Những hiểu biết về sinh học phân tử của SARS-CoV-2 (COVID-19) trong nghiên cứu phát triển thuốc dựa trên mục tiêu

Springer Science and Business Media LLC - Tập 29 - Trang 1777-1791 - 2020
P. Chellapandi1, S. Saranya1
1Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India

Tóm tắt

Đại dịch bệnh coronavirus (COVID-19) do virus corona gây hội chứng hô hấp cấp tính nặng 2 (SARS-CoV-2) gây ra. COVID-19 là một tình trạng khẩn cấp về sức khỏe toàn cầu và cho đến nay chưa có vaccine hoặc thuốc kháng virus nào được phê duyệt lâm sàng. Việc nghiên cứu bài bản về SARS-CoV-2 là cần thiết một cách cấp bách để hiểu rõ về sinh bệnh học và cơ chế virulence của nó, cũng như để khám phá các liệu pháp kháng virus dựa trên mục tiêu. Trong số nhiều luận điểm nghiên cứu, hiện nay sinh tin học nhấn mạnh những giả thuyết mới có thể kiểm tra được cho việc định vị lại hệ thống thuốc và thiết kế nhằm chống lại COVID-19. Tổng cộng có 121 bài báo liên quan đến khía cạnh sinh tin học của virus này đã được thu thập từ PubMed Central. Nội dung của mỗi nghiên cứu đã được xem xét một cách toàn diện, được quản lý thủ công và bao gồm ở đây. Thú vị thay, 109 tài liệu liên quan đến COVID-19 được công bố trong năm 2020 (từ tháng 1 đến tháng 6) đã được đưa vào đánh giá này. Bài viết hiện tại nhấn mạnh việc phát triển nguồn tài nguyên mới về cấu trúc gen, tiến hóa, các mục tiêu điều trị, thiết kế thuốc và chiến lược tái sử dụng thuốc. Tổ chức gen, chức năng của các gen mã hóa, nguồn gốc và tiến hóa của SARS-CoV-2 được mô tả chi tiết. Những hiểu biết về gen giúp hiểu rõ mối quan hệ giữa cấu trúc và chức năng của các mục tiêu thuốc bao gồm protein gai, protease chính và RNA polymerase phụ thuộc RNA của SARS-CoV-2 được thảo luận một cách sâu sắc. Nhiều phương pháp docking phân tử và dược lý hệ thống đã được điều tra về một số loại thuốc kháng virus đầy hứa hẹn chống lại SARS-CoV-2 dựa trên các đặc điểm gen, cơ chế sinh bệnh và tính đặc hiệu của vật chủ. Có lẽ, những hiểu biết sinh học phân tử hiện tại về virus này sẽ cung cấp cho các nhà nghiên cứu một hướng đi để thiết kế hoặc tái sử dụng các loại thuốc kháng virus trong tương lai và các hướng đi trong việc kiểm soát sự lây lan của COVID-19.

