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The present invention is directed to nucleoside analogues to inhibit the main protease of a coronavirus. In particular the present invention relates to a composition comprising (i) a compound selected from the group consisting of clitocine, a pharmacophore for clitocine, tautomer, mesomer, racemate, enantiomer, diastereomer, or mixture thereof, or an acceptable salt thereof, and (ii) a pharmaceutically acceptable vehicle, a carrier, an excipient or a diluent, for use in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection, in a host, in particular a mammalian host.

Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the Coronaviridae family. Coronaviruses have a characteristic morphology with a “club-shaped” surface. Their genome encodes four or five structural proteins [a spike (S) protein, an envelope (E) protein, a membrane (M) protein, a nucleocapsid (N) protein, and sometimes a hemagglutinin esterase (HE) protein], non-structural proteins that are released from polyproteins cleaved by the virus proteases, and further comprises additional open reading frames coding for proteins of unknown functions. Coronaviruses can infect humans and a large variety of animals. Examples of coronaviruses include severe acute respiratory syndrome coronavirus (SARS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), feline coronavirus (FCoV), porcine respiratory coronavirus (PRCV), porcine transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), bovine coronavirus (BCV), bovine coronavirus (BCoV), canine coronavirus (CCoV), avian coronavirus (IBV), and middle east respiratory syndrome-coronavirus (MERS-CoV).

Severe acute respiratory syndrome coronavirus (SARS-CoV-1) is a strain of virus that emerged in 2002-2004 as an outbreak in Asia and was observed to cause severe acute respiratory syndrome (SARS) or at least often caused a severe disease with people showing systemic and respiratory symptoms. Currently there is no vaccine or effective treatment for SARS-CoV-1.

The newly 2019 identified coronavirus was first named 2019-nCoV before being officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the coronavirus family, SARS-CoV-2 is a SARS-like virus but is different from SARS-CoV-1 identified in 2002. SARS-CoV-2 has been characterized to date as a single-stranded RNA betacoronavirus with a genome of 30 kb encoding as many as 14 open reading frames (ORFs) (Gordon D. E. et al, Nature, 2020 doi.org/10.1038/541586-020-2286-9). A polyprotein is encoded by the ORF1a/ORF1ab and is auto-proteolytically cleaved into 16 non-structural proteins (Nsp1-16) that form the replicase/transcriptase complex (RTC). The RTC contains enzymes including the Nsp3 [papain-like protease], Nsp5 (main protease, also named Mpro or 3CL depending on the virus), the Nsp7-Nsp8 primase complex, the primary RNA-dependent RNA polymerase (Nsp12), a helicase/triphosphatase (Nsp13), an exoribonuclease (Nsp14), an endonuclease (Nsp15) and N7- and 2′O-methyltransferases (Nsp10/Nsp16)] (Chan J. F. W. et al. Emerg. Microbes Infect., 2020, 9, 221-236). Additionally the genome expresses 13 ORFs at its end that include four structural proteins: Spike (S), Envelope (E), Membrane (M) and Nucleocapsid (N) together with 9 putative accessory factors (Fehr A. R. & Perlman, Methods. Mol. Biol., 2015, 1282, 1-23). In the RNA that encodes the predicted Nsp1-16 proteins and the structure proteins, SARS-CoV-2 is very similar to SARS-CoV-1 identified in 2002. By contrast the two viruses differ in their 3′ORFs, SARS-CoV-2 exhibiting an ORF3b and an ORF10 with very limited homology to SARS-CoV-1. This new strain of SARS virus causes an infectious respiratory disease called coronavirus disease 2019 (COVID-19). People infected with COVID-19 can be asymptomatic or show symptoms of mild, moderate or severe intensity which can be fatal. On Mar. 11, 2020, the World Health Organization (WHO) characterized COVID-19 as a pandemic affecting both industrialized and developing countries and declared COVID-19 as a Public Health Emergency of International Concern. In this context, experts gathered at WHO agreed that the development of a vaccine and/or a treatment for COVID-19, which do not exist yet, is a major priority around the world.

Feline coronavirus (FCoV) is a coronavirus that infects cats worldwide. Two forms of FCoV are found in nature: feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV) that causes the disease feline infectious peritonitis (FIP). There is currently no effective treatment for FIP.

Transmissible gastroenteritis virus or porcine transmissible gastroenteritis virus (TGEV) is a coronavirus that infects pigs and causes the disease transmissible gastroenteritis (TGE). Symptoms include severe diarrhea, vomiting and rapid dehydration. Porcine respiratory coronavirus (PRCV) is a closely related virus, which is derived from TGEV by deletion of the S-gene. Canine coronavirus and FIPV are also related to TGEV. There is no specific treatment for TGE.

Porcine epidemic diarrhea virus (PEDV) is an alpha coronavirus that infects pigs and causes the disease porcine epidemic diarrhea (PED) with a high mortality in neonatal pigs, resulting in a severe agricultural loss. Symptoms include severe diarrhea, vomiting and dehydration. There is a major outbreak in swine producing countries, in particular in Europe and Asia. There is currently no effective treatment for PED.

Bovine coronavirus (BCoV) is a coronavirus that infects a bovine animal and causes enteric and respiratory disease. Symptoms include diarrhea and respiratory illnesses. BCoV is a biologically significant respiratory pathogen in cattle (Ellis, J. The Canadian veterinary journal, 2019, 60(2), 147-152). There is currently no effective treatment.

In order to find the best drug target candidate to prevent or treat coronavirus infections, it is necessary to fully understand the characteristics of said infections. The inventors have considered various coronaviruses that have been known to infect animals for years for which no treatment is yet available and have designed an approach using the 3D-structure of viral proteases in different strains with a view to identify molecules that could target structures shared in these proteases for ligand-protease interactions, e.g. efficient binding. Targeting viral proteases is indeed one of the routes to provide treatments against COVID-19 and more broadly against coronavirus infection. Accordingly viral protease inhibition would prevent cleavage of the virus polyproteins and would thus hamper virus replication and assembly. The invention accordingly originates from molecular docking studies (virtual screening studies) and binding site analysis of protease of several coronaviruses that enabled to identify binding capability for molecules capable of inhibiting virus proteases. Besides SARS-CoV-2 study, data were obtained from other Coronaviridae to enable determining candidate ligands and their binding affinity with a view to define candidate molecules for infection treatment.

The coronavirus main protease (Mpro) plays a vital role in viral replication through the proteolytic processing of the polyproteins and is thus an attractive drug target. Its X-ray crystal structure has been recently published (X. Liu et al, PDB 2020, DOI 10.210/pdb6lu7/pdb). The coronavirus Mpro is known to cleave at 11 positions, i.e. 11 cleavage sites. For example, the SARS-CoV-1 Mpro cleaves the replicase polyproteins, pp1a and pp1b, at 11 specific positions, using core sequences in the polyprotein substrate to determine cleavage sites (T. Muramatsu, et al., Proc. Natl. Acad. Sci. USA 2016, 113, 12997-13002). The SARS-CoV-2 Mpro has 96% identity with the SARS-CoV-1 Mpro.

In the present invention, the inventors studied the molecular interactions of a high-resolution experimental structure of the Mpro of SARS-CoV-1, SARS-CoV-2, FIPV, TGEV and PEDV, or of the HE of BCoV with nucleoside analogues using docking analysis. In particular the inventors surprisingly found that clitocine and pharmacophores for clitocine had molecular interactions with an active site, i.e. a substrate binding site, in Mpro or HE of viruses involved in SARS, COVID-19, FIP, TGE, PED, and enteric and respiratory disease. Thus clitocine and pharmacophores for clitocine may inhibit the Mpro or HE, in particular Mpro, of a coronavirus and/or clitocine and some of the pharmacophores may inhibit the RNA dependent RNA polymerase of the virus and be regarded as drug candidate for use in the treatment and/or the prevention of coronavirus infections or illness related to infection, in particular respiratory illness.

Clitocine is a natural amino nucleoside, especially an adenosine nucleoside analogue, that has been first isolated from the mushroom Clitocybe inversa (Kubo et al., Tet. Lett., 1986, 27: 4277). Clitocine has been reported as a potential novel therapeutic agent to overcome drug resistance in cancer therapy (Sun et al., Apoptosis, 2014, 19(5), 871-882) and has been shown to have growth inhibitory activity against lung, colon and gastric human cancer cells (Vaz et al., Food and Chemical Toxicology, 2010, 48(10), 2881-2884). EP3067053 and U.S. Ser. No. 16/342,640 patent applications disclose the use of clitocine as a therapeutic compound for diseases associated with a nonsense mutation.

The invention relates to a compound selected from the group consisting of clitocine, a pharmacophore for clitocine, tautomer, mesomer, racemate, enantiomer, diastereomer, or mixture thereof, or an acceptable salt thereof, for use in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection, in a host, in particular a mammalian host.

The invention also relates to a composition, in particular a pharmaceutical composition, comprising (i) clitocine, a pharmacophore for clitocine, tautomer, mesomer, racemate, enantiomer, diastereomer, or mixture thereof, or an acceptable salt thereof, and (ii) a pharmaceutically acceptable vehicle, a carrier, an excipient or a diluent, for use in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family, i.e. a coronavirus infection, or an illness related to such infection, in a host, in particular a mammalian host.

As used herein, the term “nucleoside analogues” refers to nucleosides containing a nucleic acid analogue and a sugar.

Clitocine (CAS Registry number 105798-74-1; PubChem CID129111, CHEBI:205898) as used herein is also known as (2R,3R,4S,5R)-2-[(6-amino-5-nitropyrimidin-4-yl)amino]-5-(hydroxymethyl)oxolane-3,4-diol (IUPAC name); or 6-amino-5-nitro-4-(ribofuranosylamino)pyrimidine; or beta-D-ribofuranosylamine, N-(6-amino-5-nitro-4-pyrimidinyl); or 2-(6-amino-5-nitro-pyrimidin-4-ylamino)-5-hydroxymethyl-tetrahydro-furan-3,4-diol, or (2R,3R,4S,5R)-2-(6-amino-5-nitro-pyrimidin-4-ylamino)-5-hydroxymethyl-tetrahydro-furan-3,4-diol. Clitocine has the molecular formula of C₉H₁₃N₅O₆, which is represented by the general formula (I) below:

[Image Omitted]

Clitocine as used herein can be the alpha-anomer of clitocine, the beta-anomer of clitocine, or a mixture of alpha and beta anomers. Preferably, clitocine is the beta anomer represented by the formula (II) below:

[Image Omitted]

Clitocine may be obtained by synthesis according to published procedure (Moss R. J. et al, 1988, J Med Chem 31: 786-790; Korean patent application KR20060102602). Clitocine is commercially available and can be purchased for example from Muse Chem (USA), MedKoo Biosciences, Inc. (USA), Angene and Interchim.

In a particular embodiment of the invention, when the clitocine is used or when the clitocine is the compound of the composition, the treatment targets a coronavirus that is a coronavirus infecting an animal (a non-human mammal) for prevention and/or treatment of the infection or the disease related thereto. In a particular embodiment the coronavirus is FIPV.

As used herein, the term “a pharmacophore for clitocine” refers to a compound comprising the functional properties of clitocine of binding to a protease, in particular Mpro, or HE of a coronavirus, especially of SARS-CoV-1, SARS-CoV-2, FIPV, TGEV, PEDV or BCoV, and optionally structural features of clitocine. In a particular embodiment, the pharmacophore for clitocine according to the invention exhibits the same biological activity as clitocine as inhibitor of the Mpro or HE activity. In a preferred embodiment, the pharmacophore for clitocine binds a protease, in particular Mpro or 3CL of a coronavirus. In another particular embodiment, the pharmacophore for clitocine is active in preventing and/or treating an infection by a virus from the Coronaviridae family, i.e. a coronavirus infection, or an illness related to such infection, in a host, in particular a mammalian host, especially a human host. In a particular embodiment of the invention, the pharmacophore for clitocine encompasses clitocine derivatives or an adenosine analogue whose pharmacophore features are similar to the pharmacophore features of clitocine. As used herein, the term “clitocine derivatives” refers to compounds that are derived from clitocine by a chemical reaction, i.e. by substitution of one or more substituents such as, for example, halogen, alkyl, alkoxy, aryl, heteroaryl, haloalkyl, haloalkoxy, alkoxycarbonyl, alkanoyl, aroyl, formyl, nitrile, nitro, amido, alkylthio, alkylsulfinyl, alkylsulfonyl, arylthio, arylsulfinyl, arylsulfonyl, amino, alkylamino, arylamino, dialkylamino and diarylamino.

A molecule, in particular a pharmacophore for clitocine is considered to be an inhibitor of Mpro or HE of a coronavirus, preferably an inhibitor of Mpro, when it prevents or lessens the activity of Mpro or HE, respectively preferably the activity of Mpro, on the maturation of the coronavirus, in vitro or in vivo, in particular the activity of Mpro of SARS-CoV-1, SARS-CoV-2, FIPV, TGEV, PEDV or the activity of HE of BCoV. In a particular embodiment the compound is an adenosine analogue. In a particular embodiment the adenosine analogue is clitocine or mizoribine. In a particular embodiment, the activity of the inhibitor may be determined by measurement of the IC50 values that should preferably be lower than 50 mM, advantageously lower than 10 mM.

