Insilico Screening for Identification of Hits against SARS-Cov-2 Variant of Concern B.1.617 and NSP12 Mutants by Molecular Docking and Simulation Studies

1 Rajnik M, Cascella M, Cuomo A, Dulebohn SC, Di Napoli R. Features, evaluation, and treatment of coronavirus (COVID-19). Uniformed Services University Of The Health Sciences; 2021 Mar 1. Search in Google Scholar

2 Sheng J, Shao A. The epidemiological and clinical features of COVID-19 and lessons from this global infectious public health event; 2020. Search in Google Scholar

3 Singhal T. A Review of Coronavirus Disease-2019 (COVID-19). Indian J Pediatr 2020; 87(4): 281-286. Search in Google Scholar

4 Wang W, Tang J, Wei F. Updated understanding of the outbreak of 2019 novel coronavirus (2019-nCoV) in Wuhan, China. J Med Virol 2020; 92(4): 441-447. Search in Google Scholar

5 Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. International journal of antimicrobial agents 2020; 55(3):105924. Search in Google Scholar

6 Prompetchara E, Ketloy C, Palaga T. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pacific journal of allergy and immunology 2020;38(1):1-9. Search in Google Scholar

7 Fan Y, Zhao K, Shi Z. L, Zhou P. Bat coronaviruses in China. Viruses 2019;11(3):210. Search in Google Scholar

8 Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic acids research 2018; 46(D1):D708-717. Search in Google Scholar

9 Sexton NR, Smith EC, Blanc H, Vignuzzi M, Peersen OB, Denison MR. Homology-based identification of a mutation in the coronavirus RNA-dependent RNA polymerase that confers resistance to multiple mutagens. Journal of virology 2016; 90(16):7415-7428. Search in Google Scholar

10 Simmons G, Zmora P, Gierer S, Heurich A, Pöhlmann S. Proteolytic activation of the SARS-coronavirus spike protein: cutting enzymes at the cutting edge of antiviral research. Antiviral research 2013;100(3):605-614. Search in Google Scholar

11 Fehr AR, Perlman S, Maier HJ, Bickerton E, Britton P. An overview of their replication and pathogenesis; section 2 genomic organization. Methods in Molecular Biology 2015;1282:1-23. Search in Google Scholar

12 Yadav R, Chaudhary JK, Jain N, Chaudhary PK, Khanra S, Dhamija P, Sharma A, Kumar A, Handu S. Role of structural and non-structural proteins and therapeutic targets of SARS-CoV-2 for COVID-19. Cells 2021;10(4):821. Search in Google Scholar

13 Lei J, Kusov Y, Hilgenfeld R. Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. Antiviral research 2018;149:58-74. Search in Google Scholar

14 Walensky RP, Walke HT, Fauci AS. SARS-CoV-2 variants of concern in the United States—Challenges and opportunities. Jama 2021;325(11):1037-1038. Search in Google Scholar

15 Shastri J, Parikh S, Agrawal S, Chatterjee N, Pathak M, Chaudhary S, Sharma C, Kanakan A, Srinivasa Vasudevan J, Maurya R, Fatihi S. Clinical, serological, whole genome sequence analyses to confirm SARS-CoV-2 reinfection in patients from Mumbai, India. Frontiers in medicine 2021; 215. Search in Google Scholar

16 Yadav PD, Sapkal GN, Abraham P, Ella R, Deshpande G, Patil DY, Nyayanit DA, Gupta N, Sahay RR, Shete AM, Panda S. Neutralization of variant under investigation B. 1.617. 1 with sera of BBV152 vaccinees. Clinical Infectious Diseases 2022; 74(2):366-368. Search in Google Scholar

17 Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, Rakshit P, Singh S, Abraham P, Panda S, Team NI. SARSCoV-2 spike mutations, L452R, T478K, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Microorganisms 2021;9(7):1542. Search in Google Scholar

18 https://lifechemicals.com/screening-libraries/hts-compound-collection Search in Google Scholar

19 Cheeseright TJ, Mackey MD, Melville JL, Vinter JG. FieldScreen: virtual screening using molecular fields. Application to the DUD data set. Journal of chemical information and modeling 2008;48(11):2108-2117. Search in Google Scholar

20 Bordoli L, Schwede T. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. Homology Modeling: Methods and Protocols 2012;107-36. Search in Google Scholar

21 Biswas N, Kumar K, Mallick P, Das S, Kamal IM, Bose S, Choudhury A, Chakrabarti S. Structural and drug screening analysis of the non-structural proteins of severe acute respiratory syndrome coronavirus 2 virus extracted from Indian coronavirus disease 2019 patients. Frontiers in genetics 2021;12:626642. (DbNSP, http://www.hpppi.iicb.res.in/covid19/index.php) Search in Google Scholar

22 Bauer MR, Mackey MD. Electrostatic complementarity as a fast and effective tool to optimize binding and selectivity of protein–ligand complexes. Journal of medicinal chemistry 2019;62(6):3036-3050. Search in Google Scholar

23 Kalhotra P, Chittepu VC, Osorio-Revilla G, Gallardo-Velazquez T. Field-template, QSAR, ensemble molecular docking, and 3D-RISM solvation studies expose potential of FDA-approved marine drugs as SARS-CoVID-2 main protease inhibitors. Molecules 2021; 26(4):936. Search in Google Scholar

24 Rao P, Patel R, Shukla A, Parmar P, Rawal RM, Saraf M, Goswami D. Identifying structural–functional analogue of GRL0617, the only well-established inhibitor for papain-like protease (PLpro) of SARS-CoV2 from the pool of fungal metabolites using docking and molecular dynamics simulation. Molecular diversity 2021; 6:1-21. Search in Google Scholar

25 Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, COVID-19 Genomics UK (COG-UK) Consortium, Peacock SJ. SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology 2021;19(7):409-424. Search in Google Scholar

26 Gan HH, Twaddle A, Marchand B, Gunsalus KC. Structural modeling of the SARS-CoV-2 spike/human ACE2 complex interface can identify high-affinity variants associated with increased transmissibility. Journal of Molecular Biology 2021;433(15):167051. Search in Google Scholar

27 Hoffmann M, Hofmann-Winkler H, Krüger N, Kempf A, Nehlmeier I, Graichen L, Arora P, Sidarovich A, Moldenhauer AS, Winkler MS, Schulz S. SARS-CoV-2 variant B. 1.617 is resistant to bamlanivimab and evades antibodies induced by infection and vaccination. Cell reports 2021; 36(3):109415. Search in Google Scholar

28 Jaspe RC, Sulbaran Y, Loureiro CL, D’Angelo P, Rodríguez L, Garzaro DJ, Rangel HR, Pujol FH. Importance of E484K and N501Y mutations in SARS-CoV-2 for genomic surveillance: rapid detection by restriction enzyme analysis. medRxiv 2021;:2021-05. Search in Google Scholar

29 Focosi D, Maggi F. Neutralising antibody escape of SARS- CoV-2 spike protein: risk assessment for antibody-based Covid-19 therapeutics and vaccines. Reviews in medical virology 2021; 31(6):e2231. Search in Google Scholar

30 Cole AL, Hossain S, Cole AM, Phanstiel IV O. Synthesis and bioevaluation of substituted chalcones, coumaranones and other flavonoids as anti-HIV agents. Bioorganic & medicinal chemistry 2016; 24(12):2768-2776. Search in Google Scholar