Từ khóa

#COVID-19 #SARS-CoV-2 #sinh tin học #tái sử dụng thuốc #dược lý hệ thống #thuốc kháng virus

Tài liệu tham khảo

Ahn DG, Shin HJ, Kim MH, Lee S, Kim HS, myoung J, Kim BT, Kim SJ (2020) Current status of epidemiology, diagnosis, therapeutics, and vaccines for novel coronavirus disease 2019 (COVID-19). J Microbiol Biotechnol 30:313–324 Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF (2020) The proximal origin of SARS-CoV-2. Nat Med. https://doi.org/10.1038/s41591-020-0820-9 Angeletti S, Benvenuto D, Bianchi M, Giovanetti M, Pascarella S, Ciccozzi M (2020) COVID-2019: the role of the nsp2 and nsp3 in its pathogenesis. J Med Virol. https://doi.org/10.1002/jmv.25719 Arabi YM, Deeb A, Al-Hameed, Mandourah Y, Almekhlafi GA, Sindi AA, Al-Omari A, Shalhoub S, Mady A, Alraddadi B, Almotairi A, Al Khatib K, Abdulmomen A, Qushmaq I, Solaiman O, Al-Aithan AM, Al-Raddadi R, Ragab A, Al Harthy A, Kharaba A, Jose J, Dabbagh T, Fowler RA, Balkhy HH, Merson L, Hayden FG; Saudi Critical Care Trials group (2019) Macrolides in critically ill patients with Middle East Respiratory Syndrome. Int J Infect Dis 81:184–190. Ashour HM, Elkhatib WF, Rahman MM, Elshabrawy HA (2020) Insights into the recent 2019 novel coronavirus (SARS-CoV-2) in light of past human coronavirus outbreaks. Pathogens 9:186 Bagdonaite I, Wandall HH (2018) Global aspects of viral glycosylation. Glycobiology 28:443–467 Baig AM, Khaleeq A, Ali U, Syeda H (2020) Evidence of the COVID-19 virus targeting the CNS: TIssue Distribution, Host-virus Interaction, and Proposed Neurotropic Mechanisms. ACS Chem Neurosci 11:995–998 Banerjee AK, Begum F, Ray U (2020) Mutation hot spots in Spike protein of COVID-19. Preprints 2020:2020040281. https://doi.org/10.20944/preprints202004.0281.v1 Baruah V, Bose S (2020) Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV. J Med Virol 92:495–500 Bharathi M, Chellapandi P (2019) Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1. Biochem Biophysics Rep 20:100698 Bösl K, Ianevski A, Than TT, Andersen PI, Kuivanen S, Teppor M, Zusinaite E, Dumpis u, Vitkauskiene A, Cox RJ, Kallio-Kokko H, Bergqvist A, Tenson T, Merits A, Oksenych V, Bjoras M, Anthonsen MW, Shum D, Kaarbo M, Vapalahti O, Windisch MP, Superti-Furga G, Snijder B, Kainov D, Kandasamy RK (2019) Common nodes of virus-host interaction revealed through an integrated network analysis. Front Immunol 10:2186 Cagliani R, Forni D, Clerici M, Sironi M (2020) Computational inference of selection underlying the evolution of the novel coronavirus, SARS-CoV-2. J Virol. https://doi.org/10.1128/JVI.00411-20 Caly L, Druce JD, Catton MG, Jans DA, Wagstaff KM (2020) The FDA-approved drug Ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Res 104787 Cao B, Wang Y, Wen D, Liu W, Wang J, Fan G, Ruan L, Song B, Cai Y, Wei M, Li X, Xia J, Chen N, Xiang J, Yu T, Bai T, Xie X, Zhang L, Li C, Yuan Y, Chen H, Li H, Huang H, Tu S, Gong F, Liu Y, Wei Y, Dong C, Zhou F, Gu X, Xu J, Liu Z, Zhang Y, Li H, Shang L, Wang K, Li K, Zhou X, Dong X, Qu Z, Lu S, Hu X, Ruan S, Luo S, Wu J, Peng L, Cheng F, Pan L, Zou J, Jia C, Wang J, Liu X, Wang S, Wu X, Ge Q, He J, Zhan H, Qiu F, Guo L, Huang C, Jaki T, Hayden FG, Horby PW, Zhang D, Wang C (2020) A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19. N Engl J Med. https://doi.org/10.1056/NEJMoa2001282 Cascella M, Rajnik M, Cuomo A, Dulebohn SC, Di Napoli R (2020). Features, evaluation and treatment coronavirus (COVID-19). In: StatPearls. StatPearls Publishing, Treasure Island, FL Ceraolo C, Giorgi FM (2020) Genomic variance of the 2019-nCoV coronavirus. J Med