The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes pathological pulmonary symptoms. Most efforts to develop vaccines and drugs against this virus target the spike glycoprotein, particularly its S1 subunit, which is recognised by angiotensin-converting enzyme 2. Here we use the in-house developed tool CaverDock to perform virtual screening against spike glycoprotein using a cryogenic electron microscopy structure (PDB-ID: 6VXX) and the representative structures of five most populated clusters from a previously published molecular dynamics simulation. The dataset of ligands was obtained from the ZINC database and consists of drugs approved for clinical use worldwide. Trajectories for the passage of individual drugs through the tunnel of the spike glycoprotein homotrimer, their binding energies within the tunnel, and the duration of their contacts with the trimer's three subunits were computed for the full dataset. Multivariate statistical methods were then used to establish structure-activity relationships and select top candidate for movement inhibition. This new protocol for the rapid screening of globally approved drugs (4359 ligands) in a multi-state protein structure (6 states) showed high robustness in the rate of finished calculations. The protocol is universal and can be applied to any target protein with an experimental tertiary structure containing protein tunnels or channels. The protocol will be implemented in the next version of CaverWeb (https://loschmidt.chemi.muni.cz/caverweb/) to make it accessible to the wider scientific community.

Institute of Computer Science Masaryk University Brno Czech Republic

International Clinical Research Centre St Ann's Hospital Brno Czech Republic

Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of Science Masaryk University Brno Czech Republic

Zobrazit více v PubMed

Cascella M., Rajnik M., Cuomo A., Dulebohn S.C., Di Napoli R. StatPearls Publishing; Treasure Island (FL): 2020. StatPearls. PubMed

Murthy S., Gomersall C.D., Fowler R.A. Care for critically ill patients with COVID-19. JAMA. 2020;323(15):1499. doi: 10.1001/jama.2020.3633. PubMed DOI

Heymann D.L., Shindo N. Shindo and WHO scientific and technical advisory group for infectious hazards, COVID-19: what is next for public health? Lancet. 2020;395(10224):542–545. PubMed PMC

Hui D.S., I Azhar E., Madani T.A., Ntoumi F., Kock R., Dar O. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — the latest 2019 novel coronavirus outbreak in Wuhan, China. Int J Inf Dis. 2020;91:264–266. PubMed PMC

Mengist H.M., Fan X., Jin T. Designing of improved drugs for COVID-19: Crystal structure of SARS-CoV-2 main protease M pro. Signal Transd Targeted Therapy. 2020;5:1–2. PubMed PMC

Jin Z., Du X., Xu Y., Deng Y., Liu M., Zhao Y. Structure of M pro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582(7811):289–293. PubMed

H. Pearson, Caution raised over SARS vaccine, Nature, DOI:10.1038/news050110-3.

D.S. Goodsell, M. Voigt, Ch. Zardecki, S.K. Burley, Integrative illustration for coronavirus outreach, PLOS Biology, https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000815, (accessed 10 September 2020). PubMed PMC

Li Y.-D., Chi W.-Y., Su J.-H., Ferrall L., Hung C.-F., Wu T.-C. Coronavirus vaccine development: from SARS and MERS to COVID-19. J Biomed Sci. 2020;27:104. PubMed PMC

Tseng C.-T., Sbrana E., Iwata-Yoshikawa N., Newman P.C., Garron T., Atmar R.L. Immunization with SARS coronavirus vaccines leads to pulmonary immunopathology on challenge with the SARS virus. PLoS ONE. 2012;7(4):e35421. doi: 10.1371/journal.pone.0035421. PubMed DOI PMC

Yang Z.-y., Werner H.C., Kong W.-p., Leung K., Traggiai E., Lanzavecchia A. Evasion of antibody neutralization in emerging severe acute respiratory syndrome coronaviruses. PNAS. 2005;102(3):797–801. PubMed PMC

Erhabor G.E. COVID-19 VACCINE IS HERE!!! West Afr J Med. 2020;37:712–713. PubMed

Oliver S., Gargano J., Marin M., Wallace M., Curran K.G., Chamberland M. The advisory committee on immunization practices’ interim recommendation for use of moderna COVID-19 vaccine – United States, December 2020. MMWR Morb Mortal Wkly Rep. 2021;69(5152):1653–1656. PubMed PMC

The Advisory Committee on Immunization Practices’ Interim Recommendation for Use of Pfizer-BioNTech COVID-19 Vaccine - United States, December 2020 - PubMed, https://pubmed.ncbi.nlm.nih.gov/33332292/, (accessed 25 April 2021). PubMed PMC

A New Vaccine to Battle Covid-19 - PubMed, https://pubmed.ncbi.nlm.nih.gov/33378607/, (accessed 25 April 2021).