In a particular embodiment of the pharmacophore for clitocine, such pharmacophore comprises the functional properties of clitocine of binding to a protease, in particular Mpro of a coronavirus, especially of SARS-CoV-1, SARS-CoV-2, FIPV, TGEV, PEDV or BCoV and comprises, in addition, the functional property of binding to a RdRp (RNA dependent RNA polymerase) of the coronavirus. In a particular embodiment the RdRp is the 6M71 (NCBI YP_009725307.1—SEQ ID NO. 8), or variants thereof such as the 7BV1 (Accession NCBI 7BV1_A; SEQ ID NO. 9), the 7BV2 (Accession NCBI 7BV2_A; SEQ ID NO. 10) and/or the 7BW4 (Accession NCBI 7BW4_A; SEQ ID NO. 11) of the SARS-CoV-2.

In a particular embodiment, the pharmacophore for clitocine is mizoribine. The mizoribine (CID 104762; CAS 50924-49-7) as used herein also known as 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-hydroxy-1H-imidazole-4-carboxamide (UPAC name) or N′-(β-D-Ribofuranosyl)-5-hydroxyimidazole-4-carboxamide has the molecular formula of C₉H₁₃N₃O₆, and is represented by the following general formula (III):

[Image Omitted]

Using an in silico approach, the inventors evaluated the activity of the inhibitor by estimating the inhibition constant (Ki) value in molecular docking. The inhibition constant values were virtually calculating the chemical activity interaction towards the protein. All the docking results showed values ranging from a minimum of around ˜3.81 μM to a maximum of around 50 μM.

As used herein, the term “tautomer” refers to structural isomers differing only in the positions of hydrogen atoms and electrons. Examples of tautomers include, but are not limited to, ketone-enol, enamine-imine, amide-imidic acid, lactam-lactim, nitroso-oxime, ketene-ynol, amino acid, or phosphite-phosphonate.

As used herein, the term “mesomer” or “meso compound” refers to a stereoisomer that has two or more chiral centers but is optically inactive.

As used herein, the term “racemate” or “racemic mixtures” refers to a mixture of two enantiomers in equal proportions.

As used herein, the term “enantiomer” refers stereoisomers that are mirror images, i.e. mirror image isomers.

As used herein, the term “diastereomer” refers to isomers of compounds with more than one chiral center that are not mirror images of one another.

As used herein, the term “an acceptable salt thereof” refers to any non-toxic salts of a compound of the invention that do not interfere with the activity of the composition.

As used herein, the term “pharmaceutically acceptable vehicle” encompasses any substance that does not interfere with the activity of the composition. A vehicle is any substance or combination of substances physiologically appropriate for its use in a composition in contact with a host, in particular a mammalian host, preferably a human host, and thus non-toxic. Pharmaceutically acceptable vehicles are well known in the art.

As used herein, the term “carrier” encompasses any standard pharmaceutical carriers such as phosphate buffered saline solutions, water, emulsions, tablets and capsules.

As used herein, the term “excipient” encompasses any pharmaceutically acceptable excipients such as binding agents, fillers, lubricants, disintegrants and wetting agents.

As used herein, the term “diluent” encompasses an inert agent that is designed to increase the weight of the composition.

In a particular embodiment of the invention, said infection or disease related thereto is selected from the group consisting of SARS, COVID-19, FIP, TGE, PED, enteric and respiratory disease, and MERS, preferably is selected from the group consisting of SARS, COVID-19, FIP, TGE, PED, and enteric and respiratory disease.

In another particular embodiment of the invention, the virus from the Coronaviridae family is selected from the group consisting of SARS-CoV-1, SARS-CoV-2, FIPV, TGEV, PEDV, BCoV, FCoV, PRCV, BCV, CCoV and MERS-CoV. Preferably, the virus from the Coronaviridae family is selected from the group consisting of SARS-CoV-1, SARS-CoV-2, FIPV, TGEV, PEDV and BCoV.

In a preferred embodiment of the invention, the composition comprises clitocine. In a preferred embodiment the composition comprises mizoribine. In a particular embodiment, the composition comprises clitocine and mizoribine, In a particular embodiment the clitocine and the mizoribine are provided as an association of separate compounds for use in combination regimen (or combination treatment) as disclosed herein.

In another preferred embodiment of the invention, the compound is selected from the group consisting of compounds 2-90, preferably from the group consisting of compounds 2-76, even more preferably from the group consisting of compounds 2-43 as disclosed herein. In another more preferred embodiment of the invention, the compound is selected from the group consisting of compounds 2-10, 11 and 77-90. In another more preferred embodiment of the invention, the compound is selected from the group consisting of compounds 2-10. In a particular embodiment the compound is selected from one of these groups that contain in addition, mizoribine.

In a preferred embodiment of the invention, the mammalian host is a human host. In a particular embodiment when the treated host is a human, the compound used for treatment is not clitocine. In a particular embodiment when the treated host is a human, the compound used for treatment is mizoribine.

In another preferred embodiment of the invention, the mammalian host is selected from the group consisting of a pig, a bovine animal, a horse, a cat, a dog, a rabbit, a rodent, a bird and a bat, preferably is a pig, a bovine animal or a cat.

When using a compound that is a pharmacophore for clitocine, the compound may be selected in the particular groups of compounds identified herein and may advantageously be further selected for optimized binding properties toward the Mpro or HE of the specific coronavirus that one intends to treat in the host in need of such treatment. In a particular embodiment, the compound, in particular the pharmacophore for clitocine is selected for binding properties toward the Mpro of a coronavirus as disclosed herein, and is further selected for its binding capacity to RdRp of the same coronavirus. In a particular embodiment the Mpro is from the SARS-Cov-2 (PDB:6LU7) and the RdRp is the 6M71, the 7BV1, 7BV2 and/or the 7BW4 of the SARS-CoV-2. The binding capability of clitocine and mizoribine (illustrative of the pharmacophores for clitocine) has been determined and is shown in the figures.

In a particular embodiment of the invention, the composition is for use in association with another therapeutic agent, in particular an antibiotic, in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection according to the invention.

The present invention also relates to a method to prevent and/or treat an infection by a virus from the Coronaviridae family, i.e. a coronavirus infection, or a disease related to such infection, in a host, in particular a mammalian host, preferably a human host, or an animal host known to be sensible to infection by especially one of the herein cited coronaviruses, comprising administering a pharmaceutically effective quantity of the composition according to the invention. In a particular embodiment, the coronavirus is a virus infecting an animal, especially a non-human mammal, in particular is a virus selected from the group of FIPV, TGEV, PEDV, BCoV, FCoV, PRCV, BCV and CCoV, especially is FIPV. In another embodiment, the coronavirus is a virus infecting a human, in particular is the SARS-Cov-2.

As used herein, the term “to prevent” refers to a method by which the coronavirus infection is obstructed or delayed.

As used herein, the term “to treat” refers to a method by which the symptoms of the coronavirus infection are either alleviated, i.e. decrease of the coronavirus infection in the host (especially of the measured virus load) or improvement of the clinical condition of the patient, or completely eliminated. In particular the composition and the method of the invention are used to treat the respiratory disease associated with coronavirus infection, in particular with SARS or COVID-19 in a human host.

As used herein, the term “a pharmaceutically effective quantity” refers to an amount which is sufficient to prevent and/or treat a patient or an animal at risk for developing or diagnosed with a coronavirus infection, thus producing the desired therapeutic effect.

The present invention also relates to a method to inhibit the main protease (Mpro) or a hemagglutinin esterase (HE) and/or RdRp of a virus from the Coronaviridae family, i.e. a coronavirus, in a host, in particular a mammalian host, preferably a human host, comprising administering a pharmaceutically effective quantity of the composition according to the invention.

In a particular embodiment when clitocine and mizoribine are used to prevent and/or to treat a coronavirus infection, in particular the respiratory disease associated with a coronavirus infection, in particular with SARS such as SARS-CoV-2 or COVID-19 in a human host, both compounds may be used in a single composition for administration to the host or alternatively may be administered in a combination regimen, in particular may be administered separately in time.

In a preferred embodiment of the invention, the Mpro of a virus from the Coronaviridae family has an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6, and the BCoV-HE has the amino acid sequence of SEQ ID NO: 7.

As used herein, the term “to inhibit the main protease (Mpro) of a coronavirus” refers to preventing or lessening the activity of Mpro on the maturation of the coronavirus, in particular with SARS or COVID-19. The activity of the inhibitor may be determined by measurement of the IC50 values that should preferably be lower than 50 mM.

In a particular aspect, the invention relates to clitocine in association with mizoribine for use in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection, in a mammalian host, in particular a human host according to any one of the features disclosed herein, wherein the clitocine and mizoribine are for administration in a combination regimen to the host.

The term “association” refers to the combination for use of the compounds, especially of clitocine an mizoribine, wherein the use is for prevention and/or treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection, in a mammalian host, in particular a human host according to any one of the features disclosed herein. Accordingly the associated compounds may be provided to the host as separate compositions and/or may be administered to the host separately in time, to the extent that their use accordingly achieves a combination regimen for the prevention and/or treatment of the infection or related disease. Accordingly a use of compounds “in association” according to the invention relates to administration of more than one active compound, in particular two compounds wherein the administered compounds influence the health status of the host by preventing and/or treating an infection by a virus from the Coronaviridae family or an illness related to such infection, wherein the host is a mammalian host, in particular a human host. The term “association” encompasses a combination regimen.

In a particular embodiment, the clitocine in association with the mizoribine is for use for separate administration in time to the mammalian host, in particular to the human host.

In a particular embodiment, the clitocine is for use in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection, in a mammalian host, in particular a human host according to any one of the features disclosed herein, and said clitocine is used for administration in a combination regimen with mizoribine.

The invention also relates to the mizoribine for use in the prevention and/or the treatment of an infection by a virus from the Coronaviridae family or an illness related to such infection in a mammalian host, in particular to a human host, according to any one of the features disclosed herein, wherein the mizoribine is used for administration in a combination regimen with clitocine.

In a particular embodiment, the association of clitocine and mizoribine is for use as disclosed herein for the prevention of the treatment of an infection with SARS-CoV-2 or an illness related to such infection such as COVID-19, in a human host.

The invention also relates to a composition suitable for administration to a mammalian host infected with a coronavirus, in particular with SARS-CoV-2, wherein the composition comprises clitocine and mizoribine.

In another aspect, the invention relates to an association of compounds formulated for separate administration in time wherein the compounds are clitocine and mizoribine.

The Examples below illustrate the activity of clitocine and of pharmacophore for clitocine such as mizoribine, on SARS-CoV-2 production.

The inventors collected compounds against CID_129111 in PubChem database based on Tanimoto similarity coefficient analysis. The compounds (.sdf format) were also collected according to the CID number and the structures were converted into 3D coordinates using Open Bable software. The inventors observed the pharmacophore model of clitocine and identified the chemical features of the compounds.

The 3D structure of clitocine (CID 129111) is represented in FIG. 19, and its pharmacophore structure is represented in FIG. 20.

First of all, the inventors carried out a fingerprint Tanimoto-based 2-dimensional similarity search (Tanimoto threshold=100%) of clitocine (compound CID129111) and identified 10 compounds (compounds 1-10) as disclosed in Table 1 including clitocine as compound 1.

TABLE 1

List of identified compounds 1-10 and their pharmacophore

features (HBA = Hydrogen Bond Acceptor; HBD = Hydrogen Bond Donor; AR = Aromatic Ring).

Com-
PubChem

pound
CID
Compound name
IUPAC name
Pharmacophore features

1
129111
Clitocine
(2R,3R,4S,5R)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

2
11644921
2-[(6-Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
2-[(6-amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

3
13965719
(3R,4S,5R)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(3R,4S,5R)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

4
13965721
(2R,3R,4R,5R)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2R,3R,4R,5R)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

5
58996359
(2S,3S,4R,5S)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2S,3S,4R,5S)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

6
60139991
(2S,3R,4S,5R)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2S,3R,4S,5R)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

7
71136912
(2R,5R)-2-[(6-Amino- 5-nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2R,5R)-2-[(6-amino- 5-nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

8
90294771
(2R,3S,5R)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2R,3S,5R)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

9
91572539
(3R,4R,5R)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(3R,4R,5R)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

10
137704644
(3S,4R,5S)-2-[(6- Amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(3S,4R,5S)-2-[(6- amino-5- nitropyrimidin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

The inventors carried out a fingerprint Tanimoto-based 2-dimensional similarity search (Tanimoto threshold=95%) of clitocine (compound CID129111) and identified 43 compounds (compounds 1-43, including clitocine as compound 1) as disclosed in Table 2.