Virol 92:522–528 Chan JF, Kok KH, Zhu Z, Chu H, To KK, Yuan S, Yuen KY (2020a) Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect 9:221–236 Chan JF, Yip CC, To KK, Tang TH, Wong SC, Leung k, Fung AY, Ng AC, Zou Z, Tsoi h, Choi GK, Tam AR, Cheng VC, Chan KH, Tsang OT, Yuen K (2020b) Improved molecular diagnosis of COVID-19 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain reaction assay validated in vitro and with clinical specimens. J Clin Microbiol. https://doi.org/10.1128/JCM.00310-20 Chatterjee S, Maity A, Chowdhury S, Islam MA, Muttinini RK, Sen D (2020) In silico analysis and identification of promising hits against 2019 novel coronavirus 3C-like main protease enzyme. J Biomol Struct Dyn. 1-14 Chellapandi P, Prisilla A (2018) Clostridium botulinum type A-virulome-gut interactions: a systems biology insight. Human Microbiome. Hum Microb J 7:15–22 Chellapandi P, Prathiviraj R, Prisilla A (2019) Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints. J Comput Aided Mol Des 33:419–436 Chen YW, Yiu CB, Wong KY (2020) Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Res 9:129 Clasman JR, Everett RK, Srinivasan K, Mesecar AD (2020) Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease. Antivir Res 174:104661 Cleemput S, Dumon W, Fonseca V, Karim WA, Giovanetti M, Alcantara LC, Deforche K, de Oliveira T (2020) Genome detective coronavirus typing tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa145 Cortegiani A, Ingoglia G, Ippolito M, Giarratano A, Einav S (2020) A systematic review on the efficacy and safety of chloroquine for the treatment of COVID-19. J Crit Care 57:279–283 Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E (2020) The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antivir Res 176:104742 De Clercq E, Li G (2016) Approved antiviral drugs over the past 50 years. Clin Microbiol Rev 29:695–747 Elfiky AA (2020a) Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sci 248:117477 Elfiky AA (2020b) Ribavirin, remdesivir, sofosbuvir, galidesivir, and tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study. Life Sci 253:117592 Fahmi M, Kubota Y, Ito M (2020) Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV. Infect Genet Evol 81:104272 Forster P, Forster L, Renfrew C, Forster M (2020) Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci USA 117:9241–9243 Fox D (2020) What you need to know about the Wuhan coronavirus. Nature. https://doi.org/10.1038/d41586-020-00209-y Frieman M, Yount B, Heise M, Kopecky-Bromberg SA, Palese P, Baric RS (2007) Severe acute respiratory syndrome coronavirus ORF6 antagonizes STAT1 function by sequestering nuclear import factors on the rough endoplasmic reticulum/Golgi membrane. J Virol 81:9812–9824 Fu Y, Cheng Y, Wu Y (2020) Understanding SARS-CoV-2-mediated inflammatory responses: from mechanisms to potential therapeutic tools. Virol Sin. https://doi.org/10.1007/s12250-020-00207-4 Gao J, Zhenxue T, Yang X (2020a) Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Biosci Trends 14:72–73 Gao Y, Yan L, Huang Y, Liu F, Zhao Y, Cao L, Wang T, Sun Q, Ming Z, Zhang L, Ge J, Zheng L, Zhang Y, Wang H, Zhu Y, Zhu C, Hu T, Hua T, Zhang B, Yang X, Li J, Yang H, Liu Z, Xu W, Guddat LW, Wang Q, Lou Z, Rao Z (2020b) Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science 368:779–782 Ghosh AK, Brindisi M, Shahabi D, Chapman ME, Mesecar AD (2020) Drug development and medicinal chemistry efforts toward SARS-Coronavirus and Covid-19 therapeutics. ChemMedChem 15:907–932 Goh GK, Dunker AK, Foster JA, Uversky VN (2020) Rigidity of the outer shell predicted by a protein