Oxford-AstraZeneca COVID-19 vaccine efficacy - PubMed, https://pubmed.ncbi.nlm.nih.gov/33306990/, (accessed 25 April 2021).

Chernyshev A. Pharmaceutical targeting the envelope protein of SARS-CoV-2: the screening for inhibitors in approved. Drugs. 2020 doi: 10.26434/chemrxiv.12286421.v1. DOI

Jiménez-Alberto A., Ribas-Aparicio R.M., Aparicio-Ozores G., Castelán-Vega J.A. Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Comput Biol Chem. 2020;88:107325. doi: 10.1016/j.compbiolchem.2020.107325. PubMed DOI PMC

Miroshnychenko K., Shestopalova A.V. Combined use of amentoflavone and ledipasvir could interfere with binding of spike glycoprotein of SARS-CoV-2 to ACE2. Results Mol Dock Study. 2020 doi: 10.26434/chemrxiv.12377870.v1. PubMed DOI PMC

Bennet B.M., Wolf J., Laureano R., Sellers R.S. Review of current vaccine development strategies to prevent coronavirus disease 2019 (COVID-19) Toxicol Pathol. 2020;48(7):800–809. PubMed

Klein S.L., Creisher P.S., Burd I. COVID-19 vaccine testing in pregnant females is necessary. J Clin Invest. 2020;48:800–809. doi: 10.1172/JCI147553. PubMed DOI PMC

Mehrotra D.V., Janes H.E., Fleming T.R., Annunziato P.W., Neuzil K.M., Carpp L.N. Clinical endpoints for evaluating efficacy in COVID-19 vaccine trials. Ann Intern Med. 2021;174(2):221–228. PubMed PMC

Park K.S., Sun X., Aikins M.E., Moon J.J. Non-viral COVID-19 vaccine delivery systems. Adv Drug Deliv Rev. 2021;169:137–151. PubMed PMC

Wibawa T. COVID-19 vaccine research and development: ethical issues. Trop Med Int Health. 2021;26(1):14–19. PubMed PMC

Glowacka I., Bertram S., Muller M.A., Allen P., Soilleux E., Pfefferle S. Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response. J Virol. 2011;85(9):4122–4134. PubMed PMC

South A.M., Brady T.M., Flynn J.T. ACE2 (Angiotensin-Converting Enzyme 2), COVID-19, and ACE Inhibitor and Ang II (Angiotensin II) receptor blocker use during the pandemic. Hypertension. 2020;76(1):16–22. PubMed PMC

Chowdhury R, Maranas CD, Biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity, bioRxiv, 2020, 2020.03.30.015891. PubMed PMC

Wrapp D., Wang N., Corbett K.S., Goldsmith J.A., Hsieh C.-L., Abiona O. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020;367(6483):1260–1263. PubMed PMC

Satarker S., Nampoothiri M. Structural proteins in severe acute respiratory syndrome coronavirus-2. Arch Med Res. 2020;51(6):482–491. PubMed PMC

Siu Y.L., Teoh K.T., Lo J., Chan C.M., Kien F., Escriou N. The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles. J Virol. 2008;82(22):11318–11330. PubMed PMC

Ou X., Liu Y., Lei X., Li P., Mi D., Ren L. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun. 2020;11:1620. PubMed PMC

Marques S.M., Daniel L., Buryska T., Prokop Z., Brezovsky J., Damborsky J. Enzyme Tunnels and gates as relevant targets in drug design. Med Res Rev. 2017;37(5):1095–1139. PubMed

Lv Z., Chu Y., Wang Y. HIV protease inhibitors: a review of molecular selectivity and toxicity. HIV AIDS (Auckl) 2015;7:95–104. PubMed PMC