TABLE 2

List of identified compounds 1-43

PubChem

Compound
CID
Compound name
IUPAC name

1
129111
Clitocine
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol

11
9795869
(2R,3S,4R,5R)-2-Aminomethyl-5-(6-
(2R,3S,4R,5R)-2-(aminomethyl)-5-[(6-

amino-5-nitro-pyrimidin-4-ylamino)-
amino-5-nitropyrimidin-4-

tetrahydro-furan-3,4-diol
yl)amino]oxolane-3,4-diol

12
10017723
(2R,3S,4R,5R)-5-[(6-Amino-5-
(2R,3S,4R,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-2-
nitropyrimidin-4-yl)amino]-2-

(hydroxymethyl)-3-methyloxolane-3,4-
(hydroxymethyl)-3-methyloxolane-3,4-

diol
diol

13
10038815
(2R,3S,5R)-5-[(6-Amino-5-
(2R,3S,5R)-5-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-2-
4-yl)amino]-2-(hydroxymethyl)oxolan-3-

(hydroxymethyl)oxolan-3-ol
ol

14
10065264
(2R,3R,4S,5R)-2-[[6-(2-
(2R,3R,4S,5R)-2-[[6-(2-

Hydroxyethylamino)-5-nitropyrimidin-4-
hydroxyethylamino)-5-nitropyrimidin-4-

yl]amino]-5-(hydroxymethyl)oxolane-
yl]amino]-5-(hydroxymethyl)oxolane-3,4-

3,4-diol
diol

15
10085552
(2R,3S,4S,5R)-2-[(6-Amino-5-
(2R,3S,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-5-
nitropyrimidin-4-yl)amino]-4-fluoro-5-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

16
10334340
(2R,3R,4S,5S)-2-[(6-Amino-5-
(2R,3R,4S,5S)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(fluoromethyl)oxolane-3,4-diol
(fluoromethyl)oxolane-3,4-diol

17
10378472
(2R,3R,4S,5R)-2-(6-Amino-5-nitro-
(2R,3R,4S,5R)-2-[(6-amino-5-

pyrimidin-4-ylamino)-5-methyl-
nitropyrimidin-4-yl)amino]-5-

tetrahydro-furan-3,4-diol
methyloxolane-3,4-diol

18
10402587
(2R,3R,4S,5R)-2-[(6-Amino-5-
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-(2-
nitropyrimidin-4-yl)amino]-5-(2-

hydroxyethyl)oxolane-3,4-diol
hydroxyethyl)oxolane-3,4-diol

19
10424240
(2R,3S,4R,5R)-2-[(6-Amino-5-
(2R,3S,4R,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-5-
nitropyrimidin-4-yl)amino]-4-fluoro-5-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

20
10424919
(2R,3R,4S,5R)-2-[(6-Amino-5-
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-(1-
nitropyrimidin-4-yl)amino]-5-(1-

hydroxyethyl)oxolane-3,4-diol
hydroxyethyl)oxolane-3,4-diol

21
10446869
(2R,3R,4S,5R)-5-[(6-Amino-5-
(2R,3R,4S,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-2-
nitropyrimidin-4-yl)amino]-4-fluoro-2-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

22
10470946
(2R,3R,4S,5R)-2-[[6-(Ethylamino)-5-
(2R,3R,4S,5R)-2-[[6-(ethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

2
11644921
2-[(6-Amino-5-nitropyrimidin-4-
2-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-5-(hydroxymethyl)oxolane-
5-(hydroxymethyl)oxolane-3,4-diol

3,4-diol

3
13965719
(3R,4S,5R)-2-[(6-Amino-5-
(3R,4S,5R)-2-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-5-
4-yl)amino]-5-(hydroxymethyl)oxolane-

(hydroxymethyl)oxolane-3,4-diol
3,4-diol

4
13965721
(2R,3R,4R,5R)-2-[(6-Amino-5-
(2R,3R,4R,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

23
58996355
(2R,3R,4R,5R)-5-[(6-Amino-5-
(2R,3R,4R,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-2-
nitropyrimidin-4-yl)amino]-4-fluoro-2-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

24
58996356
(2R,3R,4S,5R)-2-[[6-(Dimethylamino)-
(2R,3R,4S,5R)-2-[[6-(dimethylamino)-5-

5-nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

25
58996357
(2R,3S,4R,5R)-2-(Hydroxymethyl)-5-
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-[[6-

[[6-(methylamino)-5-nitropyrimidin-4-
(methylamino)-5-nitropyrimidin-4-

yl]amino]oxolane-3,4-diol
yl]amino]oxolane-3,4-diol

5
58996359
(2S,3S,4R,5S)-2-[(6-Amino-5-
(2S,3S,4R,5S)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

26
58996362
(2R,3S,5R)-2-[(6-Amino-5-
(2R,3S,5R)-2-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-4,4-difluoro-
4-yl)amino]-4,4-difluoro-5-

5-(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

6
60139991
(2S,3R,4S,5R)-2-[(6-Amino-5-
(2S,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

27
69221289
5-[(6-Amino-5-nitropyrimidin-4-
5-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-4-fluoro-2-
4-fluoro-2-(hydroxymethyl)oxolan-3-ol

(hydroxymethyl)oxolan-3-ol

28
69225115
2-[(6-Amino-5-nitropyrimidin-4-
2-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-5-(2-hydroxyethyl)oxolane-
5-(2-hydroxyethyl)oxolane-3,4-diol

3,4-diol

29
69225288
2-[(6-Amino-5-nitropyrimidin-4-
2-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-5-methyloxolane-3,4-diol
5-methyloxolane-3,4-diol

30
69225538
5-[(6-Amino-5-nitropyrimidin-4-
5-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-2-(hydroxymethyl)oxolan-3-
2-(hydroxymethyl)oxolan-3-ol

ol

31
69225577
2-[(6-Amino-5-nitropyrimidin-4-
2-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-4,4-difluoro-5-
4,4-difluoro-5-(hydroxymethyl)oxolan-3-

(hydroxymethyl)oxolan-3-ol
ol

32
69225578
2-(Aminomethyl)-5-[(6-amino-5-
2-(aminomethyl)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]oxolane-3,4-
nitropyrimidin-4-yl)amino]oxolane-3,4-

diol
diol

33
69225751
2-[(6-Amino-5-nitropyrimidin-4-
2-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-5-(1-hydroxyethyl)oxolane-
5-(1-hydroxyethyl)oxolane-3,4-diol

3,4-diol

34
69226163
5-[(6-Amino-5-nitropyrimidin-4-
5-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-2-(hydroxymethyl)-3-
2-(hydroxymethyl)-3-methyloxolane-3,4-

methyloxolane-3,4-diol
diol

35
69226282
2-[(6-Amino-5-nitropyrimidin-4-
2-[(6-amino-5-nitropyrimidin-4-yl)amino]-

yl)amino]-4-fluoro-5-
4-fluoro-5-(hydroxymethyl)oxolan-3-ol

(hydroxymethyl)oxolan-3-ol

36
69717518
(3R,4S,5R)-2-[[6-(Ethylamino)-5-
(3R,4S,5R)-2-[[6-(ethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

37
69717520
(2S,3R,4S,5R)-2-[[6-(Ethylamino)-5-
(2S,3R,4S,5R)-2-[[6-(ethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

7
71136912
(2R,5R)-2-[(6-Amino-5-nitropyrimidin-
(2R,5R)-2-[(6-amino-5-nitropyrimidin-4-

4-yl)amino]-5-(hydroxymethyl)oxolane-
yl)amino]-5-(hydroxymethyl)oxolane-3,4-

3,4-diol
diol

8
90294771
(2R,3S,5R)-2-[(6-Amino-5-
(2R,3S,5R)-2-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-5-
4-yl)amino]-5-(hydroxymethyl)oxolane-

(hydroxymethyl)oxolane-3,4-diol
3,4-diol

38
90860724
(2R,3R,5S)-2-[(6-Amino-5-
(2R,3R,5S)-2-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-5-
4-yl)amino]-5-

[azido(hydroxy)methyl]oxolan-3-ol
[azido(hydroxy)methyl]oxolan-3-ol

39
90900219
(2R,3S,4R)-2-(Hydroxymethyl)-5-[[6-
(2R,3S,4R)-2-(hydroxymethyl)-5-[[6-

(methylamino)-5-nitropyrimidin-4-
(methylamino)-5-nitropyrimidin-4-

yl]amino]oxolane-3,4-diol
yl]amino]oxolane-3,4-diol

40
91074498
(3R,4S,5R)-2-[[6-(Dimethylamino)-5-
(3R,4S,5R)-2-[[6-(dimethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

41
91088753
(3R,4S,5R)-2-[[6-(2-
(3R,4S,5R)-2-[[6-(2-hydroxyethylamino)-

Hydroxyethylamino)-5-nitropyrimidin-4-
5-nitropyrimidin-4-yl]amino]-5-

yl]amino]-5-(hydroxymethyl)oxolane-
(hydroxymethyl)oxolane-3,4-diol

3,4-diol

42
91521750
(3R,4S,5S)-2-[(6-Amino-5-
(3R,4S,5S)-2-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-5-
4-yl)amino]-5-(fluoromethyl)oxolane-3,4-

(fluoromethyl)oxolane-3,4-diol
diol

9
91572539
(3R,4R,5R)-2-[(6-Amino-5-
(3R,4R,5R)-2-[(6-amino-5-nitropyrimidin-

nitropyrimidin-4-yl)amino]-5-
4-yl)amino]-5-(hydroxymethyl)oxolane-

(hydroxymethyl)oxolane-3,4-diol
3,4-diol

43
10123433
(2R,3R,4S,5R)-2-[[6-
(2R,3R,4S,5R)-2-[[6-

6
[Ethyl(methyl)amino]-5-nitropyrimidin-
[ethyl(methyl)amino]-5-nitropyrimidin-4-

4-yl]amino]-5-(hydroxymethyl)oxolane-
yl]amino]-5-(hydroxymethyl)oxolane-3,4-

3,4-diol
diol

10
13770464
(3S,4R,5S)-2-[(6-Amino-5-
(3S,4R,5S)-2-[(6-amino-5-nitropyrimidin-

4
nitropyrimidin-4-yl)amino]-5-
4-yl)amino]-5-(hydroxymethyl)oxolane-

(hydroxymethyl)oxolane-3,4-diol
3,4-diol

The inventors carried out a fingerprint Tanimoto-based 2-dimensional similarity search (Tanimoto threshold=90%) of clitocine (compound CID129111) and identified 76 compounds (compounds 1-76, including clitocine as compound 1) as disclosed in Table 3.

TABLE 3

List of identified compounds 1-76

PubChem

Compound
CID
Compound name
IUPAC name

1
129111
Clitocine
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol

44
592060
9-beta-d-Arabinofuranosyl-adenine-N'-
2-(6-amino-9-oxidopurin-9-ium-9-yl)-

oxide
5-(hydroxymethyl)oxolane-3,4-diol

11
9795869
(2R,3S,4R,5R)-2-Aminomethyl-5-(6-amino-
(2R,3S,4R,5R)-2-(aminomethyl)-5-

5-nitro-pyrimidin-4-ylamino)-tetrahydro-
[(6-amino-5-nitropyrimidin-4-

furan-3,4-diol
yl)amino]oxolane-3,4-diol

45
9971159
(2R,4S,5R)-5-[(6-Amino-5-nitropyrimidin-4-
(2R,4S,5R)-5-[(6-amino-5-

yl)amino]-4-hydroxy-2-
nitropyrimidin-4-yl)amino]-4-hydroxy-

(hydroxymethyl)oxolan-3-one
2-(hydroxymethyl)oxolan-3-one

12
10017723
(2R,3S,4R,5R)-5-[(6-Amino-5-
(2R,3S,4R,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-2-
nitropyrimidin-4-yl)amino]-2-

(hydroxymethyl)-3-methyloxolane-3,4-diol
(hydroxymethyl)-3-methyloxolane-

3,4-diol

13
10038815
(2R,3S,5R)-5-[(6-Amino-5-nitropyrimidin-4-
(2R,3S,5R)-5-[(6-amino-5-

yl)amino]-2-(hydroxymethyl)oxolan-3-ol
nitropyrimidin-4-yl)amino]-2-

(hydroxymethyl)oxolan-3-ol

14
10065264
(2R,3R,4S,5R)-2-[[6-(2-
(2R,3R,4S,5R)-2-[[6-(2

Hydroxyethylamino)-5-nitropyrimidin-4-
hydroxyethylamino)-5-nitropyrimidin-

yl]amino]-5-(hydroxymethyl)oxolane-3,4-
4-yl]amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

15
10085552
(2R,3S,4S,5R)-2-[(6-Amino-5-
(2R,3S,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-5-
nitropyrimidin-4-yl)amino]-4-fluoro-5-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

46
10086834
(2R,3R,4S,5R)-2-[(6-Amino-5-
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(azidomethyl)oxolane-3,4-diol
(azidomethyl)oxolane-3,4-diol

47
10107264
(2R,3S,4R,5R)-2-(Hydroxymethyl)-5-[(5-
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-

nitropyrimidin-4-yl)amino]oxolane-3,4-diol
[(5-nitropyrimidin-4-

yl)amino]oxolane-3,4-diol

16
10334340
(2R,3R,4S,5S)-2-[(6-Amino-5-
(2R,3R,4S,5S)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(fluoromethyl)oxolane-3,4-diol
(fluoromethyl)oxolane-3,4-diol

17
10378472
(2R,3R,4S,5R)-2-(6-Amino-5-nitro-
(2R,3R,4S,5R)-2-[(6-amino-5-

pyrimidin-4-ylamino)-5-methyl-tetrahydro-
nitropyrimidin-4-yl)amino]-5-

furan-3,4-diol
methyloxolane-3,4-diol

48
10381774
[(3Ar,4R,6R,6aR)-4-[(6-amino-5-
[(3aR,4R,6R,6aR)-4-[(6-amino-5-

nitropyrimidin-4-yl)amino]-2,2-dimethyl-
nitropyrimidin-4-yl)amino]-2,2-

3a,4,6,6a-tetrahydrofuro[3,4-d][1,3]dioxol-
dimethyl-3a,4,6,6a-

6-yI]methanol
tetrahydrofuro[3,4-d][1,3]dioxol-6-

yl]methanol

18
10402587
(2R,3R,4S,5R)-2-[(6-Amino-5-
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-(2-
nitropyrimidin-4-yl)amino]-5-(2-

hydroxyethyl)oxolane-3,4-diol
hydroxyethyl)oxolane-3,4-diol

49
10402931
(2R,3R,5R)-5-[(6-Amino-5-nitropyrimidin-4-
(2R,3R,5R)-5-[(6-amino-5-

yl)amino]-4,4-difluoro-2-
nitropyrimidin-4-yl)amino]-4,4-

(hydroxymethyl)oxolan-3-ol
difluoro-2-(hydroxymethyl)oxolan-3-

ol

19
10424240
(2R,3S,4R,5R)-2-[(6-Amino-5-
(2R,3S,4R,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-5-
nitropyrimidin-4-yl)amino]-4-fluoro-5-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

