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Research Article

Insights from computational studies on the potential of natural compounds as inhibitors against SARS-CoV-2 spike omicron variant

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Pages 953-968 | Received 30 Sep 2022, Accepted 21 Nov 2022, Published online: 05 Dec 2022

References

  • A. Al-Romaima, Y. Liao, J. Feng, X. Qin, and G. Qin, Advances in the treatment of novel coronavirus disease (COVID-19) with Western medicine and traditional Chinese medicine: A narrative review, J. Thorac. Dis. 12 (2020), pp. 6054–6069. doi:10.21037/jtd-20-1810.
  • C.C. Lai, T.P. Shih, W.C. Ko, H.J. Tang, and P.R. Hsueh, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges, Int. J. Antimicrob. Agents 55 (2020), pp. 105924. doi:10.1016/j.ijantimicag.2020.105924.
  • Coronavirus disease (COVID-19) situation reports; software available at https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
  • R. Yadav, J.K. Chaudhary, N. Jain, P.K. Chaudhary, S. Khanra, P. Dhamija, A. Sharma, A. Kumar, and S. Handu, Role of structural and non-structural proteins and therapeutic targets of SARS-CoV-2 for COVID-19, Cells 10 (2021), pp. 821. doi:10.3390/cells10040821.
  • T. Shu, M. Huang, D. Wu, Y. Ren, X. Zhang, Y. Han, J. Mu, R. Wang, Y. Qiu, D.Y. Zhang, and X. Zhou, SARS-Coronavirus-2 Nsp13 possesses NTPase and RNA helicase activities that can be inhibited by bismuth salts, Virol. Sin. 35 (2020), pp. 321–329. doi:10.1007/s12250-020-00242-1.
  • Z. Zhang, N. Nomura, Y. Muramoto, T. Ekimoto, T. Uemura, K. Liu, M. Yui, N. Kono, J. Aoki, M. Ikeguchi, T. Noda, S. Iwata, U. Ohto, and T. Shimizu, Structure of SARS-CoV-2 membrane protein essential for virus assembly, Nat. Commun. 131 (2022), pp. 1–12.
  • F. Chaudhry, S. Lavandero, X. Xie, B. Sabharwal, Y.Y. Zheng, A. Correa, J. Narula, and P. Levy, Manipulation of ACE2 expression in COVID-19, Open Hear. 7 (2020), pp. e001424.
  • J. Luan, Y. Lu, X. Jin, and L. Zhang, Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection, Biochem. Biophys. Res. Commun. 526 (2020), pp. 165–169. doi:10.1016/j.bbrc.2020.03.047.
  • W.T. Harvey, A.M. Carabelli, B. Jackson, R.K. Gupta, E.C. Thomson, E.M. Harrison, C. Ludden, R. Reeve, A. Rambaut, S.J. Peacock, and D.L. Robertson, SARS-CoV-2 variants, spike mutations and immune escape, Nat. Rev. Microbiol. 19 (2021), pp. 409–424. doi:10.1038/s41579-021-00573-0.
  • C. Yi, X. Sun, Z. Ling, and B. Sun, Jigsaw puzzle of SARS-CoV-2 RBD evolution and immune escape, Cell. Mol. Immunol. 2022 (2022), pp. 1–4.
  • H.M. Mengist, A.J. Kombe Kombe, D. Mekonnen, A. Abebaw, M. Getachew, and T. Jin, Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity, Semin. Immunol. 55 (2021), pp. 101533. doi:10.1016/j.smim.2021.101533.
  • R. Zhou, H. Chen, J. Chen, X. Chen, Y. Wen, and L. Xu, Extract from astragalus membranaceus inhibit breast cancer cells proliferation via PI3K/AKT/mTOR signaling pathway, BMC Complement. Altern. Med. 18 (2018), pp. 1–8. doi:10.1186/s12906-018-2148-2.
  • S.E. Greasley, S. Noell, O. Plotnikova, R.A. Ferre, W. Liu, B. Bolanos, K. Fennell, J. Nicki, T. Craig, Y. Zhu, A.E. Stewart, and C.M. Steppan, Structural basis for Nirmatrelvir in vitro efficacy against SARS-CoV-2 variants, bioRxiv, (2022), pp. 2022.01.17.476556.