intrinsic disorder model sheds light on the COVID-19 (Wuhan-2019-nCoV) infectivity. Biomolecules 10:331 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O’Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, Zastrow MV, Taunton J, Schwartz O, Vignuzzi M, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJA (2020) SARS-CoV-2-Human protein-protein interaction map reveals drug targets and potential drug repurposing. bioRxiv preprint. https://doi.org/10.1101/2020.03.22.002386 Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A (2020) A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host Microbe 27:671–680 Guo YR, Cao QD, Hong ZS, Tan YY, Chen SD, Jin HJ, Tan KS, Wang DY, Yan Y (2020) The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak - an update on the status. Mil Med Res 7:11 Gupta MK, Vemula S, Donde R, Gouda G, Behera L, Vadde R (2020) In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. J Biomol Struct Dyn 1–17. https://doi.org/10.1080/07391102.2020.1751300 Harrison C (2020) Coronavirus puts drug repurposing on the fast track. Nat Biotechnol. https://doi.org/10.1038/d41587-020-00003-1. Hasan A, Paray BA, Hussain A, Qadir FA, Attar F, Aziz FM, Sharifi M, Derakhshankhah H, Rasti B, Mehrabi M, Shahpasand K, Saboury AA, Falahati M (2020) A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. J Biomol Struct Dyn 1–9. https://doi.org/10.1080/07391102.2020.1754293. Hussain M, Jabeen N, Raza F, Shabbir S, Baig AA, Amanullah A, Aziz B (2020) Structural variations in human ACE2 may influence its binding with SARS-CoV-2 spike protein. J Med Virol. https://doi.org/10.1002/jmv.25832 Ibrahim IM, Abdelmalek DH, Elshahat ME, Elfiky AA (2020) COVID-19 spike-host cell receptor GRP78 binding site prediction. J Infect 80:554–562 Jeon S, Ko M, Lee J, Choi I, Byun SY, Park S, Shum D, Kim S (2020) Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs. Antimicrob Agents Chemother 64:e00819–20. Kandeel M, Al-Nazawi M (2020) Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sci 117627. https://doi.org/10.1016/j.lfs.2020.117627 Kandeel M, Ibrahim A, Fayez M, Al-Nazawi M (2020) From SARS and MERS CoVs to SARS-CoV-2: moving toward more biased codon usage in viral structural and nonstructural genes. J Med Virol 92:660–666 Ke YY, Peng TT, Yeh TK, Huang WZ, Chang SE, Wu SH, Hung HC, Hsu TA, Lee SJ, Song JS, Lin WH, Chiang TJ, Lin JH, Sytwu HK, Chen CT (2020) Artificial intelligence approach fighting COVID-19 with repurposing drugs. Biomed J. https://doi.org/10.1016/j.bj.2020.05.001 Khan RJ, Jha RK, Amera GM, Jain M, Singh E, Pathak A, Singh RP, Muthukumaran J, Singh AK (2020a) Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2’-O-ribose methyltransferase. J Biomol Struct Dyn 1–14. https://doi.org/10.1080/07391102.2020.1753577 Khan S, Siddique R, Shereen MA, Ali A, Liu J, Bai Q, Bashir N, Xue M (2020b) The emergence of a novel coronavirus (SARS-CoV-2), their biology and therapeutic options. J Clin Microbiol 58. https://doi.org/10.1128/JCM00187-20 Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M, Godzik A, Michalska K, Joachimiak A (2020) Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci 29:1596–1605. https://doi.org/10.1002/pro.3873 Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC; Sheffield COVID-19 Genomics Group (2020) Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. https://doi.org/10.1016/j.cell.2020.06.043 Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, Zhang Q, Shi X, Wang Q, Zhang L, Wang X (2020) Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581:215–220 Li G, De Clercq (2020) Therapeutic options