In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants

References

• Aier, I., Varadwaj, P. K., & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6(1), 34984–34910. https://doi.org/10.1038/srep34984
   PubMed Web of Science ®Google Scholar
• Alimohamadi, Y., Sepandi, M., Taghdir, M., & Hosamirudsari, H. (2020). Determine the most common clinical symptoms in COVID-19 patients: A systematic review and meta-analysis. Journal of Preventive Medicine and Hygiene, 61(3), E304–E312.
   PubMedGoogle Scholar
• Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, N.Y.), 300(5626), 1763–1767.
   PubMed Web of Science ®Google Scholar
• Andreano, E., Piccini, G., Licastro, D., Casalino, L., Johnson, N. V., Paciello, I., Dal Monego, S., Pantano, E., Manganaro, N., Manenti, A., Manna, R., Casa, E., Hyseni, I., Benincasa, L., Montomoli, E., Amaro, R. E., McLellan, J. S., & Rappuoli, R. (2021). SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Proceedings of the National Academy of Sciences, 118(36), e2103154118. https://doi.org/10.1073/pnas.2103154118
   PubMed Web of Science ®Google Scholar
• Arya, R., Kumari, S., Pandey, B., Mistry, H., Bihani, S. C., Das, A., Prashar, V., Gupta, G. D., Panicker, L., & Kumar, M. (2021). Structural insights into SARS-CoV-2 proteins. Journal of Molecular Biology, 433(2), 166725. https://doi.org/10.1016/j.jmb.2020.11.024
   PubMed Web of Science ®Google Scholar
• Awad, I. E., Abu-Saleh, A., Sharma, S., Yadav, A., & Poirier, R. A. (2022). High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein. Journal of Biomolecular Structure & Dynamics, 40(5), 2099–2112. https://doi.org/10.1080/07391102.2020.1835721
   PubMed Web of Science ®Google Scholar
• Bafna, K., Krug, R. M., & Montelione, G. T. (2020). Structural similarity of SARS-CoV2 Mpro and HCV NS3/4A proteases suggests new approaches for identifying existing drugs useful as COVID-19 therapeutics. Frontiers in Chemistry, 1070.
   Google Scholar
• Balmeh, N., Mahmoudi, S., & Fard, N. A. (2021). Manipulated bio antimicrobial peptides from probiotic bacteria as proposed drugs for COVID-19 disease. Informatics in Medicine Unlocked, 23, 100515. https://doi.org/10.1016/j.imu.2021.100515
   PubMedGoogle Scholar
• Barh, D., Tiwari, S., Andrade, B. S., Giovanetti, M., Costa, E. A., Kumavath, R., Ghosh, P., Góes-Neto, A., Alcantara, L. C. J., & Azevedo, V. (2020). Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain. F1000Research, 9, 576. https://doi.org/10.12688/f1000research.24074.1
   PubMedGoogle Scholar
• Barton, M. I., MacGowan, S. A., Kutuzov, M. A., Dushek, O., Barton, G. J., & Van Der Merwe, P. A. (2021). Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. eLife, 10, e70658. https://doi.org/10.7554/eLife.70658
   PubMed Web of Science ®Google Scholar
• Bharadwaj, S., Dubey, A., Yadava, U., Mishra, S. K., Kang, S. G., & Dwivedi, V. D. (2021). Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro. Briefings in Bioinformatics, 22(2), 1361–1377. https://doi.org/10.1093/bib/bbaa382
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006, November 11–17). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, FL.