  • J. Li, S. Lai, G.F. Gao, and W. Shi, The emergence, genomic diversity and global spread of SARS-CoV-2, Nature 600 (2021), pp. 408–418. doi:10.1038/s41586-021-04188-6.
  • H. Akkız, The biological functions and clinical significance of SARS-CoV-2 variants of corcern, Front. Med. P (2022), pp. 101972.
  • N.L. Miller, T. Clark, R. Raman, and R. Sasisekharan, Insights on the mutational landscape of the SARS-CoV-2 omicron variant receptor-binding domain, Cell Reports Med. 3 (2022), pp. 100527. doi:10.1016/j.xcrm.2022.100527.
  • S. Qin, M. Cui, S. Sun, J. Zhou, Z. Du, Y. Cui, and H. Fan, Genome characterization and potential risk assessment of the novel SARS-CoV-2 variant omicron (B.1.1.529), Zoonoses 1 (2021). doi:10.15212/ZOONOSES-2021-0024.
  • P. Han, L. Li, S. Liu, Q. Wang, D. Zhang, Z. Xu, P. Han, X. Li, Q. Peng, C. Su, B. Huang, D. Li, R. Zhang, M. Tian, L. Fu, Y. Gao, X. Zhao, K. Liu, J. Qi, J. Qi, G.F. Gao, and P. Wang, Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2, Cell 185 (2022), pp. 630–640.e10. doi:10.1016/j.cell.2022.01.001.
  • M. Macchiagodena, M. Pagliai, and P. Procacci, Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease, J. Mol. Graph. Model. 110 (2022), pp. 108042. doi:10.1016/j.jmgm.2021.108042.
  • S. Ding, I. Ullah, S.Y. Gong, J.R. Grover, M. Mohammadi, Y. Chen, D. Vézina, G. Beaudoin-Bussières, V.T. Verma, G. Goyette, F. Gaudette, J. Richard, D. Yang, A.B. Smith, M. Pazgier, M. Côté, C. Abrams, P. Kumar, W. Mothes, P.D. Uchil, A. Finzi, and C. Baron, VE607 stabilizes SARS-CoV-2 spike in the “RBD-up” conformation and inhibits viral entry, iScience 25 (2022), pp. 104528. doi:10.1016/j.isci.2022.104528.
  • F. Mosquera-Yuqui, N. Lopez-Guerra, and E.A. Moncayo-Palacio, Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: Molecular docking and molecular dynamics simulations, J. Biomol. Struct. Dyn. 40 (2022), pp. 2010–2023. doi:10.1080/07391102.2020.1835716.
  • A. Alqethami, A.Y. Aldhebiani, and I. Teixidor-toneu, Medicinal plants used in Jeddah, Saudi Arabia : A gender perspective, J. Ethnopharmacol. 257 (2020), pp. 112899. doi:10.1016/j.jep.2020.112899.
  • J. Roshni, R. Vaishali, K. Ganesh, N. Dharani, K.J. Alzahrani, H.J. Banjer, A.H. Alghamdi, A. Theyab, S.S. Ahmed, and S. Patil, Multi-target potential of Indian phytochemicals against SARS-CoV-2: A docking, molecular dynamics and MM-GBSA approach extended to omicron B.1.1.529, J. Infect. Public Health 15 (2022), pp. 662–669. doi:10.1016/j.jiph.2022.05.002.
  • G. Kumar Paul, S. Mahmud, A.A. Aldahish, M. Afroze, S. Biswas, S. Briti Ray Gupta, M. Hasan Razu, S. Zaman, M. Salah Uddin, M.H. Nahari, M. Merae Alshahrani, M. Abdul Rahman Alshahrani, M. Khan, and M. Abu Saleh, Computational screening and biochemical analysis of Pistacia integerrima and Pandanus odorifer plants to find effective inhibitors against Receptor-Binding Domain (RBD) of the spike protein of SARS-Cov-2, Arab. J. Chem. 15 (2022), pp. 103600. doi:10.1016/j.arabjc.2021.103600.
  • C.H. Kim, Anti–SARS-CoV-2 natural products as potentially therapeutic agents, Front. Pharmacol. 12 (2021), pp. 1015. doi:10.3389/fphar.2021.590509.