20
10424919
(2R,3R,4S,5R)-2-[(6-Amino-5-
(2R,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-(1-
nitropyrimidin-4-yl)amino]-5-(1-

hydroxyethyl)oxolane-3,4-diol
hydroxyethyl)oxolane-3,4-diol

50
10445180
(2R,3R,4S,5R)-2-[(5,6-Diaminopyrimidin-4-
(2R,3R,4S,5R)-2-[(5,6-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
diaminopyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

21
10446869
(2R,3R,4S,5R)-5-[(6-Amino-5-
(2R,3R,4S,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-2-
nitropyrimidin-4-yl)amino]-4-fluoro-2-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

22
10470946
(2R,3R,4S,5R)-2-[[6-(Ethylamino)-5-
(2R,3R,4S,5R)-2-[[6-(ethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

2
11644921
2-[(6-Amino-5-nitropyrimidin-4-yl)amino]-5-
2-[(6-amino-5-nitropyrimidin-4-

(hydroxymethyl)oxolane-3,4-diol
yl)amino]-5-(hydroxymethyl)oxolane-

3,4-diol

51
11724091
[(2R,3S,4R,5R)-5-[(6-Amino-5-
[(2R,3S,4R,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-3,4-
nitropyrimidin-4-yl)amino]-3,4-

dihydroxyoxolan-2-yl]methyl acetate
dihydroxyoxolan-2-yl]methyl acetate

3
13965719
(3R,4S,5R)-2-[(6-Amino-5-nitropyrimidin-4-
(3R,4S,5R)-2-[(6-amino-5-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
nitropyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

4
13965721
(2R,3R,4R,5R)-2-[(6-Amino-5-
(2R,3R,4R,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

52
13965723
[(3Ar,6R,6aR)-4-[(6-amino-5-nitropyrimidin-
[(3aR,6R,6aR)-4-[(6-amino-5-

4-yl)amino]-2,2-dimethyl-3a,4,6,6a-
nitropyrimidin-4-yl)amino]-2,2-

tetrahydrofuro[3,4-d][1,3]dioxol-6-
dimethyl-3a,4,6,6a-

yl]methanol
tetrahydrofuro[3,4-d][1,3]dioxol-6-

yl]methanol

53
15539937
[(2R,3S)-5-[(6-Amino-5-nitropyrimidin-4-
[(2R,3S)-5-[(6-amino-5-

yl)amino]-3-[tert-
nitropyrimidin-4-yl)amino]-3-[tert-

butyl(dimethyl)silyl]oxyoxolan-2-yl]methanol
butyl(dimethyl)silyl]oxyoxolan-2-

yl]methanol

54
44317554
(2R,3R,4S,5S)-2-[(6-Amino-5-
(2R,3R,4S,5S)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(bromomethyl)oxolane-3,4-diol
(bromomethyl)oxolane-3,4-diol

55
54314153
(2R,3R,5S)-2-(6-Amino-9-oxidopurin-9-ium-
(2R,3R,5S)-2-(6-amino-9-

9-yl)-5-(hydroxymethyl)oxolan-3-ol
oxidopurin-9-ium-9-yl)-5-

(hydroxymethyl)oxolan-3-ol

56
54341839
(2R,3R,4S,5R)-2-(6-Amino-9-oxidopurin-9-
(2R,3R,4S,5R)-2-(6-amino-9-

ium-9-yl)-5-(hydroxymethyl)oxolane-3,4-
oxidopurin-9-ium-9-yl)-5-

diol
(hydroxymethyl)oxolane-3,4-diol

23
58996355
(2R,3R,4R,5R)-5-[(6-Amino-5-
(2R,3R,4R,5R)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]-4-fluoro-2-
nitropyrimidin-4-yl)amino]-4-fluoro-2-

(hydroxymethyl)oxolan-3-ol
(hydroxymethyl)oxolan-3-ol

24
58996356
(2R,3R,4S,5R)-2-[[6-(Dimethylamino)-5-
(2R,3R,4S,5R)-2-[[6-

nitropyrimidin-4-yl]amino]-5-
(dimethylamino)-5-nitropyrimidin-4-

(hydroxymethyl)oxolane-3,4-diol
yl]amino]-5-(hydroxymethyl)oxolane-

3,4-diol

25
58996357
(2R,3S,4R,5R)-2-(Hydroxymethyl)-5-[[6-
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-

(methylamino)-5-nitropyrimidin-4-
[[6-(methylamino)-5-nitropyrimidin-4-

yl]amino]oxolane-3,4-diol
yl]amino]oxolane-3,4-diol

5
58996359
(2S,3S,4R,5S)-2-[(6-Amino-5-
(2S,3S,4R,5S)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

26
58996362
(2R,3S,5R)-2-[(6-Amino-5-nitropyrimidin-4-
(2R,3S,5R)-2-[(6-amino-5-

yl)amino]-4,4-difluoro-5-
nitropyrimidin-4-yl)amino]-4,4-

(hydroxymethyl)oxolan-3-ol
difluoro-5-(hydroxymethyl)oxolan-3-

ol

6
60139991
(2S,3R,4S,5R)-2-[(6-Amino-5-
(2S,3R,4S,5R)-2-[(6-amino-5-

nitropyrimidin-4-yl)amino]-5-
nitropyrimidin-4-yl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

27
69221289
5-[(6-Amino-5-nitropyrimidin-4-yl)amino]-4-
5-[(6-amino-5-nitropyrimidin-4-

fluoro-2-(hydroxymethyl)oxolan-3-ol
yl)amino]-4-fluoro-2-

(hydroxymethyl)oxolan-3-ol

57
69222181
5-[(6-Amino-5-nitropyrimidin-4-yl)amino]-
5-[(6-amino-5-nitropyrimidin-4-

4,4-difluoro-2-(hydroxymethyl)oxolan-3-ol
yl)amino]-4,4-difluoro-2-

(hydroxymethyl)oxolan-3-ol

58
69222394
2-(Hydroxymethyl)-5-[(5-nitropyrimidin-4-
2-(hydroxymethyl)-5-[(5-

yl)amino]oxolane-3,4-diol
nitropyrimidin-4-yl)amino]oxolane-

3,4-diol

59
69223701
Acetic acid; [(2R,3S,4R,5R)-5-[(6-amino-5-
acetic acid; [(2R,3S,4R,5R)-5-[(6-

nitropyrimidin-4-yl)amino]-3,4-
amino-5-nitropyrimidin-4-yl)amino]-

dihydroxyoxolan-2-yl]methyl acetate
3,4-dihydroxyoxolan-2-yl]methyl

acetate

28
69225115
2-[(6-Amino-5-nitropyrimidin-4-yl)amino]-5-
2-[(6-amino-5-nitropyrimidin-4-

(2-hydroxyethyl)oxolane-3,4-diol
yl)amino]-5-(2-hydroxyethyl)oxolane-

3,4-diol

60
69225277
5-[(6-Amino-5-nitropyrimidin-4-yl)amino]-4-
5-[(6-amino-5-nitropyrimidin-4-

hydroxy-2-(hydroxymethyl)oxolan-3-one
yl)amino]-4-hydroxy-2-

(hydroxymethyl)oxolan-3-one

29
69225288
2-[(6-Amino-5-nitropyrimidin-4-yl)amino]-5-
2-[(6-amino-5-nitropyrimidin-4-

methyloxolane-3,4-diol
yl)amino]-5-methyloxolane-3,4-diol

30
69225538
5-[(6-Amino-5-nitropyrimidin-4-yl)amino]-2-
5-[(6-amino-5-nitropyrimidin-4-

(hydroxymethyl)oxolan-3-ol
yl)amino]-2-(hydroxymethyl)oxolan-

3-ol

31
69225577
2-[(6-Amino-5-nitropyrimidin-4-yl)amino]-
2-[(6-amino-5-nitropyrimidin-4-

4,4-difluoro-5-(hydroxymethyl)oxolan-3-ol
yl)amino]-4,4-difluoro-5-

(hydroxymethyl)oxolan-3-ol

32
69225578
2-(Aminomethyl)-5-[(6-amino-5-
2-(aminomethyl)-5-[(6-amino-5-

nitropyrimidin-4-yl)amino]oxolane-3,4-diol
nitropyrimidin-4-yl)amino]oxolane-

3,4-diol

33
69225751
2-[(6-Amino-5-nitropyrimidin-4-yl)amino]-5-
2-[(6-amino-5-nitropyrimidin-4-

(1-hydroxyethyl)oxolane-3,4-diol
yl)amino]-5-(1-hydroxyethyl)oxolane-

3,4-diol

34
69226163
5-[(6-Amino-5-nitropyrimidin-4-yl)amino]-2-
5-[(6-amino-5-nitropyrimidin-4-

(hydroxymethyl)-3-methyloxolane-3,4-diol
yl)amino]-2-(hydroxymethyl)-3-

methyloxolane-3,4-diol

35
69226282
2-[(6-Amino-5-nitropyrimidin-4-yl)amino]-4-
2-[(6-amino-5-nitropyrimidin-4-

fluoro-5-(hydroxymethyl)oxolan-3-ol
yl)amino]-4-fluoro-5-

(hydroxymethyl)oxolan-3-ol

61
69234609
(2R,3S,4R,5R)-2-(Hydroxymethyl)-5-[(5-
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-

nitropyrimidin-2-yl)amino]oxolane-3,4-diol
[(5-nitropyrimidin-2-

yl)amino]oxolane-3,4-diol

36
69717518
(3R,4S,5R)-2-[[6-(Ethylamino)-5-
(3R,4S,5R)-2-[[6-(ethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

37
69717520
(2S,3R,4S,5R)-2-[[6-(Ethylamino)-5-
(2S,3R,4S,5R)-2-[[6-(ethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

62
69722004
Acetic acid; [(2R,3S,4R)-5-[(6-amino-5-
acetic acid; [(2R,3S,4R)-5-[(6-amino-

nitropyrimidin-4-yl)amino]-3,4-
5-nitropyrimidin-4-yl)amino]-3,4-

dihydroxyoxolan-2-yl]methyl acetate
dihydroxyoxolan-2-yl]methyl acetate

63
69722005
[(2R,3S,4R)-5-[(6-Amino-5-nitropyrimidin-4-
[(2R,3S,4R)-5-[(6-amino-5-

yl)amino]-3,4-dihydroxyoxolan-2-yl]methyl
nitropyrimidin-4-yl)amino]-3,4-

acetate
dihydroxyoxolan-2-yl]methyl acetate

64
69773457
2-[5-[(6-Amino-5-nitropyrimidin-4-
2-[5-[(6-amino-5-nitropyrimidin-4-

yl)amino]oxolan-2-yl]ethanol
yl)amino]oxolan-2-yl]ethanol

65
70917149
5-[(5,6-Diaminopyrimidin-4-yl)amino]-2-
5-[(5,6-diaminopyrimidin-4-

(hydroxymethyl)oxolan-3-ol
yl)amino]-2-(hydroxymethyl)oxolan-

3-ol

66
71051136
(3R,4S,5R)-2-[(5,6-Diaminopyrimidin-4-
(3R,4S,5R)-2-[(5,6-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
diaminopyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

7
71136912
(2R,5R)-2-[(6-Amino-5-nitropyrimidin-4-
(2R,5R)-2-[(6-amino-5-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
nitropyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

67
71163925
[(2R,3S,4R)-5-[(6-Amino-5-nitropyrimidin-4-
[(2R,3S,4R)-5-[(6-amino-5-

yl)amino]-3,4-dihydroxyoxolan-2-yl]methyl
nitropyrimidin-4-yl)amino]-3,4-

dimethyl phosphate
dihydroxyoxolan-2-yl]methyl

dimethyl phosphate

68
71221536
(2R,3S,5R)-5-[(5,6-Diaminopyrimidin-4-
(2R,3S,5R)-5-[(5,6-

yl)amino]-4-(2-hydroxyethoxy)-2-
diaminopyrimidin-4-yl)amino]-4-(2-

(hydroxymethyl)oxolan-3-ol
hydroxyethoxy)-2-

(hydroxymethyl)oxolan-3-ol

69
77996097
2-[(5,6-Diaminopyrimidin-4-yl)amino]-5-
2-[(5,6-diaminopyrimidin-4-

(hydroxymethyl)oxolane-3,4-diol
yl)amino]-5-(hydroxymethyl)oxolane-

3,4-diol

70
88887092
[(2S,5R)-5-[[6-Amino-5-
[(2S,5R)-5-[[6-amino-5-

(hydroxyamino)pyrimidin-4-
(hydroxyamino)pyrimidin-4-

yl]amino]oxolan-2-yl]methanol
yl]amino]oxolan-2-yl]methanol

71
89226248
2-[(2S)-5-[(6-Amino-5-nitropyrimidin-4-
2-[(2S)-5-[(6-amino-5-nitropyrimidin-

yl)amino]oxolan-2-yl]ethanol
4-yl)amino]oxolan-2-yl]ethanol

8
90294771
(2R,3S,5R)-2-[(6-Amino-5-nitropyrimidin-4-
(2R,3S,5R)-2-[(6-amino-5-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
nitropyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