   Google Scholar
• Brant, A. C., Tian, W., Majerciak, V., Yang, W., & Zheng, Z. M. (2021). SARS-CoV-2: From its discovery to genome structure, transcription, and replication. Cell & Bioscience, 11(1), 1–17. https://doi.org/10.1186/s13578-021-00643-z
   PubMed Web of Science ®Google Scholar
• Brister, J. R., Ako-Adjei, D., Bao, Y., & Blinkova, O. (2015). NCBI viral genomes resource. Nucleic Acids Research, 43(D1), D571–D577. Epub 2014 Nov 26. https://doi.org/10.1093/nar/gku1207
   PubMed Web of Science ®Google Scholar
• Campagna, S., Saint, N., Molle, G., & Aumelas, A. (2007). Structure and mechanism of action of the antimicrobial peptide piscidin. Biochemistry, 46(7), 1771–1778. https://doi.org/10.1021/bi0620297
   PubMed Web of Science ®Google Scholar
• Cannalire, R., Stefanelli, I., Cerchia, C., Beccari, A. R., Pelliccia, S., & Summa, V. (2020). SARS-CoV-2 entry inhibitors: Small molecules and peptides targeting virus or host cells. International Journal of Molecular Sciences, 21(16), 5707. https://doi.org/10.3390/ijms21165707
   PubMed Web of Science ®Google Scholar
• Cao, L., Goreshnik, I., Coventry, B., Case, J. B., Miller, L., Kozodoy, L., Chen, R. E., Carter, L., Walls, A. C., Park, Y.-J., Strauch, E.-M., Stewart, L., Diamond, M. S., Veesler, D., & Baker, D. (2020). De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science (New York, N.Y.), 370(6515), 426–431.
   PubMed Web of Science ®Google Scholar
• Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., Wang, J., Wang, Y., Niu, X., Yang, S., Liang, H., Sun, H., Li, T., Yu, Y., Cui, Q., … Xie, X. S. (2022). Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature, 602(7898), 657–663.
   PubMed Web of Science ®Google Scholar
• Chowdhury, S. M., Talukder, S. A., Khan, A. M., Afrin, N., Ali, M. A., Islam, R., Parves, R., Al Mamun, A., Sufian, M. A., Hossain, M. N., Hossain, M. A., & Halim, M. A. (2020). Antiviral peptides as promising therapeutics against SARS-CoV-2. The Journal of Physical Chemistry. B, 124(44), 9785–9792. https://doi.org/10.1021/acs.jpcb.0c05621
   PubMed Web of Science ®Google Scholar
• da Costa, C. H. S., de Freitas, C. A. B., Alves, C. N., & Lameira, J. (2022). Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants. Scientific Reports, 12(1), 1–10. https://doi.org/10.1038/s41598-022-12479-9
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
   Google Scholar
• Dominguez, C., Boelens, R., & Bonvin, A. M. (2003). HADDOCK: A protein − protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society, 125(7), 1731–1737. https://doi.org/10.1021/ja026939x
   PubMed Web of Science ®Google Scholar
• Du, Q. S., Wang, S. Q., Zhu, Y., Wei, D. Q., Guo, H., Sirois, S., & Chou, K. C. (2004). Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide. Peptides, 25(11), 1857–1864. https://doi.org/10.1016/j.peptides.2004.06.018
   PubMed Web of Science ®Google Scholar
• Ferreira, G. M., Kronenberger, T., Tonduru, A. K., Hirata, R. D. C., Hirata, M. H., & Poso, A. (2021). SARS-COV-2 Mpro conformational changes induced by covalently bound ligands. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.1080/07391102.2021.1970626
   Google Scholar
• Giovanetti, M., Cella, E., Benedetti, F., Rife Magalis, B., Fonseca, V., Fabris, S., Campisi, G., Ciccozzi, A., Angeletti, S., Borsetti, A., Tambone, V., Sagnelli, C., Pascarella, S., Riva, A., Ceccarelli, G., Marcello, A., Azarian, T., Wilkinson, E., de Oliveira, T., … Ciccozzi, M. (2021). SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy. Communications Biology, 4(1), 1–9. https://doi.org/10.1038/s42003-021-02025-0
   PubMed Web of Science ®Google Scholar
• Goyal, B., & Goyal, D. (2020). Targeting the dimerization of the main protease of coronaviruses: A potential broad-spectrum therapeutic strategy. ACS Combinatorial Science, 22(6), 297–305. https://doi.org/10.1021/acscombsci.0c00058
   PubMed Web of Science ®Google Scholar
• Greaney, A. J., Loes, A. N., Crawford, K. H., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021). Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host & Microbe, 29(3), 463–476.e6. https://doi.org/10.1016/j.chom.2021.02.003
   PubMed Web of Science ®Google Scholar
• Guo, Y. R., Cao, Q. D., Hong, Z. S., Tan, Y. Y., Chen, S. D., Jin, H. J., Tan, K. S., Wang, D. Y., & Yan, Y. (2020). The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak–an update on the status. Military Medical Research, 7(1), 1–10. https://doi.org/10.1186/s40779-020-00240-0
   PubMed Web of Science ®Google Scholar
• Gupta, S., Wang, W., Hayek, S. S., Chan, L., Mathews, K. S., Melamed, M. L., Brenner, S. K., Leonberg-Yoo, A., Schenck, E. J., Radbel, J., Reiser, J., Bansal, A., Srivastava, A., Zhou, Y., Finkel, D., Green, A., Mallappallil, M., Faugno, A. J., Zhang, J., … Leaf, D. E. (2021). Association between early treatment with tocilizumab and mortality among critically ill patients with COVID-19. JAMA Internal Medicine, 181(1), 41–51.