  • K. Gopinath, E.M. Jokinen, S.T. Kurkinen, and O.T. Pentikäinen, Screening of natural products targeting SARS-CoV-2–ACE2 receptor interface – A MixMD based HTVS pipeline, Front. Chem. 8 (2020), pp. 1084. doi:10.3389/fchem.2020.589769.
  • M. Nedyalkova, M. Vasighi, S. Sappati, A. Kumar, S. Madurga, and V. Simeonov, Inhibition ability of natural compounds on receptor-binding domain of SARS-CoV2: An in silico approach, Pharmaceuticals 14 (2021), pp. 1328. doi:10.3390/ph14121328.
  • P. Kar, N.R. Sharma, B. Singh, A. Sen, and A. Roy, Natural compounds from Clerodendrum spp. as possible therapeutic candidates against SARS-CoV-2: An in silico investigation, J. Biomol. Struct. Dyn. 39 (2021), pp. 4774–4785. doi:10.1080/07391102.2020.1780947.
  • P. Kar, M.M. Saleh-E-In, N. Jaishee, A. Anandraj, E. Kormuth, B. Vellingiri, C. Angione, P.K.S.M. Rahman, S. Pillay, A. Sen, D. Naidoo, A. Roy, and Y.E. Choi, Computational profiling of natural compounds as promising inhibitors against the spike proteins of SARS-CoV-2 wild-type and the variants of concern, viral cell-entry process, and cytokine storm in COVID-19, J. Cell. Biochem. 123 (2022), pp. 964–986. doi:10.1002/jcb.30243.
  • A. Mehmood, S. Nawab, Y. Wang, A. Chandra Kaushik, and D.Q. Wei, Discovering potent inhibitors against the Mpro of the SARS-CoV-2. A medicinal chemistry approach, Comput. Biol. Med. 143 (2022), pp. 105235. doi:10.1016/j.compbiomed.2022.105235.
  • L.G. Ferreira, R.N. Dos Santos, G. Oliva, and A.D. Andricopulo, Molecular docking and structure-based drug design strategies, Molecules 20 (2015), pp. 13384–13421. doi:10.3390/molecules200713384.
  • G. Madhavi Sastry, M. Adzhigirey, T. Day, R. Annabhimoju, and W. Sherman, Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments, J. Comput. Aided Mol. Des. 27 (2013), pp. 221–234. doi:10.1007/s10822-013-9644-8.
  • S.E. Omer, T.M. Ibrahim, O.A. Krar, A.M. Ali, A.A. Makki, W. Ibraheem, and A.A. Alzain, Drug repurposing for SARS-CoV-2 main protease: Molecular docking and molecular dynamics investigations, Biochem. Biophys. Rep. 29 (2022), pp. 101225. doi:10.1016/j.bbrep.2022.101225.
  • R.A. Friesner, R.B. Murphy, M.P. Repasky, L.L. Frye, J.R. Greenwood, T.A. Halgren, P.C. Sanschagrin, and D.T. Mainz, Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes, J. Med. Chem. 49 (2006), pp. 6177–6196. doi:10.1021/jm051256o.
  • A.A. Alzain, F.A. Elbadwi, and F.O. Alsamani, Discovery of novel TMPRSS2 inhibitors for COVID-19 using in silico fragment-based drug design, molecular docking, molecular dynamics, and quantum mechanics studies, Inf. Med. Unl. 29 (2022), pp. 100870.
  • K.J. Bowers, D.E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, and D.E. Shaw, Scalable algorithms for molecular dynamics simulations on commodity clusters, ACM/IEEE SC 2006 Conference (SC'06) (2007), pp. 43.
  • H. Arya and M.S. Coumar, Chapter 4 - Lead Identification and Optimization, in The Design & Development of Novel Drugs and Vaccines, T.K. Bhatt and N.D. Nimesh, eds., Academic Press, 2021, pp. 31–63.
  • D.E.V. Pires, T.L. Blundell, and D.B. Ascher, pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures, J. Med. Chem. 58 (2015), pp. 4066–4072. doi:10.1021/acs.jmedchem.5b00104.
  • B. Kar, B. Dehury, M.K. Singh, S. Pati, and D. Bhattacharya, Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study, J. Mol. Graph. Model. 114 (2022), pp. 108192. doi:10.1016/j.jmgm.2022.108192.