for the 2019 novel coronavirus (2019-nCoV). Nat Rev Drug Discov 19:149–150 Li H, Zhou Y, Zhang M, Wang H, Zhao Q, Liu J (2020b) Updated Approaches against SARS-CoV-2. Antimicrob Agents Chemother 64:e00483–20 Li JY, You Z, Wang Q, Zhou ZJ, Qiu Y, Luo R, Ge XY (2020a) The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future. Microbes Infect 22:80–85 Li X, Wang W, Zhao X, Zai J, Zhao Q, Li Y, Chaillon A (2020c) Transmission dynamics and evolutionary history of 2019-nCoV. J Med Virol 92:501–511 Li Y, Zhang J, Wang N, Li H, Shi Y, Guo G, Liu K, Zeng H, Zou Q (2020d) Therapeutic drugs targeting 2019-nCoV main protease by high-throughput screening. bioRxiv Preprint. https://doi.org/10.1101/2020.01.28.922922 Li Y, Zhou W, Yang L, You R (2020e) Physiological and pathological regulation of ACE2, the SARS-CoV-2 receptor. Pharm Res 157:104833 Licastro D, Rajasekharan S, Dal Monego S, Segat L, D’Agaro P, Marcello A (2020) Isolation and full-length genome characterization of SARS-CoV-2 from COVID-19 cases in Northern Italy. J Virol 94:e00543–20. https://doi.org/10.1128/JVI.00543-20 Liu J, Cao R, Xu M, Wang X, Zhang H, Hu H, Li Y, Hu Z, Zhong W, Wang M (2020b) Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro. Cell Discov 6:16 Liu S, Zheng Q, Wang Z (2020c) Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa224 Liu X, Zhang B, Jin Z, Yang H, Rao Z (2020a) The crystal structure of COVID-19 main protease in complex with an inhibitor N3. PDB https://doi.org/10.2210/pdb6lu7/pdb Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W (2020) Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395:565–574 Luan J, Lu Y, Jin X, Zhang L (2020) Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem Biophys Res Commun 526:165–169 Lung J, Lin YS, Yang YH, Chou YL, Shu LH, Cheng YC, Liu HT, Wu CY (2020) The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase. J Med Virol 92:693–697 Ma J, Huo XQ, Chen X, Zhu WX, Yao MC, Qiao YJ, Zhang YL (2020) Study on screening potential traditional Chinese medicines against 2019-nCoV based on Mpro and PLP. Zhongguo Zhong Yao Za Zhi 45:1219–1224 Morse JS, Lalonde T, Xu S, Liu WR (2020) Learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV. Chembiochem 21:730–738 Murugan R, Prathiviraj R, Mothay Dipti, Chellapandi P (2019) Substrate-imprinted docking of Agrobacterium tumefaciens uronate dehydrogenase for increased substrate selectivity. Int J Biol Macromol 140:1214–1225 Nabirotchkin S, Peluffo AE, Rinaudo P, Yu J, Hajj R, Cohen D (2020) Next-generation drug repurposing using human genetics and network biology. Curr Opin Pharmacol 11:1–15. Nutho B, Mahalapbutr P, Hengphasatporn K, Pattaranggoon NC, Simanon N, Shigeta Y, Hannongbua S, Rungrotmongkol T (2020) Why are lopinavir and ritonavir effective against the newly emerged coronavirus 2019? Atomistic insights into the inhibitory mechanisms. Biochemistry 59:1769–1779 Ortega JT, Serrano ML, Pujol FH, Rangel HR (2020) Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: an in silico analysis. EXCLI J 19:410–417 Paasche A, Zipper A, Schäfer S, Ziebuhr J, Schirmeister T, Engels B (2014) Evidence for substrate binding-induced zwitter ion formation in the catalytic Cys-His dyad of the SARS-CoV main protease. Biochemistry 53:5930–5946 Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R (2020) Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med 18:179 Paraskevis D, Kostaki EG, Magiorkinis G, Panayiotakopoulos G, Sourvinos G, Tsiodras S (2020) Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infect Genet Evol 79:104212 Phadke M, Saunik S (2020) COVID-19 