CONTEXT: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 infection and responsible for millions of victims worldwide, remains a significant threat to public health. Even after the development of vaccines, research interest in the emergence of new variants is still prominent. Currently, the focus is on the search for effective and safe drugs, given the limitations and side effects observed for the synthetic drugs administered so far. In this sense, bioactive natural products that are widely used in the pharmaceutical industry due to their effectiveness and low toxicity have emerged as potential options in the search for safe drugs against COVID-19. Following this line, we screened 10 bioactive compounds derived from cholesterol for molecules capable of interacting with the receptor-binding domain (RBD) of the spike protein from SARS-CoV-2 (SC2Spike), responsible for the virus's invasion of human cells. Rounds of docking followed by molecular dynamics simulations and binding energy calculations enabled the selection of three compounds worth being experimentally evaluated against SARS-CoV-2. METHODS: The 3D structures of the cholesterol derivatives were prepared and optimized using the Spartan 08 software with the semi-empirical method PM3. They were then exported to the Molegro Virtual Docking (MVD®) software, where they were docked onto the RBD of a 3D structure of the SC2Spike protein that was imported from the Protein Data Bank (PDB). The best poses obtained from MVD® were subjected to rounds of molecular dynamics simulations using the GROMACS software, with the OPLS/AA force field. Frames from the MD simulation trajectories were used to calculate the ligand's free binding energies using the molecular mechanics - Poisson-Boltzmann surface area (MM-PBSA) method. All results were analyzed using the xmgrace and Visual Molecular Dynamics (VMD) software.

Department of Chemical Engineering Military Institute of Engineering Rio de Janeiro RJ Brazil

Department of Chemistry Faculty of Science University of Hradec Kralove Hradec Kralove Czech Republic

INRS Centre Armand Frappier Santé Biotechnologie 531 Boulevard Des Prairies Laval QC Canada

Laboratory of Molecular Modeling Applied to Chemical and Biological Defense Military Institute of Engineering Rio de Janeiro RJ Brazil

Zobrazit více v PubMed

Jo S, Kim S, Shin DH, et al. Inhibition of SARS-CoV 3CL protease by flavonoids. J Enzym Inhib Med Ch. 2020;35(1):145–151. doi: 10.1080/14756366.2019.1690480. PubMed DOI PMC

Bambini S, Rappuoli R. The use of genomics in microbial vaccine development. Drug Discov Today. 2009;14(5–6):252–260. doi: 10.1016/j.drudis.2008.12.007. PubMed DOI PMC

Cao L, Goreshnik I, Coventry B, et al. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science. 2020;370(6515):426–431. doi: 10.1126/science.abd9909. PubMed DOI PMC

da Silva AA, Wiedemann LSM, Veiga-Junior VF. Natural products’ role against COVID-19. RSC Adv. 2020;10(39):23379–23393. doi: 10.1039/D0RA03774E. PubMed DOI PMC

Sepay N, Sekar A, Halder UC, et al. Anti-COVID-19 terpenoid from marine sources: a docking, admet and molecular dynamics study. J Mol Struct. 2021;1228:129433. doi: 10.1016/j.molstruc.2020.129433. PubMed DOI PMC

Sanders DW, Jumper CC, Ackerman PJ, et al. SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation. Elife. 2021;10:e65962. doi: 10.7554/eLife.65962. PubMed DOI PMC

Yan R, Zhang Y, Li Y, et al. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science. 2020;367(6485):1444–1448. doi: 10.1126/science.abb2762. PubMed DOI PMC

Camargo CA, Jr, Martineau AR. Vitamin D to prevent COVID-19: recommendations for the design of clinical trials. FEBS J. 2020;287(17):3689–3692. doi: 10.1111/febs.15534. PubMed DOI

Speeckaert M, Speeckaert R, Delanghe J. Vitamin D and vitamin D binding protein: the inseparable duo in COVID-19. J Endocrinol Invest. 2021;44:2323–2324. doi: 10.1007/s40618-021-01573-w. PubMed DOI PMC