  • A. Khan, H. Waris, M. Rafique, M. Suleman, A. Mohammad, S.S. Ali, T. Khan, Y. Waheed, C. Liao, and D.Q. Wei, The omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data, Int. J. Biol. Macromol. 200 (2022), pp. 438–448. doi:10.1016/j.ijbiomac.2022.01.059.
  • J. Ai, H. Zhang, Y. Zhang, K. Lin, Y. Zhang, J. Wu, Y. Wan, Y. Huang, J. Song, Z. Fu, H. Wang, J. Guo, N. Jiang, M. Fan, Y. Zhou, Y. Zhao, Q. Zhang, Q. Liu, J. Lv, P. Li, C. Qiu, and W. Zhang, Omicron variant showed lower neutralizing sensitivity than other SARS-CoV-2 variants to immune sera elicited by vaccines after boost, Emerg. Microbes Infect. 11 (2022), pp. 337–343. doi:10.1080/22221751.2021.2022440.
  • M.D. Sacco, Y. Hu, M.V. Gongora, F. Meilleur, M.T. Kemp, X. Zhang, J. Wang, and Y. Chen, The P132H mutation in the main protease of omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition, Cell Res. 2022 (2022), pp. 1–3.
  • D.R. Owen, C.M.N. Allerton, A.S. Anderson, L. Aschenbrenner, M. Avery, S. Berritt, B. Boras, R.D. Cardin, A. Carlo, K.J. Coffman, A. Dantonio, L. Di, H. Eng, R.A. Ferre, K.S. Gajiwala, S.A. Gibson, S.E. Greasley, B.L. Hurst, and E.P. Kadar, An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19, Science 374 (2021), pp. 1586–1593. doi:10.1126/science.abl4784.
  • I. Celik, R. Yadav, Z. Duzgun, S. Albogami, A.M.E.-S. Fatimawali, T. Bin Emran, T.E. Tallei, and T. Bin Emran, Interactions of the receptor binding domain of SARS-CoV-2 variants with hACE2: Insights from molecular docking analysis and molecular dynamic simulation, Biology 10 (2021), pp. 880. doi:10.3390/biology10090880.
  • A. Khan, D.Q. Wei, K. Kousar, J. Abubaker, S. Ahmad, J. Ali, F. Al-Mulla, S.S. Ali, N. Nizam-Uddin, A.M. Sayaf, and A. Mohammad, Preliminary structural data revealed that the SARS-CoV-2 B.1.617 variant’s RBD binds to ACE2 receptor stronger than the wild type to enhance the infectivity, ChemBioChem 22 (2021), pp. 2641–2649. doi:10.1002/cbic.202100191.
  • B. Usadel, U. Schlüter, M. Mølhøj, M. Gipmans, R. Verma, J. Kossmann, W.D. Reiter, and M. Pauly, Identification and characterization of a UDP glucuronate4-epimerase in arabidopsis, FEBS Lett. 569 (2004), pp. 327–331. doi:10.1016/j.febslet.2004.06.005.
  • R. Vignesh, V. Velu, and S.M. Sureban, Could nutraceutical approaches possibly attenuate the cytokine storm in COVID-19 patients? Front. Cell. Infect. Microbiol. 11 (2021), pp. 320. doi:10.3389/fcimb.2021.667733.
  • M. Volino-Souza, G.V. de Oliveira, C.A. Conte-Junior, and T.S. Alvares, Covid-19 quarantine: Impact of lifestyle behaviors changes on endothelial function and possible protective effect of beetroot juice, Front. Nutr. 7 (2020), pp. 204. doi:10.3389/fnut.2020.582210.
  • A. Ganesan, The impact of natural products upon modern drug discovery, Curr. Opin. Chem. Biol. 12 (2008), pp. 306–317. doi:10.1016/j.cbpa.2008.03.016.
  • Y. Kapelyukh, C.J. Henderson, N. Scheer, A. Rode, and C.R. Wolf, Defining the contribution of CYP1A1 and CYP1A2 to drug metabolism using humanized CYP1A1/1A2 and Cyp1a1/Cyp1a2 knockout mice, Drug Metab. Dispos. 47 (2019), pp. 907–918. doi:10.1124/dmd.119.087718.
  • E. Zeiger, The test that changed the world: The Ames test and the regulation of chemicals, Mutat. Res. Toxicol. Environ. Mutagen. 841 (2019), pp. 43–48. doi:10.1016/j.mrgentox.2019.05.007.

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