treatment by repurposing drugs until the vaccine is in sight. Drug Dev Res. https://doi.org/10.1002/ddr.21666 Phan T (2020) Genetic diversity and evolution of SARS-CoV-2. Infect Genet Evol 81:104260 Prajapat M, Sarma P, Shekhar N, Avti P, Sinha S, Kaur H, Kumar S, Bhattacharyya A, Kumar H, Bansal S, Medhi B (2020) Drug targets for corona virus: A systematic review. Indian J Pharmacol 52:56–65 Prathiviraj R, Chellapandi P (2020a) Deciphering molecular virulence mechanism of Mycobacterium tuberculosis Dop isopeptidase based on its sequence-structure-function link. Protein J 39:33–45 Prathiviraj R, Chellapandi P (2020b) Modelling a global regulatory network of Methanothermobacter thermautotrophicus strain ΔH. Netw Model Anal Health Inf Bioinform 9:17 Prathiviraj R, Berchmans Sheela, Chellapandi P (2019) Analysis of modularity in proteome-wide protein interaction networks of Methanothermobacter thermautotrophicus strain ΔH across metal-loving bacteria. J Proteins Proteom 10:179–190 Prompetchara E, Ketloy C, Palaga T (2020) Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol 38:1–9 Rabaan AA, Al-Ahmed SH, Haque S, Sah R, Tiwari R, Malik YS, Dhama K, Yatoo MI, Bonilla-Aldana DK, Rodriguez-Morales AJ (2020) SARS-CoV-2, SARS-CoV, and MERS-COV: a comparative overview. Infez Med 28:174–184 Ralph R, Lew J, Zeng T, Francis M, Xue B, Roux M, Toloue Ostadgavahi A, Rubino S, Dawe NJ, Al-Ahdal MN, Kelvin DJ, Richardson CD, Kindrachuk J, Falzarano D, Kelvin AA (2020) 2019-nCoV (Wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness. J Infect Dev Ctries 14:3–17 Rehman SU, Shafique L, Ihsan A, Liu Q (2020) Evolutionary trajectory for the emergence of novel coronavirus SARS-CoV-2. Pathogens 9:240 Reina J (2020) Remdesivir, the antiviral hope against SARS-CoV-2. Rev Esp Quimioter 33:176–179 Robson B (2020) Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus. Comput Biol Med 119:103670 Rothan HA, Byrareddy SN (2020) The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J Autoimmun 109:102433 Shah B, Modi P, Sagar SR (2020) In silico studies on therapeutic agents for COVID-19: drug repurposing approach. Life Sci 252:117652 Shanmugaraj B, Siriwattananon K, Wangkanont K, Phoolcharoen W (2020) Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19). Asian Pac J Allergy Immunol 38:10–18 Shi J, Song J (2006) The catalysis of the SARS 3C-like protease is under extensive regulation by its extra domain. FEBS J 273:1035–1045 Sigrist CJ, Bridge A, Le Mercier P (2020) A potential role for integrins in host cell entry by SARS-CoV-2. Antivir Res 177:104759 Singhal T (2020) A review of coronavirus disease-2019 (COVID-19). Indian J Pediatr 87:281–286 Sohrabi C, Alsafi Z, O’Neill N, Khan M, Kerwan A, Al-Jabir A, Iosifidis C, Agha R (2020) World Health Organization declares global emergency: a review of the 2019 novel coronavirus (COVID-19). Int J Surg 76:71–76 Srinivasan S, Cui H, Gao Z, Liu M, Lu S, Mkandawire W, Narykov O, Sun M, Korkin D (2020) Structural genomics of SARS-CoV-2 indicates evolutionary conserved functional regions of viral proteins. Viruses 12:360 Tian X, Li C, Huang A, Xia S, Lu S, Shi Z, Lu L, Jiang S, Yang Z, Wu Y, Ying T (2020) Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. Emerg Microbes Infect 9:382–385 Ton AT, Gentile F, Hsing M, Ban F, Cherkasov A (2020) Rapid identification of potential inhibitors of SARS-CoV-2 main protease by deep docking of 1.3 Billion compounds. Mol Inform. https://doi.org/10.1002/minf.202000028 Tu YF, Chien CS, Yarmishyn AA, Lin YY, Luo YH, Lin YT, Lai WY, Yang DM, Chou SJ, Yang YP, Wang ML, Chiou SH (2020) A