Alshahawey M. A genetic insight into vitamin D binding protein and COVID-19. Med Hypotheses. 2021;149:110531. doi: 10.1016/j.mehy.2021.110531. PubMed DOI PMC

Meltzer DO, Best TJ, Zhang H, et al. Solway, association of vitamin D status and other clinical characteristics with COVID-19 test results. JAMA Netw open. 2020;3(9):e2019722–e2019722. doi: 10.1001/jamanetworkopen.2020.19722. PubMed DOI PMC

Levental I, Lingwood D, Grzybek M, et al. Palmitoylation regulates raft affinity for the majority of integral raft proteins. Proc Natl Acad Sci. 2010;107(51):22050–22054. doi: 10.1073/pnas.1016184107. PubMed DOI PMC

Martin BR. Chemical approaches for profiling dynamic palmitoylation. Biochem Soc Trans. 2013;41(1):43–49. doi: 10.1042/BST20120271. PubMed DOI PMC

Sobocińska J, Roszczenko-Jasińska P, Ciesielska A, et al. Protein palmitoylation and its role in bacterial and viral infections. Front Immunol. 2018;8:2003. doi: 10.3389/fimmu.2017.02003. PubMed DOI PMC

Daniels LB, Sitapati AM, Zhang J, et al. Relation of statin use prior to admission to severity and recovery among COVID-19 inpatients. Am J Card. 2020;136:149–155. doi: 10.1016/j.amjcard.2020.09.012. PubMed DOI PMC

Zhang XJ, Qin JJ, Cheng X, et al. In-hospital use of statins is associated with a reduced risk of mortality among individuals with COVID-19. Cell Metab. 2020;32(2):176–187. e4. doi: 10.1016/j.cmet.2020.06.015. PubMed DOI PMC

Andricopulo AD, Salum LB, Abraham DJ. Structure-based drug design strategies in medicinal chemistry. Curr Top Med Chem. 2009;9(9):771–790. doi: 10.2174/156802609789207127. PubMed DOI

Reynolds CH. Impact of computational structure-based methods on drug discovery. Curr Pharm Des. 2014;20(20):3380–3386. doi: 10.2174/138161282020140528105532. PubMed DOI

Dhankhar P, Dalal V, Kumar V. Screening of severe acute respiratory syndrome coronavirus 2 RNA-dependent RNA polymerase inhibitors using computational approach. J Comput Biol. 2021;28(12):1228–1247. doi: 10.1089/cmb.2020.0639. PubMed DOI PMC

Kumar KA, Sharma M, Dalal V, et al. Multifunctional inhibitors of SARS-CoV-2 by MM/PBSA, essential dynamics, and molecular dynamic investigations. J Mol GraphModel. 2021;107:107969. doi: 10.1016/j.jmgm.2021.107969. PubMed DOI PMC

Dhankhar P, Dalal V, Singh V, et al. Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. J Biomol Struct Dyn. 2022;40(9):4084–4099. doi: 10.1080/07391102.2020.1852968. PubMed DOI PMC

Almeida JSFD, Botelho FD, de Souza FR, et al. Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets. J Biomol Struct Dyn. 2022;40(11):5229–5242. doi: 10.1080/07391102.2020.1869096. PubMed DOI PMC

Aghamohammadi M, Sirouspour M, Goncalves AS, et al. Modeling studies on the role of vitamins B1 (thiamin), B3 (nicotinamide), B6 (pyridoxamine), and caffeine as potential leads for the drug design against COVID-19. J Mol Model. 2022;28(12):380. doi: 10.1007/s00894-022-05356-9. PubMed DOI PMC

Farahani MD, França TCC, Alapour S, et al. Jumping from fragment to drug via smart scaffolds. ChemMedChem. 2022;17(10):e202200092. doi: 10.1002/cmdc.202200092. PubMed DOI