72
90695347
(3R,4S,5R)-2-[(6-Amino-5-nitropyrimidin-4-
(3R,4S,5R)-2-[(6-amino-5-

yl)amino]-5-(azidomethyl)oxolane-3,4-diol
nitropyrimidin-4-yl)amino]-5-

(azidomethyl)oxolane-3,4-diol

38
90860724
(2R,3R,5S)-2-[(6-Amino-5-nitropyrimidin-4-
(2R,3R,5S)-2-[(6-amino-5-

yl)amino]-5-[azido(hydroxy)methyl]oxolan-
nitropyrimidin-4-yl)amino]-5-

3-ol
[azido(hydroxy)methyl]oxolan-3-ol

39
90900219
(2R,3S,4R)-2-(Hydroxymethyl)-5-[[6-
(2R,3S,4R)-2-(hydroxymethyl)-5-[[6-

(methylamino)-5-nitropyrimidin-4-
(methylamino)-5-nitropyrimidin-4-

yl]amino]oxolane-3,4-diol
yl]amino]oxolane-3,4-diol

40
91074498
(3R,4S,5R)-2-[[6-(Dimethylamino)-5-
(3R,4S,5R)-2-[[6-(dimethylamino)-5-

nitropyrimidin-4-yl]amino]-5-
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol
(hydroxymethyl)oxolane-3,4-diol

41
91088753
(3R,4S,5R)-2-[[6-(2-Hydroxyethylamino)-5-
(3R,4S,5R)-2-[[6-(2-

nitropyrimidin-4-yl]amino]-5-
hydroxyethylamino)-5-nitropyrimidin-

(hydroxymethyl)oxolane-3,4-diol
4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol

42
91521750
(3R,4S,5S)-2-[(6-Amino-5-nitropyrimidin-4-
(3R,4S,5S)-2-[(6-amino-5-

yl)amino]-5-(fluoromethyl)oxolane-3,4-diol
nitropyrimidin-4-yl)amino]-5-

(fluoromethyl)oxolane-3,4-diol

9
91572539
(3R,4R,5R)-2-[(6-Amino-5-nitropyrimidin-4-
(3R,4R,5R)-2-[(6-amino-5-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
nitropyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

43
101234336
(2R,3R,4S,5R)-2-[[6-[Ethyl(methyl)amino]-
(2R,3R,4S,5R)-2-[[6-

5-nitropyrimidin-4-yl]amino]-5-
[ethyl(methyl)amino]-5-

(hydroxymethyl)oxolane-3,4-diol
nitropyrimidin-4-yl]amino]-5-

(hydroxymethyl)oxolane-3,4-diol

73
101262263
N-[4-Amino-6-[[(2R,3R,4S,5R)-3,4-
N-[4-amino-6-[[(2R,3R,4S,5R)-3,4-

dihydroxy-5-(hydroxymethyl)oxolan-2-
dihydroxy-5-(hydroxymethyl)oxolan-

yl]amino]pyrimidin-5-yl]formamide
2-yl]amino]pyrimidin-5-yl]formamide

74
135019247
[(2S,3R,5R)-5-[(6-Amino-5-nitropyrimidin-4-
[(2S,3R,5R)-5-[(6-amino-5-

yl)amino]-3-azidooxolan-2-yl]methanol
nitropyrimidin-4-yl)amino]-3-

azidooxolan-2-yl]methanol

75
135258154
2-[[6-Amino-5-(methylamino)pyrimidin-4-
2-[[6-amino-5-

yl]amino]-5-(hydroxymethyl)oxolan-3-ol
(methylamino)pyrimidin-4-yl]amino]-

5-(hydroxymethyl)oxolan-3-ol

10
137704644
(3S,4R,5S)-2-[(6-Amino-5-nitropyrimidin-4-
(3S,4R,5S)-2-[(6-amino-5-

yl)amino]-5-(hydroxymethyl)oxolane-3,4-
nitropyrimidin-4-yl)amino]-5-

diol
(hydroxymethyl)oxolane-3,4-diol

76
141378328
(2R,3S,4R,5R)-2-(Hydroxymethyl)-5-[6-
(2R,3S,4R,5R)-2-(hydroxymethyl)-5-

(methylamino)-9-oxidopurin-9-ium-9-
[6-(methylamino)-9-oxidopurin-9-

yl]oxolane-3,4-diol
ium-9-yl]oxolane-3,4-diol

The inventors carried out a fingerprint Tanimoto-based 3-dimensional similarity search (Tanimoto threshold=100%) of clitocine (compound CID129111) and identified 267 compounds. Then the inventors predicted the pharmacophore features of 15 compounds including clitocine that were randomly selected from said 267 identified compounds, as disclosed in Table 4, and analyzed the pharmacophore alignment using feature and alignment point. For example, the inventors showed a similarity of pharmacophore features between clitocine (CID_129111 corresponding to compound 1 of Table 1) and CID9795869 [(2R,3S,4R,5R)-2-Aminomethyl-5-(6-amino-5-nitro-pyrimidin-4-ylamino)-tetrahydro-furan-3,4-diol corresponding to compound 11 of Table 2] (FIG. 21).

TABLE 4

List of the 15 selected compounds, i.e. compounds 1, 11 and 77-90.

Com-
PubChem

pound
CID
Compound name
IUPAC name
Pharmacophore features

77
6245
Tubercidin
(2R,3R,4S,5R)-2-(4- aminopyrrolo[2,3- d]pyrimidin-7-yl)-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

78
8975
2-Fluoroadenosine
(2R,3R,4S,5R)-2-(6- amino-2-fluoropurin-9- yl)-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

79
60961
Adenosine
(2R,3R,4S,5R)-2-(6- aminopurin-9-yl)-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

80
439182
5′-Deoxyadenosine
(2R,3R,4S,5R)-2-(6- aminopurin-9-yl)-5- methyloxolane- 3,4-diol

[Image Omitted]

81
447199
Formycin
(2S,3R,4S,5R)-2-(7- amino-2H-pyrazolo[4,3- d]pyrimidin-3-yl)-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

82
448403
5′-Fluoro-5′- deoxyadenosine
(2R,3R,4S,5S)-2-(6- aminopurin-9-yl)-5 (fluoromethyl)oxolane- 3,4-diol

[Image Omitted]

83
472638
3-Cyclopentene-1,2- diol, 5-(6-amino-9H- purin-9-yl)-3-((1R)-1- hydroxy-2-propynyl)-, (1S,2R,5R)-
(1S,2R,5R)-5-(6- aminopurin-9-yl)-3- [(1R)-1-hydroxyprop-2- ynyl]cyclopent-3-ene- 1,2-diol

[Image Omitted]

11
9795869
(2R,3S,4R,5R)-2- Aminomethyl-5-(6- amino-5-nitro- pyrimidin-4-ylamino)- tetrahydro-furan-3,4- diol
(2R,3S,4R,5R)-2- (aminomethyl)-5-[(6- amino-5-nitropyrimidin- 4-yl)amino]oxolane- 3,4-diol

[Image Omitted]

84
10334232
(2R,3R,4S,5R)-2-[(6- Amino-5- nitropyridazin-4- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2R,3R,4S,5R)-2-[(6- amino-5-nitropyridazin- 4-yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

85
10446747
(2R,3R,4S,5R)-2-[(5- Amino-4- nitropyridazin-3- yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol
(2R,3R,4S,5R)-2-[(5- amino-4-nitropyridazin- 3-yl)amino]-5- (hydroxymethyl) oxolane- 3,4-diol

[Image Omitted]

86
10753174
5′-Deoxytubercidin
(2R,3R,4S,5R)-2-(4- aminopyrrolo[2,3- d]pyrimidin-7-yl)-5- methyloxolane-3,4-diol

[Image Omitted]

87
46876860
(3R,4S,5S)-2-(6- Aminopurin-9-yl)-5- (difluoromethyl) oxolane- 3,4-diol
(3R,4S,5S)-2-(6- aminopurin-9-yl)-5- (difluoromethyl) oxolane- 3,4-diol

[Image Omitted]

88
101875585
(2R,3S,4S,5S)-2-(6- Aminopurin-9-yl)-4,5- difluoro-5- (hydroxymethyl) oxolan- 3-ol
(2R,3S,4S,5S)-2-(6- aminopurin-9-yl)-4,5- difluoro-5- (hydroxymethyl) oxolan- 3-ol

[Image Omitted]

89
102006363
5,5-Difluoromethyl Adenosine
(2R,4S,5S)-2-(6- aminopurin-9-yl)-5- (difluoromethyl) oxolane- 3,4-diol

[Image Omitted]

90
118717403
(2R,3S,4R,5S)-2-(6- Aminopurin-9-yl)-4,5- difluoro-5- (hydroxymethyl) oxolan- 3-ol
(2R,3S,4R,5S)-2-(6- aminopurin-9-yl)-4,5- difluoro-5- (hydroxymethyl)oxolan- 3-ol

[Image Omitted]

Other features and advantages of the invention will be apparent from the examples which follow and will also be illustrated in the figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Sequence and structural differences between SARS-CoV-2 and SARS-CoV-1. 1A. The multiple sequence alignment of SARS-CoV-2 (6LU7) and SARS-CoV-1 (3V3M) showed 96% of sequence identity as (*). Other dissimilar residues are indicated in the box. 1B. Structural superimposition of the crystal structures of SARS-CoV-2 (White) and SARS-CoV-1 (Black). The modified sequence is shown in surface mesh view between the two proteins.

FIG. 2. Protein domains of SARS-CoV-2 with CID_129111. The ligand interacted towards the substrate-binding pocket of SARS-CoV-2.

FIG. 3. Molecular docking of 6LU7 and 7BQY with CID_129111. 3A. Molecular docking of 6LU7 showed the best-fit interactions with the S1 position. Interactions: Van der Waals: F140, H163, H164; Conventional Hydrogen Bond: L141, G143, S144, Q189; Carbon Hydrogen Bond: E166, M165; Pi-Sigma: N142; Pi-Alkyl: C145. 3B. Molecular docking of 7BQY showed a similar interaction with few other sites (S1, S2, S4). Interactions: Van der Waals: H41, Y118, F140, H163, H164, E166; Conventional Hydrogen Bond: L141, G143, S144, Q189; Carbon Hydrogen Bond: M165; Pi-Sigma: N142, Pi-Alkyl: C145. Both docking analyses 3A and 3B showed the Pi-sigma (N142) and Pi-Alkyl (C145) interactions.

FIG. 4. Repetition of molecular docking of 6LU7 with CID_129111. Said repetition showed the conventional H-bond (M165, T190) and carbon H-bond (E166, Q189) interactions as well as the Pi-Alkyl (M165) interaction in the S1′, S1, S2, S4 positions corresponding to the substrate-binding pocket in SARS-CoV-2.

FIG. 5. Interaction of 6LU7A with CID_129111 (Site-specific docking). Several conventional H bond (L141, G143, S144, E166) and carbon H-bond (M165, Q189) interactions as well as a Pi-Alkyl (C145) interaction were observed in the catalytic site. Van der Waals interactions were also observed (F140, N142, H163, H164, H172).

FIG. 6. Binding site analysis of FIPV (5EU8). The substrate-binding site (white cartoon bubble shape) was predicted by CASTp server, and the binding site residues were indicated in the box.

FIG. 7. Sequence and structural differences between SARS-CoV-2 and FIPV. 7A. The multiple sequence alignment of SARS-CoV-2 (6LU7) and FIPV (5EU8) showed 44.70% of sequence identity as (*). Other dissimilar residues are indicated in the box. 7B. Structural superimposition of the crystal structures of SARS-CoV-2 (White) and FIPV (Black).

FIG. 8. Two different approaches of FIPV (5EU8) docking analysis. 8A. Site-specific docking of SBD pocket with 25 Å radius. 8B. Global flexible ligand binding with the large radius of 60 Å.

FIG. 9. Site-specific ligand interaction with FIPV (5EU8). 9A-9B showed the protein-ligand interaction in molecular surface. 9C. SBD site interaction of main H-bond residues with Pi-Sigma (L164), Pi-Alkyl (L166) residues on surface. 9D. 2Dmap of CID_129111 residue interaction with FIPV. Interactions: Van der Weals: S48, P188, M190, Q191; Conventional Hydrogen Bond: T47, E165, G167, S189; Carbon Hydrogen Bond: L166, Q187; Pi-Sigma: L164; Pi-Alkyl: L166.

FIG. 10. 2Dmap of CID_129111 interaction with FIPV (5EU8). The conventional and carbon H-bond interactions were indicated in dotted lines. Conventional Hydrogen Bond: V26, E118, G142; Carbon Hydrogen Bond: N25, H41, G142. The ligand was present in the catalytic site, as shown by the marked residues H41 and C144 (see the arrows).