Bosch B.J., Martina B.E.E., van der Zee R., Lepault J., Haijema B.J., Versluis C. Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides. PNAS. 2004;101(22):8455–8460. PubMed PMC

Vincent M.J., Bergeron E., Benjannet S., Erickson B.R., Rollin P.E., Ksiazek T.G. Chloroquine is a potent inhibitor of SARS coronavirus infection and spread. Virol J. 2005;2:69. PubMed PMC

Du L., Yang Y., Zhou Y., Lu L.u., Li F., Jiang S. MERS-CoV spike protein: a key target for antivirals. Expert Opin Therapeutic Targets. 2017;21(2):131–143. PubMed PMC

Walls A.C., Park Y.-J., Tortorici M.A., Wall A., McGuire A.T., Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020;181(2):281–292.e6. PubMed PMC

Singh A., Mishra A. Leucoefdin a potential inhibitor against SARS CoV-2 Mpro. J Biomol Struct Dyn. 2020:1–6. PubMed PMC

Lokhande K.B., Doiphode S., Vyas R., Swamy K.V. Molecular docking and simulation studies on SARS-CoV-2 Mpro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19. J Biomol Struct Dyn. 2020:1–12. PubMed PMC

Stoddard S.V., Stoddard S.D., Oelkers B.K., Fitts K., Whalum K., Whalum K. Optimization rules for SARS-CoV-2 Mpro antivirals: ensemble docking and exploration of the coronavirus protease active site. Viruses. 2020;12(9):942. doi: 10.3390/v12090942. PubMed DOI PMC

Ibrahim M.A.A., Abdeljawaad K.A.A., Abdelrahman A.H.M., Hegazy M.-E.-F. Natural-like products as potential SARS-CoV-2 Mpro inhibitors: in-silico drug discovery. J Biomol Struct Dyn. 2020:1–13. PubMed PMC

Bhanu P., Kumar N.H., Kumar S.H., Relekar M., Anand D.A., Kumar J. Comparative molecular docking analysis of the SARS CoV-2 Spike glycoprotein with the human ACE-2 receptors and thrombin. Bioinformation. 2020;16:532–538. PubMed PMC

Vardhan S., Sahoo S.K. in-silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19. Comput Biol Med. 2020;124:103936. doi: 10.1016/j.compbiomed.2020.103936. PubMed DOI PMC

Kim S.Y., Jin W., Sood A., Montgomery D.W., Grant O.C., Fuster M.M. Characterization of heparin and severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) spike glycoprotein binding interactions. Antiviral Res. 2020;181:104873. doi: 10.1016/j.antiviral.2020.104873. PubMed DOI PMC

Pandey P., Rane J.S., Chatterjee A., Kumar A., Khan R., Prakash A. Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in-silico study for drug development. J Biomol Struct Dyn. 2020:1–11. PubMed PMC

Choudhary S., Malik Y.S., Tomar S. Identification of SARS-CoV-2 cell entry inhibitors by drug repurposing using in silico structure-based virtual screening approach. Front Immunol. 2020 doi: 10.3389/fimmu.2020.01664. PubMed DOI PMC

Romeo A., Iacovelli F., Falconi M. Targeting the SARS-CoV-2 spike glycoprotein prefusion conformation: virtual screening and molecular dynamics simulations applied to the identification of potential fusion inhibitors. Virus Res. 2020;286:198068. PubMed PMC

Chodera J.D., Mobley D.L., Shirts M.R., Dixon R.W., Branson K., Pande V.S. Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol. 2011;21(2):150–160. PubMed PMC

Cabeza de Vaca I., Zarzuela R., Tirado-Rives J., Jorgensen W.L. Robust free energy perturbation protocols for creating molecules in solution. J Chem Theory Comput. 2019;15(7):3941–3948. PubMed PMC

Guallar V., Lu C., Borrelli K., Egawa T., Yeh S.-R. Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis THE ROLE OF G8 TRYPTOPHAN. J Biol Chem. 2009;284(5):3106–3116. PubMed PMC

Lucas M.F., Guallar V. An atomistic view on human hemoglobin carbon monoxide migration processes. Biophys J. 2012;102(4):887–896. PubMed PMC