review of SARS-CoV-2 and the ongoing clinical trials. Int J Mol Sci 21:2657 Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D (2020) Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181:281–292 Wan Y, Shang J, Graham R, Baric RS, Li F (2020) Receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol 94:e00127–20. https://doi.org/10.1128/JVI.00127-20 Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G (2020a) Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res 30:269–271 Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, Lu G, Qiao C, Hu Y, Yuen KY, Wang Q, Zhou H, Yan J, Qi J (2020b) Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell 181:894–904.e9. https://doi.org/10.1016/j.cell.2020.03.045 Wen F, Yu H, Guo J, Li Y, Luo K, Huang S (2020) Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2. J Infect 80:671–693 Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265–269 Xia S, Liu M, Wang C, Xu W, Lan Q, Feng S, Qi F, Bao L, Du L, Liu S, Qin C, Sun F, Shi Z, Zhu Y, Jiang S, Lu L (2020) Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res 30:343–355 Xu X, Han M, Li T, Sun W, Wang D, Fu B, Zhou Y, Zheng X, Yang Y, Li X, Zhang X, Pan A, Wei H (2020a) Effective treatment of severe COVID-19 patients with tocilizumab. Proc Natl Acad Sci USA 117:10970–10975 Xu Z, Peng C, Shi Y, Zhu Z, Mu K, Wang X, Zhu W (2020b) 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. https://doi.org/10.1101/2020.01.27.921627 Yang P, Wang X (2020) COVID-19: a new challenge for human beings. Cell Mol Immunol 17:555–557 Yao X, Ye F, Zhang M, Cui C, Huang B, Niu P, Liu X, Zhao L, Dong E, Song C, Zhan S, Lu R, Li H, Tan W, Liu D (2020) In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clin Infect Dis ciaa237. https://doi.org/10.1093/cid/ciaa237 Yin C (2020) Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics 112:3588–3596 Yoshimoto FK (2020) The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the cause of COVID-19. Protein J 39:198–216 Yu H, Wang XC, Li J, Qian X, Yu XF, Sun Z, Chen JF, Kao QJ, Wang HQ, Pan JC. (2020) Genomic analysis of a 2019-novel coronavirus (2019-nCoV) strain in the first COVID-19 patient found in Hangzhou. Zhonghua Yu Fang Yi Xue Za Zhi 54:486-490. Chinese. https://doi.org/10.3760/cma.j.cn112150-20200217-00128 Zhang L, Li L, Yan L, Ming Z, Jia Z, Lou Z, Rao Z (2018) Structural and biochemical characterization of endoribonuclease Nsp15 encoded by middle east respiratory syndrome coronavirus. J Virol 92:e00893–18. https://doi.org/10.1128/JVI.00893-18 Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R (2020b) Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science 368:409–412 Zhang T, Cui X, Zhao X, Wang J, Zheng J, Zheng G, Guo W, Cai C, He S, Xu Y (2020c) Detectable SARS-CoV-2 Viral RNA in feces of three children during recovery period of COVID-19 pneumonia. J Med Virol 92:909–914 Zhang T, Wu Q, Zhang Z (2020a) Probable pangolin origin of SARS-CoV-2 Associated with the COVID-19 outbreak. Curr Biol 30:1346–1351.e2 Zhao WM, Song SH, Chen ML, Zou D, Ma LN, Ma YK, Li RJ, Hao LL, Li CP, Tian DM, Tang BX, Wang YQ, Zhu JW, Chen HX, Zhang Z, Xue YB, Bao YM (2020) The 2019 novel coronavirus resource. Yi Chuan 42:212–221 Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL (2020b) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270–273 Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F (2020a) Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov 6:14 Zumla A, Chan JFW, Azhar EI, Hui DSC, Yuen KY (2016) Coronaviruses-drug discovery and therapeutic options. Nat Rev Drug Discov 15:327–347