Thomsen R, Christensen MH. MolDock: a new technique for high-accuracy molecular docking. J Med Chem. 2006;49(11):3315–3321. doi: 10.1021/jm051197e. PubMed DOI

Stewart JJ. Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements. J Mol Model. 2004;10(2):155–164. doi: 10.1007/s00894-004-0183-z. PubMed DOI

Reed AE, Weinstock RB, Weinhold F. Natural population analysis. J Chem Phys. 1985;83:735–746. doi: 10.1063/1.449486. DOI

Singh V, Dhankhar P, Dalal V, et al. Drug-repurposing approach to combat Staphylococcus aureus: biomolecular and binding interaction study. ACS Omega. 2022;7(43):38448–38458. doi: 10.1021/acsomega.2c03671. PubMed DOI PMC

Singh V, Dhankhar P, Dalal V, et al. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: a potential drug target. J Mol Graph Model. 2022;116:108262. doi: 10.1016/j.jmgm.2022.108262. PubMed DOI

Kumari R, Rathi R, Pathak SR, et al. Computational investigation of potent inhibitors against YsxC: structure-based pharmacophore modeling, molecular docking, molecular dynamics, and binding free energy. J Biomol Struct Dyn. 2023;41(3):930–941. doi: 10.1080/07391102.2021.2015446. PubMed DOI

O’Boyle NM, Banck M, James CA, et al. Open Babel: an open chemical toolbox. J Cheminformatics. 2011;3(1):1–14. PubMed PMC

Da Silva AWS, Vranken WF. ACPYPE-Antechamber python parser interface. BMC Res Notes. 2012;5(1):1–8. PubMed PMC

Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996;118(45):11225–11236. doi: 10.1021/ja9621760. DOI

Kaminski GA, Friesner RA, Tirado-Rives J, et al. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B. 2001;105(28):6474–6487. doi: 10.1021/jp003919d. DOI

Abraham MJ, Murtola T, Schulz R. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1:19–25. doi: 10.1016/j.softx.2015.06.001. DOI

Pronk S, Páll S, Schulz R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013;29(7):845–854. doi: 10.1093/bioinformatics/btt055. PubMed DOI PMC

Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79(2):926–935. doi: 10.1063/1.445869. DOI

Van Gunsteren WF, Berendsen HJ. Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew Chem Int Ed English. 1990;29(9):992–1023. doi: 10.1002/anie.199009921. DOI

Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:014101 PubMed

Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys. 1981;52(12):7182–7190. doi: 10.1063/1.328693. DOI

Gupta DN, Dalal V, Savita BK, et al. In-silico screening and identification of potential inhibitors against 2Cys peroxiredoxin of Candidatus Liberibacter asiaticus. J Biomol Struct Dyn. 2022;40(19):8725–8739. doi: 10.1080/07391102.2021.1916597. PubMed DOI

Kumari R, Dalal V. Identification of potential inhibitors for LLM of Staphylococcus aureus: structure-based pharmacophore modeling, molecular dynamics, and binding free energy studies. J Biomol Struct Dyn. 2022;40(20):9833–9847. doi: 10.1080/07391102.2021.1936179. PubMed DOI

Humphrey W, Dalke A, Schulten K. VMD: Visual Molecular Dynamics. Graphics. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5. PubMed DOI

Kumari R, Kumar R; O.S.D.D. Consortium et al (2014) g _ mmpbsa - a GROMACS tool for MM-PBSA and its optimization for high-throughput binding energy calculations. J Chem Inf Model 54(7):1951–1962 PubMed

Kumari R, Dhankhar P, Dalal V. Structure-based mimicking of hydroxylated biphenyl congeners (OHPCBs) for human transthyretin, an important enzyme of thyroid hormone system. J Mol Graph Model. 2021;105:107870. doi: 10.1016/j.jmgm.2021.107870. PubMed DOI