Pinto G.P., Vavra O., Filipovic J., Stourac J., Bednar D., Damborsky J. Fast screening of inhibitor binding/unbinding using novel software tool CaverDock. Front Chem. 2019 doi: 10.3389/fchem.2019.00709. PubMed DOI PMC

Filipovic J., Vávra O., Plhák J., Bednar D., Marques S.M., Brezovsky J., Matyska L., Damborsky J. CaverDock: a novel method for the fast analysis of ligand transport. IEEE/ACM Trans Comput Biol Bioinf. 2019:1. PubMed

Vavra O., Filipovic J., Plhak J., Bednar D., Marques S.M., Brezovsky J., Stourac J., Matyska L., Damborsky J. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. 2019;35:4986–4993. PubMed

Chovancova E., Pavelka A., Benes P., Strnad O., Brezovsky J., Kozlikova B. 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol. 2012;8(10):e1002708. PubMed PMC

Trott O., Olson A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem. 2010;31:455–461. PubMed PMC

Stourac J., Vavra O., Kokkonen P., Filipovic J., Pinto G., Brezovsky J., Damborsky J., Bednar D. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res. 2019;47:W414–W422. PubMed PMC

Stourac J., Vavra O., Kokkonen P., Filipovic J., Pinto G., Schenkmayerova A. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. J Biotechnol. 2019;305:S72. doi: 10.1016/j.jbiotec.2019.05.251. PubMed DOI PMC

D.E. Shaw Research, Molecular Dynamics Simulations Related to SARS-CoV-2, https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/.

Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H. The protein data bank. Nucleic Acids Res. 2000;28:235–242. PubMed PMC

Sterling T., Irwin J.J. ZINC 15 – ligand discovery for everyone. J Chem Inf Model. 2015;55(11):2324–2337. PubMed PMC

Yang Y.I., Shao Q., Zhang J., Yang L., Gao Y.Q. Enhanced sampling in molecular dynamics. J Chem Phys. 2019;151(7):070902. doi: 10.1063/1.5109531. PubMed DOI

Harvey M.J., Giupponi G., Fabritiis G.D. ACEMD: Accelerating biomolecular dynamics in the microsecond time scale. J Chem Theory Comput. 2009;5(6):1632–1639. PubMed

Kumar S., Rosenberg J.M., Bouzida D., Swendsen R.H., Kollman P.A. THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem. 1992;13(8):1011–1021.

Laio A., Parrinello M. Escaping free-energy minima. Proc Natl Acad Sci U S A. 2002;99(20):12562–12566. PubMed PMC

Sugita Y., Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314(1-2):141–151.

Hamelberg D., Mongan J., McCammon J.A. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys. 2004;120(24):11919–11929. PubMed

Maragliano L., Vanden-Eijnden E. A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations. Chem Phys Lett. 2006;426(1-3):168–175.

Wang F., Landau D.P. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys Rev Lett. 2001;86(10):2050–2053. PubMed

Rose P.W., Bi C., Bluhm W.F., Christie C.H., Dimitropoulos D., Dutta S., Green R.K., Goodsell D.S., Prlić A., Quesada M., Quinn G.B., Ramos A.G., Westbrook J.D., Young J., Zardecki C., Berman H.M., Bourne P.E. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 2013;41:D475–D482. PubMed PMC

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data | Journal of Chemical Theory and Computation, https://pubs.acs.org/doi/10.1021/ct400341p, (accessed 9 September 2020). PubMed

D. Case, R. Betz, D. S. Cerutti, T. Cheatham, T. Darden, R. Duke, T. J. Giese, H. Gohlke, A. Götz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.-S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko and P. Kollman, Amber 16, University of California, San Francisco., 2016.

Smart O.S., Neduvelil J.G., Wang X., Wallace B.A., Sansom M.S.P. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph. 1996;14(6):354–360. PubMed

Moriwaki H., Tian Y.-S., Kawashita N., Takagi T. Mordred: a molecular descriptor calculator. J Cheminf. 2018;10:4. PubMed PMC

Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K., Goodsell D.S. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791. PubMed PMC

Höskuldsson A. PLS regression methods. J Chemom. 1988;2(3):211–228.

