Probing Antiviral Drugs Against SARS-CoV-2 Through Virus-drug Association Prediction Based on the KATZ Method

Overview

Journal Genomics

Specialty Genetics

Date 2020 Aug 4

PMID 32745502

Citations 24

Authors

Liqian Zhou

Juanjuan Wang

Guangyi Liu

Qingqing Lu

Ruyi Dong

Geng Tian

Jialiang Yang

Lihong Peng

Affiliations

Soon will be listed here.

Abstract

It is urgent to find an effective antiviral drug against SARS-CoV-2. In this study, 96 virus-drug associations (VDAs) from 12 viruses including SARS-CoV-2 and similar viruses and 78 small molecules are selected. Complete genomic sequence similarity of viruses and chemical structure similarity of drugs are then computed. A KATZ-based VDA prediction method (VDA-KATZ) is developed to infer possible drugs associated with SARS-CoV-2. VDA-KATZ obtained the best AUCs of 0.8803 when the walking length is 2. The predicted top 3 antiviral drugs against SARS-CoV-2 are remdesivir, oseltamivir, and zanamivir. Molecular docking is conducted between the predicted top 10 drugs and the virus spike protein/human ACE2. The results showed that the above 3 chemical agents have higher molecular binding energies with ACE2. For the first time, we found that zidovudine may be effective clues of treatment of COVID-19. We hope that our predicted drugs could help to prevent the spreading of COVID.

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References

Kim S, Thiessen P, Bolton E, Chen J, Fu G, Gindulyte A . PubChem Substance and Compound databases. Nucleic Acids Res. 2015; 44(D1):D1202-13. PMC: 4702940. DOI: 10.1093/nar/gkv951. View

Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y . Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 2020; 10(5):766-788. PMC: 7102550. DOI: 10.1016/j.apsb.2020.02.008. View

Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M . Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020; 30(3):269-271. PMC: 7054408. DOI: 10.1038/s41422-020-0282-0. View

Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W . Single-Cell RNA Expression Profiling of ACE2, the Receptor of SARS-CoV-2. Am J Respir Crit Care Med. 2020; 202(5):756-759. PMC: 7462411. DOI: 10.1164/rccm.202001-0179LE. View

Meyer M, Wilson P, Schomburg D . Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol. 1996; 264(1):199-210. DOI: 10.1006/jmbi.1996.0634. View

Gralinski L, Menachery V . Return of the Coronavirus: 2019-nCoV. Viruses. 2020; 12(2). PMC: 7077245. DOI: 10.3390/v12020135. View

Zhao Q, Yu H, Ming Z, Hu H, Ren G, Liu H . The Bipartite Network Projection-Recommended Algorithm for Predicting Long Non-coding RNA-Protein Interactions. Mol Ther Nucleic Acids. 2018; 13:464-471. PMC: 6205413. DOI: 10.1016/j.omtn.2018.09.020. View

Hu H, Zhang L, Ai H, Zhang H, Fan Y, Zhao Q . HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy. RNA Biol. 2018; 15(6):797-806. PMC: 6152435. DOI: 10.1080/15476286.2018.1457935. View

Simmons G, Reeves J, Rennekamp A, Amberg S, Piefer A, Bates P . Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry. Proc Natl Acad Sci U S A. 2004; 101(12):4240-5. PMC: 384725. DOI: 10.1073/pnas.0306446101. View

10.

de Wit E, van Doremalen N, Falzarano D, Munster V . SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol. 2016; 14(8):523-34. PMC: 7097822. DOI: 10.1038/nrmicro.2016.81. View

11.

. State of Knowledge and Data Gaps of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Humans. PLoS Curr. 2013; 5. PMC: 3828229. DOI: 10.1371/currents.outbreaks.0bf719e352e7478f8ad85fa30127ddb8. View

12.

Rossman J, Lamb R . Influenza virus assembly and budding. Virology. 2011; 411(2):229-36. PMC: 3086653. DOI: 10.1016/j.virol.2010.12.003. View

13.

de Jong M, Tran T, Truong H, Vo M, Smith G, Nguyen V . Oseltamivir resistance during treatment of influenza A (H5N1) infection. N Engl J Med. 2005; 353(25):2667-72. DOI: 10.1056/NEJMoa054512. View

14.

Peeri N, Shrestha N, Rahman M, Zaki R, Tan Z, Bibi S . The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: what lessons have we learned?. Int J Epidemiol. 2020; 49(3):717-726. PMC: 7197734. DOI: 10.1093/ije/dyaa033. View

15.

Lu H . Drug treatment options for the 2019-new coronavirus (2019-nCoV). Biosci Trends. 2020; 14(1):69-71. DOI: 10.5582/bst.2020.01020. View

16.

Li J, Lei K, Wu Z, Li W, Liu G, Liu J . Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs. Oncotarget. 2016; 7(29):45584-45596. PMC: 5216744. DOI: 10.18632/oncotarget.10052. View

17.

Zhang Z, Li X, Zhang W, Shi Z, Zheng Z, Wang T . Clinical Features and Treatment of 2019-nCov Pneumonia Patients in Wuhan: Report of A Couple Cases. Virol Sin. 2020; 35(3):330-336. PMC: 7091133. DOI: 10.1007/s12250-020-00203-8. View

18.

Hall Jr D, Ji H . A search for medications to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2 spike glycoprotein and 3CL protease. Travel Med Infect Dis. 2020; 35:101646. PMC: 7152904. DOI: 10.1016/j.tmaid.2020.101646. View

19.

Wheeler D, Church D, Edgar R, Federhen S, Helmberg W, Madden T . Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 2003; 32(Database issue):D35-40. PMC: 308807. DOI: 10.1093/nar/gkh073. View

20.

Tchesnokov E, Feng J, Porter D, Gotte M . Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir. Viruses. 2019; 11(4). PMC: 6520719. DOI: 10.3390/v11040326. View