   PubMed Web of Science ®Google Scholar
• Han, Y., & Král, P. (2020). Computational design of ACE2-based peptide inhibitors of SARS-CoV-2. ACS Nano, 14(4), 5143–5147. https://doi.org/10.1021/acsnano.0c02857
   PubMed Web of Science ®Google Scholar
• He, X., Lau, E. H. Y., Wu, P., Deng, X., Wang, J., Hao, X., Lau, Y. C., Wong, J. Y., Guan, Y., Tan, X., Mo, X., Chen, Y., Liao, B., Chen, W., Hu, F., Zhang, Q., Zhong, M., Wu, Y., Zhao, L., … Leung, G. M. (2020). Temporal dynamics in viral shedding and transmissibility of COVID-19. Nature Medicine, 26(5), 672–675. https://doi.org/10.1038/s41591-020-0869-5
   PubMed Web of Science ®Google Scholar
• Henninot, A., Collins, J. C., & Nuss, J. M. (2018). The current state of peptide drug discovery: Back to the future? Journal of Medicinal Chemistry, 61(4), 1382–1414. https://doi.org/10.1021/acs.jmedchem.7b00318
   PubMed Web of Science ®Google Scholar
• Honorato, R. V., Koukos, P. I., Jiménez-García, B., Tsaregorodtsev, A., Verlato, M., Giachetti, A., Rosato, A., & Bonvin, A. M. (2021). Structural biology in the clouds: The WeNMR-EOSC ecosystem. Frontiers in Molecular Biosciences, 8, 708. https://doi.org/10.3389/fmolb.2021.729513
   Web of Science ®Google Scholar
• Jacobson, M. P., Friesner, R. A., Xiang, Z., & Honig, B. (2002). On the role of crystal packing forces in determining protein sidechain conformations. Journal of Molecular Biology. 320(3), 597–608. https://doi.org/10.1016/S0022-2836(02)00470-9
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins, 55(2), 351–367. https://doi.org/10.1002/prot.10613
   PubMed Web of Science ®Google Scholar
• Jaiswal, G., & Kumar, V. (2020). In-silico design of a potential inhibitor of SARS-CoV-2 S protein. PloS One, 15(10), e0240004. https://doi.org/10.1371/journal.pone.0240004
   PubMed Web of Science ®Google Scholar
• Janik, E., Niemcewicz, M., Podogrocki, M., Majsterek, I., & Bijak, M. (2021). The emerging concern and interest SARS-CoV-2 variants. Pathogens, 10(6), 633. https://doi.org/10.3390/pathogens10060633
   PubMed Web of Science ®Google Scholar
• Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293.
   PubMed Web of Science ®Google Scholar
• Katoh, K., Misawa, K., Kuma, K. I., & Miyata, T. (2002). MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14), 3059–3066. https://doi.org/10.1093/nar/gkf436
   PubMed Web of Science ®Google Scholar
• Kawulka, K. E., Sprules, T., Diaper, C. M., Whittal, R. M., McKay, R. T., Mercier, P., Zuber, P., & Vederas, J. C. (2004). Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to α-carbon cross-links: Formation and reduction of α-thio-α-amino acid derivatives. Biochemistry, 43(12), 3385–3395. https://doi.org/10.1021/bi0359527
   PubMed Web of Science ®Google Scholar
• Khailany, R. A., Safdar, M., & Ozaslan, M. (2020). Genomic characterization of a novel SARS-CoV-2. Gene Reports, 19, 100682. https://doi.org/10.1016/j.genrep.2020.100682
   PubMed Web of Science ®Google Scholar
• 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(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: multiple ligand–protein interaction diagrams for drug discovery.