Kubinyi H, Ed., 3D QSAR in Drug Design: Volume 1: Theory Methods and Applications, Springer Netherlands, 1994.

Wold S., Dunn W.J. Multivariate quantitative structure-activity relationships (QSAR): conditions for their applicability. J Chem Inf Comput Sci. 1983;23(1):6–13.

Wold S. Validation of QSAR’s. Quant Struct-Act Relat. 1991;10(3):191–193.

Miller B.R., McGee T.D., Swails J.M., Homeyer N., Gohlke H., Roitberg A.E. MMPBSA.py: An efficient program for end-state free energy calculations. J Chem Theory Comput. 2012;8(9):3314–3321. doi: 10.1021/ct300418h. PubMed DOI

Genheden S., Ryde U. Expert Opin Drug Discov. 2015:10. PubMed PMC

D. A. Case, V. Babin, J. T. Berryman, R. M. Betz, Q. Cai, D. S. Cerutti, T. E. Cheatham III, T. A. Darden, R. E. Duke, H. Gohlke, A. W. Goetz, S. Gusarov, N. Homeyer, P. Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T. S. Lee, S. LeGrand, T. Luchko, R. Luo, B. Madej, K. M. Merz, F. Paesani, D. R. Roe, A. Roitberg, C. Sagui, R. Salomen-Ferrer, G. Seabra, G. L. Simmerling, W. Smith, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu and P. A. Kollman, AMBER 14, 2014.

Maier J.A., Martinez C., Kasavajhala K., Wickstrom L., Hauser K.E., Simmerling C. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput. 2015;11(8):3696–3713. PubMed PMC

Götz A.W., Williamson M.J., Xu D., Poole D., Le Grand S., Walker R.C. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born. J Chem Theory Comput. 2012;8(5):1542–1555. doi: 10.1021/ct200909j. PubMed DOI PMC

Le Grand S., Götz A.W., Walker R.C. Speed without compromise – a mixed precision model for GPU accelerated molecular dynamics simulations. Comput Phys Commun. 2013;184(2):374–380.

Case D.A., Betz R.M., Cerutti D.S., Cheatham T.E., III, Darden T.A., Duke R.E. University of California; San Francisco: 2016. AMBER 16.

Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO), J Comput Chem, DOI: 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A.

Wishart D.S., Knox C., Guo A.C., Shrivastava S., Hassanali M., Stothard P. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34:D668–672. PubMed PMC

Trezza A., Iovinelli D., Santucci A., Prischi F., Spiga O. An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors. Sci Rep. 2020;10:13866. PubMed PMC

Panda P.K., Arul M.N., Patel P., Verma S.K., Luo W., Rubahn H.-G. Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. Sci Adv. 2020;6(28):eabb8097. doi: 10.1126/sciadv.abb8097. PubMed DOI PMC

JCM | Free Full-Text | Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site | HTML, https://www.mdpi.com/2077-0383/9/5/1473/htm, (accessed 16 February 2021). PubMed PMC

Wei T.-z., Wang H., Wu X.-Q., Lu Y.i., Guan S.-H., Dong F.-Q. In Silico screening of potential spike glycoprotein inhibitors of SARS-CoV-2 with drug repurposing strategy. Chin J Integr Med. 2020;26(9):663–669. PubMed PMC

Awad I.E., Abu-Saleh A.-A.-A.-A., Sharma S., Yadav A., Poirier R.A. High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein. J Biomol Struct Dyn. 2020:1–14. PubMed PMC

Mirabelli C., Wotring J.W., Zhang C.J., McCarty S.M., Fursmidt R., Frum T., Kadambi N.S., Amin A.T., O’Meara T.R., Pretto C.D., Spence J.R., Huang J., Alysandratos K.D., Kotton D.N., Handelman S.K., Wobus C.E., Weatherwax K.J., Mashour G.A., O’Meara M.J., Sexton J.Z. Morphological cell profiling of SARS-CoV-2 infection identifies drug repurposing candidates for COVID-19. bioRxiv. 2020 doi: 10.1101/2020.05.27.117184. PubMed DOI PMC

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes

pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support

Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web