FIG. 11. Site-specific docking of SARS-CoV-1 (3V3M) with CID_129111. 11A. Surface view of residual interaction. 11B. 2Dmap of CID_129111 interaction. The Pi-Sulfur (C145) and the Amide-Pi-stacked (L141) contacts are shown in dark. Several conventional and carbon H-bond interactions were observed. Interactions: Van der Weals: M165, H172, Conventional Hydrogen Bond: F140, G143, S144, C145, N142, E166; Carbon Hydrogen Bond: N142, E166; Pi-Sulfur: C145; Amide-Pi Stacked: L141.

FIG. 12. 2D map of CID_129111 interaction with SARS-CoV-1 (3V3M). N142 and C145 had the H-bond and Pi interactions. Other H-bond interactions are L141 and S144. Interactions: Van der Weals: Y118, F140, G143, H163, M165, H164, E166, H172; Conventional Hydrogen Bond: L141, N142, S144, C145; Pi-Sigma: N142; Pi-Alkyl: C145.

FIG. 13. Binding site properties and the docking grid map of TGEV protein (2AMP). The binding sites of TGEV PocID2 (White) and PocID4 (Black) are indicated.

FIG. 14. Binding site properties and the docking grid map of PEDV protein (6L70).

FIG. 15. Binding site properties and the docking grid map of BCoV-HE protein (3CL5).

FIG. 16. Site-specific ligand interaction with TGEV (2AMP). 16A-16B showed the protein-ligand interaction in molecular surface. 16C. SBD site interaction of main H-bond residues with Pi-Alkyl residues on surface. 16D. 2Dmap of CID_129111 residue interaction with TGEV. Interactions: Van der Weals: H41, T47, F139, T143, H163, L164, E165 P188; Conventional Hydrogen Bond: 1140, G142 C144; Carbon Hydrogen Bond: H162; Pi-Alkyl: A141.

FIG. 17. Site-specific ligand interaction with PEDV (6L70). 17A-17B showed the protein-ligand interaction in molecular surface. 17C. SBD site interaction of docking pose 1 with H-bond residues with Amide-Pi-stacked residue. Interactions: Van der Weals: L164, G167, G169, L190, Q191; Conventional Hydrogen Bond: E165, Q187, T189; Carbon Hydrogen Bond: P188; Pi-Alkyl: L166; Amide-Pi Stacked: P188. 17D. SBD site interaction of docking pose 2 with H-bond residues with Pi-Alkyl residue. Interactions: Van der Weals: T47, Y117, F139, N141, A143, Q163; Conventional Hydrogen Bond: 1140, G142, C144, H162, E165; Carbon Hydrogen Bond: L164; Pi-Donor H Bond: C144.

FIG. 18. Site-specific ligand interaction with BCoV-HE (3CL5). 18A-18B showed the protein-ligand interaction in molecular surface. 18C. Molecular view of ligand interaction with H-bond residues. 18D. The 2D map of ligand interaction. Interactions: Van der Weals: T115, S116, Y217, G244, F245; Conventional Hydrogen Bond: K210, L212, T242; Carbon Hydrogen Bond: T114, F211, T243.

FIG. 19. 3D Structure of clitocine (CID_129111).

FIG. 20. Pharmacophore structure of clitocine (CID_129111).

FIG. 21. Similarity of pharmacophore features between clitocine (CID_129111) and CID9795869 ((2R,3S,4R,5R)-2-Aminomethyl-5-(6-amino-5-nitro-pyrimidin-4-ylamino)-tetrahydro-furan-3,4-diol; compound 11 of Table 2). 21A. Pharmacophore alignment of both compounds. 21B. Pharmacophore features of CID_129111. 21C. Pharmacophore features of CID_9795869. (HBA=Hydrogen Bond Acceptor; HBD=Hydrogen Bond Donor; AR=Aromatic Ring).

FIG. 22. Molecular docking of 3CL protease of SARS-CoV-2 with either Mizoribine (A) or clitocine (B)

FIG. 23. Molecular docking of 6M71 RNA dependent RNA polymerase (SEQ ID NO. 8) of SARS-CoV-2 with either clitocine (A) or Mizoribine (B)

FIG. 24. Molecular docking of 7BV1 RNA dependent RNA polymerase (SEQ ID NO. 9) of SARS-CoV-2 with either clitocine (A) or Mizoribine (B)

FIG. 25. Molecular docking of 7BV2 RNA dependent RNA polymerase (SEQ ID NO. 10) of SARS-CoV-2 with either clitocine (A) or Mizoribine (B)

FIG. 26. Molecular docking of 7BW4 RNA dependent RNA polymerase (SEQ ID NO. 11) of SARS-CoV-2 with either clitocine (A) or Mizoribine (B)

FIG. 27. measurement of virus production after treatment with either clitocine (A) or mizoribine (B) The determination of SARS-CoV-2 virus production was performed after treatment with increased drug concentration of clitocine (IRSEA-NACI-1) and mizoribine (IRSEA-NACI-4) and compared to a negative control (consisted in untreated sample) and a positive control using remdesivir (6 μM). IC50 and IC90 were determined. Virus production was shown to decrease significantly according to a dose response curve with both compounds.

FIG. 28. measurement of copy genome number after treatment with either clitocine (A) or mizoribine (B) The determination of genome copy number was performed by RT-qPCR on the E gene of the SARS-CoV-2 virus after treatment with increased drug concentration of clitocine (IRSEA-NACI-1) and mizoribine (IRSEA-NACI-4) and compared to a negative control (consisted in untreated sample) and a positive control using remdesivir (6 μM). IC50 and IC90 were determined. Genome copy number was shown to decrease significantly according to a dose response curve with compound IRSEA-NACI-1.

FIG. 29. Toxicity testing in Vero cells with compounds IRSEA1 (clitocine) and IRSEA4 (mizoribine) Toxicity in Vero cells was tested with increasing doses of the tested compound from 0.0001 to 1000 μM. the effect of the compounds show a certain degree of toxicity depending on the dose. The CC50 was calculated and was 3.092 μM for IRSEA1 and 191.2 μM for IRSEA4.

FIG. 30. Toxicity testing in CALU3 cells (human lung cancer epithelial cell line) with compounds NACI-1 (clitocine) and NACI-4 (mizoribine) Toxicity in CALU3 cells was tested with increasing doses of the tested compound with 2 fold dilution (A) and 10 fold dilution (B). the number of cells was normalized over non-treated (NT) condition.

EXAMPLES
Example 1. Study of Molecular Interactions of High-Resolution Experimental Structure of SARS-CoV-2, i.e. COVID-19 Virus, Mpro with CID-129111 Using Docking Analysis
Computational Methods
Protein and Ligand Collection

The crystallography structure of SARS-CoV-2 Mpro in complex with an inhibitor N3 at two different resolutions was obtained from the protein databank [PDB ID: 6LU7 (2.16 A°) & 7BQY (1.7 A°)] (Jin et al., Nature, 2020, 1-5). The 3D structure of clitocine (CID_129111) was collected from PubChem database.

The SARS-CoV-2 Mpro [PDB ID: 6LU7 (2.16 A°)] has an amino acid sequence as defined in SEQ ID NO: 1.

The SARS-CoV-2 Mpro [PDB ID: 7BQY (1.7 A°)] has an amino acid sequence as defined in SEQ ID NO: 4.

Molecular Docking Study

The molecular docking calculations were carried out using DockingServer (Bikadi and Hazai, J. Cheminform. 2009, 1, 15 and https://www.dockingserver.com). Gasteiger partial charges were added to the ligand atoms. Non-polar hydrogen atoms were merged, and rotatable bonds were defined. Docking calculations were carried out on 6LU7 and 7BQY protein models. Essential hydrogen atoms, Kollman united atom type charges, and solvation parameters were added with the aid of AutoDock tools (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). AutoDock parameter set- and distance-dependent dielectric functions were used in the calculation of the van der Waals and the electrostatic terms, respectively. Docking simulations were performed using the Lamarckian genetic algorithm (LGA) and the Solis & Wets local search method (Solis, F. J., & Wets, R. J. B. Math. Oper. Res., 1981, 6(1), 19-30). Initial position, orientation, and torsions of the ligand molecules were set randomly. The protein-ligand interaction were determined with gird size of binding site radius (like 20 or 25 Å) for the analysis of ligand affinity towards the protein.

Docking Analysis I and II (SARS-CoV-2_6 LU7A with CID_129111)

The affinity (grid) maps of 60×60×60 Å (nx, ny, and nz) grid points and cx=−26.1, cy=12.68, cz=58.85 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662) was optimized using MMFF94 gasteiger charge calculation method and the ligand had MMFF94 energy of 28.19533 kcal/mol. All rotatable torsions were released during docking. Each docking experiment was derived from 100 different runs that were set to terminate after a maximum of 2500000 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 Å, and quaternion and torsion steps of 5 were applied. The docking process was repeated for the validation of the protein-ligand interactions with the same parameters. Both analyses (I and II) were performed as a flexible docking approach with the large radius range (60 Å).

Docking Analysis III (SARS-CoV-2_7BQYA with CID_129111)

The grid maps of 30×30×30 Å (nx, ny, nz) grid points and cx=9.103367, cy=−0.928102, cz=22.691245 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The docking simulation was performed for the flexible ligands into the site-specific binding pocket (radius 30 Å). Furthermore, the same parameters for ligand and docking run were used for the analysis. The residual interactions were analyzed using UCSF chimera, LigPlot and Discovery studio visualizer tool.

Docking Analysis IV (Site-Specific-Low Radius)

The grid maps of 20×20×20 Å (nx, ny, nz) grid points and cx=−10.711837, cy=12.411388, cz=68.831286 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The docking simulation was performed for the flexible ligands into the site-specific binding pocket (low radius 20 Å).

Results and Discussion
Docking Analysis

A sequence alignment as well as the structural superimposition of the crystal structures of SARS-CoV-2 and SARS-CoV-1 are shown in FIG. 1.

The Mpro of SARS-CoV-2 (PDB: 6LU7A and 7BQYA) was docked to CID_129111 using Autodock tools. The inventors analyzed out the compound CID_129111 with the recently deposited crystal structures having 2 different resolutions (PDB: 6LU7A and 7BQYA). The inventors selected the best ligand interaction file based on hydrogen bond, docking pose and the ligand binding free energy values, and obtained top hit ligand-binding poses from the different docking analyses.

Previously, the substrate-binding pocket of SARS-CoV-2 was reported as P1, P1′, P2, P3, P4 and P5 sites of N3 inhibitor and the report suggested that the compound cinaserin occupied the substrate-binding pocket by interacting with H41 and E166 residues (Jin et al., Nature, 2020, 1-5). Another report suggested that the compound ZINC000541677852 was maintaining the key interactions of Q189, and M149 as hydrophobic and the C145, H164, E166 as H-bond interactions (Ton et al., Molecular Informatics, 2020, 1-8).

The present results also revealed that the ligand had the interaction in the same binding site of N3 inhibitor (Domain II) (FIG. 2). The first docking (Rank 1) had a lowest estimation binding free energy (−6.36 kcal/mol (6LU7A) and −6.92 kcal/mol (7BQYA)) with subsite 1 (S1) corresponding to N3 inhibitor substrate-binding pocket (Jin et al., Nature, 2020, 1-5). Furthermore, the residual interactions of ligand showed several H-bonds (L141, G143, S144, M165, Q189), Pi-Alkyl (C145) and Pi-sigma (N142) interactions (FIG. 3; Table 5 below). A similar interaction was reported in earlier studies (Ton et al., Molecular Informatics, 2020, 1-8, 2020; Jin et al., Nature, 2020, 1-5). In general, the Pi-sigma bonds were exhibiting stronger interactions than the Pi bonds, and the Pi-Alkyl bonds were depicting the least overlapping in the orbitals.

Then the inventors repeated the same analysis with 200 runs of docking simulation using SARS-CoV-2 structure (6LU7A), the ligand interaction showed the similar estimation binding-free energy of −6.33 kcal/mol in the N3 substrate binding pocket with outstanding H-bond (E166, M165, Q189, T190) residual interactions (FIG. 4).

Once again, the inventors performed the molecular docking analysis of 6LU7 to reconfirm the residual interaction within the lowest radius grid size or the site-specific interaction of ligand towards the protein SARS-CoV-2. The results reconfirmed that the ligand served strong double H-bond interaction with S1 position (L141 and E166) and one H-bond with S144. Furthermore, the other carbon H-bond interaction was displayed in the S2 (M165) and S4 (G189) positions (FIG. 5). All the docking results are shown in Table 5.

TABLE 5

The residual interaction and the binding-free energy value of SARS-CoV-2 Mpro-ligand docking.

Est.
Est.

Hydrophobic

Free
Inhibition

interactions
Grid

Energy of
Constant,

(Pi-Alkyl/Pi-
radius

Int.

Rank
PDB_ID_Chain
Binding
Ki
H bond
Sigma)
(Å)
Frequency
Surface

1
6LU7_A
−6.36
21.88 uM
L141, G143,
N142, C145
60 × 60 ×
1%
561.784

kcal/mol

S144, M165,

60

Q189

Repeat
6LU7_A
−6.33
22.85 uM
E166, M165,
M165
60 × 60 ×
1%
560.077

kcal/mol

Q189, T190

60

1
7BQY_A
−6.92
8.53 uM
L141, G143,
N142, C145
30 × 30 ×
3%
606.11

kcal/mol

S144, M165,

30

Q189

1
6LU7_A
−6.89
8.97 uM
L141, G143,
C145
20 × 20 ×
11%
599.449

kcal/mol

S144, M165,

20

E166, Q189

Earlier computational studies suggested many compounds (Lopinavir, Ritonavir, Beclabuvir, Saquinavir, Nelfinavir, Atazanavir, Ledipasvir, Elbasvir, Efavirnez) as potential drug targets for SARS-CoV-2 using computational docking simulation with preliminary clinical data (Wang et al., Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment. Biosci Trends. 2020; Sekhar Talluri. (2020) Virtual Screening Based Prediction of Potential Drugs for COVID-19. Preprint. Doi: so 10.20944/preprints202002.0418.v2; Xu et al., 2020, Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation. bioRxiv. doi:10.1101/2020.01.27.921627; Beck et al., 2020, Predicting commercially available antiviral drugs that may act on the is novel coronavirus (2019-nCoV), Wuhan, China through a drug-target interaction deep learning model. bioRxiv, Doi: 2020.01.31.929547; Gao et al., 2020, Machine intelligence design of 2019-nCoV drugs. bioRxiv. 2020.01.30.927889). The previous computational results reported a very low binding energy from −10 to −11 kcal/mol. The scoring functions were different from one to another docking software.

In the present study, the inventors screened the molecular interaction of CID_129111 with the prominent non-polar covalent bonding with SARS-CoV-2. The inventors computationally proved that the CID_129111 had stronger interaction with the protein with different docking parameters. All the results revealed that the best-fit docking poses occurred as the first ranking based on estimation binding-free energies and the residual contacts.

Conclusion

In summary, CID_129111 may act as a best drug target candidate for the new X-ray crystallography structure of SARS-CoV-2. The docking prediction and ranking of ligand binding poses were significant to understand the molecular inter-connections with the protein. The study could drive a central way to achieve the clinical and in vitro studies in the future.

Example 2. Study of Molecular Interactions of High-Resolution Experimental Structure of the Main Protease (Mpro) of FIPV and SARS-CoV-1 with CID-129111 Using Docking Analysis
Computational Methods
Protein and Ligand Collection

The crystallography structures of FIPV main protease in complex with dual inhibitors (Mpro/3CL) (PDB ID: 5EU8_2.45 Å) (Wang et al., Journal of virology, 2016, 90(4), 1910-1917) and of SARS-CoV-1 in complex with N-[(1R)-2-(tert-butylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-N-(4-tert-butylphenyl)furan-2-carboxamide inhibitor (PDB ID: 3V3M_1.96 Å) were obtained from the protein databank. The 3D structure of clitocine (CID_129111) was collected from PubChem database.

The FIPV Mpro [PDB ID: 5EU8_2.45 Å] has an amino acid sequence as defined in SEQ ID NO: 3.

The SARS-CoV-1 Mpro [PDB ID: 3V3M_1.96 Å] has an amino acid sequence as defined in SEQ ID NO: 2.

Molecular Docking Study

Molecular docking study was carried out as reported in Example 1, except that docking calculations were carried out on 5EU8 and 3V3M protein models. The inventors performed the protein-ligand interaction by increasing the binding site radius (around 20 or 25 Å to 60 Å) for the comparative prediction of ligand affinity towards the protein.

Binding Site Analysis

The inventors submitted the specific chain (A) of FIPV and SARS-CoV-1 proteins to computed atlas of surface topography of protein (CASTp) server for the prediction of binding site pockets using alpha shape method.

Substrate Binding Site Prediction

The substrate bounded protein complex models were submitted to Discovery studio visualizer. Then the inventors removed the water from the crystallography structure and selected the ligand groups for displaying the substrate-binding site (SBD), which showed as a sphere shape around the SBD site. Furthermore, the inventors collected the attribute of the sphere to find the XYZ grid for the docking analysis.

Docking Analysis I and II (FIPV with CID_129111)

The affinity (grid) maps of 25×25×25 Å (nx, ny, and nz) grid points and cx=−46.30, cy=−15.30, cz=−10.73 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The ligand (clitocine, CID_129111) was optimized using MMFF94 gasteiger charge calculation method and the ligand had MMFF94 energy of 28.19533 kcal/mol. All rotatable torsions were released during docking. Each docking experiment was derived from 100 different runs that were set to terminate after a maximum of 2500000 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 Å, and quaternion and torsion steps of 5 were applied. The docking analysis II was performed by the grid maps of 60×60×60 Å (nx, ny, nz) grid points and cx=−46.30, cy=−15.30, cz=−10.73 were selected as a grid box. Furthermore, the same parameters of ligand and docking run were used for the analysis.

Docking Analysis III and IV (SARS-CoV-1 with CID_129111)

The grid maps of 20×20×20 Å (nx, ny, nz) grid points and cx=24.44, cy=−28.68, cz=−3.94 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The docking simulation was performed for the flexible ligands into the site-specific binding pocket (radius 20 Å). The docking analysis IV was performed by the grid maps of 60×60×60 Å (nx, ny, nz) grid points and cx=24.44, cy=−28.68, cz=−3.94 were selected as a grid box. The same parameters of ligand and docking run were used for the analysis. Furthermore, the residual interactions were analyzed using UCSF chimera, Discovery studio visualizer tool.

Results and Discussion
Binding Site Analysis

The binding pockets were predicted around 1.4 radius probe in the protein model. FIPV has several sites on the domain interface, and surface sites. The inventors focused on the substrate-binding area (119.519 A²) and the volume of the pocket (63.807 A³), depicted as white cartoon bubble shape (FIG. 6). Additionally, the inventors tabulated the SBD residues of FIPV. SARS-CoV-1 has the similar binding pocket of SARS-CoV-2 with the residual changes.

The Mpro of FIPV (PDB: 5EU8) and SARS-CoV-1 (PDB: 3V3M) were docked to CID_129111 using Autodock tools. The inventors performed the sequence alignment and superimposition of SARS-CoV-2 and FIPV for the prediction of structural matches between proteins (FIG. 7).

The inventors selected the best ligand interaction file based on hydrogen bond, docking pose and the ligand binding free energy values. The inventors obtained top hit ligand-binding poses from the different docking analyses. The inventors used two main approaches of FIPV docking analysis: one based on site-specific docking of SBD pocket and another one based on the global flexible ligand binding with the largest docking radius (FIG. 8).

Regarding the structure of Mpro FIPV, it has been reported that the protein had SBD site for the accommodation of N3 complex and the dual inhibitor molecules in the bound structure. Additionally, the SBD site of FIPV was very similar to the transmissible gastroenteritis coronavirus (TGEV) SBD site in the pig. It has also been reported that the SBD sites were classified as S1, S2, S3, S4, S5 and S′ subsites. The key amino acids N25, V26, L27, H41, T47, Y53, F139, C144, H162, H163, L164, E165, G167, Q187, P188, S189, M190 were constituting the SBD sites for the inhibitors. The catalytic residues H41 and C144 were present in the FIPV structure (Wang et al., Journal of virology, 2016, 90(4), 1910-1917).

Docking Analysis I

The CID_129111 was docked to the 5EU8A structure by site-specific interaction. In the present invention, the CID_129111 had molecular interactions with the SBD site of FIPV with several strong H-bond contacts. The 4^thbinding pose had lowest estimation binding free energy (−7.15 kcal/mol with all the corresponding positions of S1, S2, S3, S4 in SBD site as reported previously (Wang et al., Journal of virology, 2016, 90(4), 1910-1917). Furthermore, the inventors observed several H-bond (T47, E165, L166, G167, Q187, S189), Pi-Sigma (L164), Pi-Alkyl (L166) interactions (Table 6 below). The similar residual interaction was reported in earlier studies (Theerawatanasirikul, S., et al. Antiviral Research, 2020, 174, 104697). The Pi-Sigma showed very strong contact with the ligand equivalent to the H-bond. This result confirmed that the ligand occupied the SBD site and created favorable strong contacts with the FIPV protein (FIG. 9).

Docking Analysis II

The CID_129111 was docked to the 5EU8A structure with 60 Å radius. The results showed that the CID_129111 compound had several H-bond contacts (N25, V26, E118, and G142), but the ligand was able to perform the interaction at the SBD site, while the inventors carried out the docking procedure using the global flexible method. The estimation binding free energy score (−6.00 kcal/mol) was little less compared to the site-specific docking (FIG. 10).

Docking Analysis III

The inventors obtained the molecular docking results of SARS-CoV-1 with CID_129111 on site-specific interaction. These results prominently depicted that CID_129111 had a very strong interaction with the SARS-CoV-1 structure (FIG. 11).

The H-bond contact (F140, N142, G143, S144, C145, E166) of ligand showed that the ligand occupied well the SBD site by building the Pi-Sulfur interaction with the C145 residue and the Amide Pi-stacked interaction in L141 residue. The docking score of FIPV was computed as −6.89 kcal/mol of binding-free energy with CID_129111 (Table 6).

TABLE 6

The residual interaction and the binding-free energy value of FIPV and SARS-CoV-1 Mpro-ligand docking.

Hydrophobic

interactions

Est.
Est.

(Pi-Alkyl/Pi-

Free
Inhibition

Sigma/Pi-
Grid

Binding

Energy of
Constant,

Sulfur/Amide-
radius

Int.

S. No
pose
Receptor_PDB_Chain
Binding
Ki
H bond
Pi-Stacked)
(Å)
Frequency
Surface

1
4
FIPV_5EU8A
−7.15
5.71 uM
T47, E165,
L164, L166
25 × 25 ×
5%
545.296

kcal/mol

L166, G167,

25

Q187, S189

2
1
FIPV_5EU8A
−6.00
40.29 uM
N25, V26,

60 × 60 ×
2%
521.906

kcal/mol

H41, E118,

60

G142

3
1
SARS-
−6.89
8.96 uM
F140, N142,
L141, C145
25 × 25 ×
17%
456.859

CoV-1_3V3MA
kcal/mol

G143, S144,

25

C145, E166

4
2
SARS-
−6.35
22.19 uM
L141, N142,
N142, C145
60 × 60 ×
2%
510.517

CoV-1_3V3MA
kcal/mol

S144, C145

60

Docking Analysis IV

The inventors obtained the molecular docking results of SARS-CoV-1 with CID_129111 on global-flexible docking analysis. The estimation binding-free energy showed −6.35 kcal/mol and the inhibition constant was of 22.19 uM in the flexible blind docking. FIG. 12 shows the H-bond residues (L141, N142, S144, C145) and hydrophobic residues (N142 and C145). These results are in accordance with the similar residual interaction that has been reported for SARS-CoV-1 studies (Jacobs et al., Journal of medicinal chemistry, 2013, 56(2), 534-546). Specifically, the C145 residue had the covalent bonding with CID_129111 as reported in the SARS-CoV-2 study (Ton et al., Molecular Informatics, 2020, 1-8).

In the prior art, several compounds have been used as a potential drug target for FIPV (Theerawatanasirikul, S., et al. Antiviral Research, 2020, 174, 104697) and SARS-CoV-1 (Jacobs et al., Journal of medicinal chemistry, 2013, 56(2), 534-546). Three molecules have also been reported as drug-like fragments (NSC87511, NSC343256, and NSC345647) for FIPV using computational docking study. The protein-ligand interactions observed by the inventors were corroborated with the previous reports of residual interactions. The inventors screened the molecules using important strategies of selecting the molecule based on binding poses of ligand interaction with the non-polar covalent bonding and the binding-free energies. All the best-fit docking poses were obtaining the estimation, binding-free energies and the best residual contacts.

Conclusion

In summary, the ligand showed strong affinity towards FIPV and SARS-CoV-1. Therefore, CID_129111 may act as a best drug target candidate for the FIPV and the SARS-CoV-1 protein models. The inventors utilized the application of in silico-based analysis of protein-ligand interactions and the ligand screening approaches.

Example 3. Study of Molecular Interactions of High-Resolution Experimental Structure of the Main Protease (Mpro) of Porcine Transmissible Gastroenteritis Virus (TGEV), Porcine Epidemic Diarrhea Virus (PEDV) and Bovine Coronavirus Hemagglutinin-Esterase (BCoV-HE) with CID-129111 Using Docking Analysis
Computational Methods
Protein and Ligand Collection

The crystallography structure of porcine transmissible gastroenteritis virus (TGEV) Mpro in complex with an inhibitor N1 (Mpro/3CL) (PDB ID: 2AMP_2.70 Å) and of porcine epidemic diarrhea virus (PEDV) Mpro with GC376 (Mpro/3CL) (PDB ID: 6L70_1.56 Å) were obtained from the protein databank. The crystallography structure of bovine coronavirus HE (BCoV-HE) in complex with 4,9-O-diacetyl sialic acid (PDB ID: 3CL5_1.80 Å) was also obtained from the protein databank. The protein chain was selected for the docking analysis. The 3D structure of clitocine (CID_129111) was collected from PubChem database.

The TGEV Mpro [PDB ID: 2AMP_2.70 Å] has an amino acid sequence as defined in SEQ ID NO: 5.

The PEDV Mpro [PDB ID: 6L70_1.56 Å] has an amino acid sequence as defined in SEQ ID NO: 6.

The BCoV-HE [PDB ID: 3CL5_1.80 Å] has an amino acid sequence as defined in SEQ ID NO: 7.

Molecular Docking Study

Molecular docking study was carried out as reported in Example 1, except that docking calculations were carried out on 2AMP, 6L70 and 3CL5 protein models. The inventors performed the protein-ligand interaction using site-specific docking (radius around 25 Å) for the prediction of ligand affinity towards the substrate-binding site of the protein.

Binding Site Analysis

The inventors submitted the specific chain (A) of TGEV, PEDV and BCoV-HE proteins to computed atlas of surface topography of protein (CASTp) server for the prediction of binding site pockets using alpha shape method.

Substrate-Binding Site Prediction

The substrate bounded protein complex models were submitted to Discovery studio visualizer. Then the inventors removed the water from the crystallography structure and selected the ligand groups for displaying the substrate-binding site (SBD), which showed as a sphere shape around SBD site. Furthermore, the inventors collected the attribute of the sphere to find the XYZ grid for the docking analysis.

Docking Analysis of TGEV (2AMP) with CID_129111

The affinity (grid) maps of 25×25×25 Å (nx, ny, and nz) grid points and cx=−8.403247, cy=−18.692871, cz=−15.677409 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The ligand (CID_129111) was optimized using MMFF94 gasteiger charge calculation method and the ligand had MMFF94 energy of 28.19533 kcal/mol. All rotatable torsions were released during docking. Each docking experiment was derived from 100 different runs that were set to terminate after a maximum of 2500000 energy evaluations. The population size was set to 150. During the search, a translational step of 0.2 Å, and quaternion and torsion steps of 5 were applied.

Docking Analysis of PEDV (6L70) with CID_129111

The grid maps of 25×25×25 Å (nx, ny, nz) grid points and cx=18.619949, cy=−13.207831, cz=−1.351508 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The docking simulation was performed for the flexible ligands into the site-specific binding pocket (radius 25 Å). Furthermore, the same parameters of ligand and docking run were used for the analysis.

Docking Analysis of BCoV-HE (3CL5) with CID_129111

The grid maps of 25×25×25 Å (nx, ny, nz) grid points and cx=19.349311, cy=−11.999508, cz=−15.461000 were selected as a grid box. The 0.375 Å spacing was generated using the Autogrid program (Morris, G. M., et al. J. Comput. Chem., 1998, 19(14), 1639-1662). The docking simulation was performed for the flexible ligands into the site-specific binding pocket (radius 25 Å). Furthermore, the same parameters of ligand and docking run were used for the analysis, and the residual interactions were analyzed using UCSF chimera, Discovery studio visualizer tool.

Results and Discussion
Binding Site Analysis

The binding pockets were predicted around 1.4 radius probe in the protein model. There are several sites on the domain interface and surface sites. The inventors focused on substrate binding area and the volume of the pocket (FIGS. 13, 14 and 15). Additionally, the inventors tabulated the SBD residues of the TGEV, PEDV and BCoV-HE. Few similar conserved residues were present in SARS-CoV-1 and SARS-CoV-2.

The inventors selected the best ligand interaction file based on hydrogen bonds, docking pose and the ligand binding free energy values. The inventors obtained top hit ligand-binding poses from the different docking analyses. In this study, the inventors focused mainly on the SBD site with short docking radius.

Docking Analysis of TGEV

CID_129111 was docked to the TGEV structure (2AMPA) using site-specific docking analysis. In this study, the inventors observed the molecular interactions of the ligand (CID_129111) in the SBD site of TGEV with several strong H-bond contacts. The first rank binding pose had very lowest estimation binding free energy (−7.39 kcal/mol) with all the corresponding position of S1, S1′ and S2 SBD site as reported previously (Wang et al., Journal of virology, 2016, 90(4), 1910-1917; Jin et al., Structure of M pro from COVID-19 virus and discovery of its inhibitors, Nature, 2020). Additionally, the interaction site was similar to the P1, P2, P3 of new SARS-CoV-2 report (Zhang, et al. Science, 2020, 368(6489), 409-412). Furthermore, the inventors observed several H-bonds (1140, G142, C144, H162), Pi-Alkyl (A141) interactions (Table 7 below). The similar residual interaction was reported in the earlier studies on feline infectious peritonitis virus (FIPV) protein (Theerawatanasirikul, S., et al. Antiviral Research, 2020, 174, 104697). This result confirmed that the ligand engaged to the SBD site and formed favorable strong contacts with the TGEV protein (FIG. 16).

Docking Analysis of PEDV

The CID_129111 was docked to the 6L70A structure with 25 Å radius. The results showed that the ligand had several strong H-bond contacts (E165, Q187, P188, T189) and Pi-Alkyl (L166, P188), Amide-Pi Stacked (P188). The ligand had the best amide bond interaction with the protein. The inventors also observed the docking pose 2 for this protein, which showed more H-bond interactions (1140, G142, C144, H162, E165) and Pi-Donor (C144). The ligand was able to perform the interaction at the SBD site and make interactions with the catalytic link with the C144 residue. An estimation binding free energy score of Pose 1=−7.13 kcal/mol and Pose 2=−7.09 kcal/mol was obtained (FIG. 17).

Docking Analysis of BCoV-HE

The inventors obtained the molecular docking results of BCoV-HE with CID_129111 on site-specific interaction. Usually the crystal structure of HE protein is complexed with 0-diacetyl sialic acid. The present result showed that the ligand occupied the corresponding SBD site (FIG. 18). The strong H-bond of ligand interactions (T114, L210, F211, L212, T242, T243) were observed in the SBD site. The docking score of BCoV-HE was computed as −6.99 kcal/mol of binding-free energy with CID_129111 (Table 7). The ligand interaction was identified only for the conventional and carbon-hydrogen bonds.

TABLE 7

The residual interaction and the binding-free energy value of FIPV and SARS-CoV Mpro-ligand docking.

Hydrophobic

Est.
Est.

interactions

Free
Inhibition

(Pi-Alkyl/Pi-
Grid

Binding

Energy of
Constant,

Donor/Amide-
radius

S. No
pose
Receptor_PDB_Chain
Binding
Ki
H bond
Pi-Stacked)
(Å)
Frequency

1
1
TGEV_2AMPA
−7.39
3.81 uM
I140, G142,
A141
25 × 25 ×
16%

kcal/mol

C144, H162

25

2
1
PEDV_6L70
−7.13
5.92 uM
E165, Q187,
L166, P188
25 ×
10%

kcal/mol

T189

25 × 25

3
2
PEDV_6L70
−7.09
6.34 uM
I140, G142,
C144
25 × 25 ×
5%

kcal/mol

C144, H162,

25

E165

4
1
BCoV-
−6.99
7.49 uM
T114, L210,

25 × 25 ×
9%

HE_3CL5
kcal/mol

F211, L212,

25

T242, T243

Several inhibitors have been used to make a crystallographic structure complex such as chloromethyl ketone (CMK) (Yang, H., et al, PLoS biology, 2005, 3(10)), GC376 (Ye, G., et al. Viruses, 2020, 12(2), 240), 0-diacetyl sialic acid and acetic acid (Zeng, Q., et al. PNAS, 2008, 105(26), 9065-9069). The protein-ligand interactions observed by the inventors were in accordance with the previous reports of residual interactions. The inventors screened the molecules using important strategies of selecting the molecule based on binding poses of ligand interaction with the non-polar covalent bonding and the binding-free energies. All the best-fit interactions were obtained in the first rank of docking poses with the estimation, binding-free energies and the SBD residual contacts.

Conclusion

In summary, the ligand showed strong affinity towards the proteins. Therefore, CID_129111 may act as a best drug target candidate for TGEV, PEDV and BCoV-HE protein models. The inventors utilised the novel computational application of the protein-ligand interactions to screen the binding affinity of ligands.

Example 4—Evaluation of Antiviral Activity of 3 Illustrative Compounds on Infection and Replication of SARS-CoV-2 and Evaluation of Cell Toxicity

The compounds designated NACI-1 (for clitocine) and NAIC-4 for mizoribine were chosen to be tested for their antiviral activity on SARS-CoV-2 and for their toxicity on various cells.

Material and Methods

Seeding of cells and treatment with compound of interest were performed with each compound in triplicate at 5 concentrations, including negative and positive controls. Infection with SARS-CoV-2 was performed at one MOI (multiplicity of infection). Viral particles were recovered in the supernatant after incubation and quantification using TCID50 (tissue culture infectious dose 50%) and RT-PCR was performed. Toxicity measurement of compounds was made on separate cell lines.

D1: cell seeding on 96 wells plate, Vero E6 cells. Growth conditions: medium DMEM high glucose (Dutsher L0104-500, lot MS008A)

D2: dilution of compounds was carried out in a mix of 100% DMSO diluted to 50% in PBS (NACL-2) or in PBS at 10 nM stock to avoid solubility issues of some compounds. Compounds were tested at 5 concentrations, from 10⁻⁴M to 10⁻⁸M by serial tenfold dilutions. Infection with SARS-CoV-2 clinical strain was performed to MOI 10⁻³.

D3: viral titers were determined by TCID50 method and calculated by the Spearman & Kärber algorithm. RT-qPCR on gene E of SARS-CoV-2 was determined by Taqman One-Step RT-qPCR.

Infection process: at T0 infection was performed with SARS-CoV-2 MOI 10⁻³(0.001). At T0+1 h virus was removed and the plates were washed with PBS (2×1 mL), 1 mL medium was then added with compound from 100 μM to 10 nM. A 24 h incubation step was carried out. At T0+25 h, 500 μL of supernatant was recovered and TCID50 processing and RT-qPCR were performed. Following 4 additional days of incubation the endpoint was obtained and TCI D50 reading and calculation was performed.

Results: Virus Production (FIG. 27)

Treatment with NACI-1 was able to induce a 3 log decrease in viral production at 10 μM with the dose response curve. At 100 μM, some toxicity was observed. If confirmed this should lead to toxicity testing to determine therapeutic window. NACI-1 displays an IC50 of 188 nM, which is 5 times lower than that of Remdesivir (known IC50 of 1 μM).

Treatment with NACI-4 was able to induce a 2 to 3 log decrease in viral production with the dose response curve. NACI-4 displays an IC50 of 660 nM, which is 3 times lower than that of NACI-1

Results: RT-qPCR (FIG. 28)

Treatment with NACI-1 was able to induce an almost 2 log decrease in copy genome at 10 μM with a dose response curve. At 100 μM some toxicity was observed. If confirmed this should lead to toxicity testing to determine therapeutic window. NACI-1 displays an IC50 of 176 nM which confirms the inhibitory effect found using TCID50. IC90 is higher due to the slope of the qPCR curve.

Treatment with NACI-4 does not impact virus genome copy number. Its MOI could be different from the MOI of NACI-1.

Results on Toxicity Testing on Vero Cells (FIG. 29)

Vero cells were plated in 96 well plates at 10 k/well. 24 h post seeding, cells were treated with each compound at the indicated concentration. 24 h post treatment, cells were fixed, nuclei were stained with Hoechst 33342 and cell number/condition determined using an internal toxicity algorithm. CC50 was calculated on internal software with DMSO taken as a control. For clitocine (i.e., NACI-1 or IRSEA1), CC50 was 3.093 μM whereas for Mizoribine (i.e., NACI-4 or IRSEA4), CC50 was 191.245 μM

Conclusions

Potent antiviral activity has been detected for NACI-1 and NACI-4 (also designated respectively as IRSEA1 and IRSEA4). NACI-1 has shown some degree of toxicity on Vero cells depending on the concentration used. NACI-2 was later disregarded because its activity on virus production was found less effective than the activity of the other compounds.

Accordingly further toxicity testing has been performed on CaLu3 cells (lung cancer epithelial cell line). The cells were grown in DMEM medium without phenol red (D1145; Sigma Aldrich) supplemented with 10% FBS (Eurobio-Scientific), 1 mM sodium pyruvate (S8636; Sigma-Aldrich), L-Glutamine (G7513; Sigma Aldrich) and Penicillin-Streptomycin solution (P0781; Sigma Aldrich).

Cells were plated at 10 per well in Corning Cell bind 96 well plates in complete DMEM. 24 h post seeding, cells were treated with test compound at the indicated concentration, in triplicate. Cells were then incubated at 37° C. and 5% CO2 for 48 h.

One-time post treatment cells were fixed with 4% formalin (Sigma) for 10 min eat RT, washed with PBS and incubated with PBS Hoechst 33342 (1 mg/mL). Data acquisition by high content microscopy was performed on a Thermo CellInsight CX7 HCS microscope using a compartmental analysis algorithm. Results are extracted, normalized over the vehicle-treated condition, and expressed as the average of the three independent wells+/−SD.

Results and conclusion: NACI-1 and 4 display respective CC50 of 108 μM, and 850 μM on human lung cancer epithelial cells (FIGS. 30A and B). These compounds accordingly are suitable for further testing for their application against infection by a coronavirus.

Binding Capability of Illustrative Compounds to RdRp 6M71 of SARS-Cov-2

Alkyl/Pi-Alkyl/Pi-

Sigma/Pi-Anion/Pi-

piT-shaped/Pi-

Est.

Carbon
Sulfur/Halogen

Free

H-bond/
(Fluorine)/Amide-

Energy

Energy of
Conventional
Pi-Donor
Pi-Stacked/Pi-

model

Compounds
CAS No
Binding
H-bond
H-bond
lone pair
Frequency
selection

Clitocine
105798-74-1
−7.95
D761
K798, S814
E811
1%
3

kcal/mol

Mizoribine
50924-49-7
−7.08
Y619, D761
D760, E811,
D760
1%
2

kcal/mol

F812

Adenosine
58-61-7
−6.75
D618, C622,

P620
5%
2

kcal/mol
D760