   Google Scholar
• Lee, J. T., Yang, Q., Gribenko, A., Perrin, B. S., Jr, Zhu, Y., Cardin, R., Liberator, P. A., Anderson, A. S., & Hao, L. (2022). Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid. Mbio, 13(4), e00869–22.
   Web of Science ®Google Scholar
• Lei, J., & Hilgenfeld, R. (2017). RNA‐virus proteases counteracting host innate immunity. FEBS Letters, 591(20), 3190–3210. https://doi.org/10.1002/1873-3468.12827
   PubMed Web of Science ®Google Scholar
• Lu, C., Wu, C., Ghoreishi, D., Chen, W., Wang, L., Damm, W., Ross, G. A., Dahlgren, M. K., Russell, E., Von Bargen, C. D., Abel, R., Friesner, R. A., & Harder, E. D. (2021). OPLS4: Improving force field accuracy on challenging regimes of chemical space. Journal of Chemical Theory and Computation, 17(7), 4291–4300. https://doi.org/10.1021/acs.jctc.1c00302
   PubMed Web of Science ®Google Scholar
• 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., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
   PubMed Web of Science ®Google Scholar
• Naqvi, A. A. T., Fatima, K., Mohammad, T., Fatima, U., Singh, I. K., Singh, A., Atif, S. M., Hariprasad, G., Hasan, G. M., & Hassan, M. I. (2020). Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochimica et Biophysica Acta. Molecular Basis of Disease, 1866(10), 165878. https://doi.org/10.1016/j.bbadis.2020.165878
   PubMed Web of Science ®Google Scholar
• Nelson-Sathi, S., Umasankar, P. K., Sreekumar, E., Nair, R. R., Joseph, I., Nori, S. R. C., Philip, J. S., Prasad, R., Navyasree, K. V., Ramesh, S., Pillai, H., Ghosh, S., Santosh Kumar, T. R., & Pillai, M. R. (2022). Mutational landscape and in silico structure models of SARS-CoV-2 spike receptor binding domain reveal key molecular determinants for virus-host interaction. BMC Molecular and Cell Biology, 23(1), 2–12. https://doi.org/10.1186/s12860-021-00403-4
   PubMed Web of Science ®Google Scholar
• Ortega, J. T., Serrano, M. L., Pujol, F. H., & Rangel, H. R. (2020). Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis. EXCLI Journal, 19, 410.
   PubMed Web of Science ®Google Scholar
• Panda, S. K., Sen Gupta, P. S., Biswal, S., Ray, A. K., & Rana, M. K. (2021). ACE-2-derived biomimetic peptides for the inhibition of spike protein of SARS-CoV-2. Journal of Proteome Research, 20(2), 1296–1303. https://doi.org/10.1021/acs.jproteome.0c00686
   PubMed Web of Science ®Google Scholar
• Park, M., Cook, A. R., Lim, J. T., Sun, Y., & Dickens, B. L. (2020). A systematic review of COVID-19 epidemiology based on current evidence. Journal of Clinical Medicine, 9(4), 967. https://doi.org/10.3390/jcm9040967
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Rajpoot, S., Ohishi, T., Kumar, A., Pan, Q., Banerjee, S., Zhang, K. Y., & Baig, M. S. (2021). A novel therapeutic peptide blocks SARS-CoV-2 spike protein binding with host cell ACE2 receptor. Drugs in R&D, 21(3), 273–283. https://doi.org/10.1007/s40268-021-00357-0
   PubMed Web of Science ®Google Scholar
• Rathi, A., Kumar, V., & Sundar, D. (2022). Insights into the potential of withanolides as Phosphodiesterase-4 (PDE4D) inhibitors. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2022.2028679
   Google Scholar
• Rogne, P., Fimland, G., Nissen-Meyer, J., & Kristiansen, P. E. (2008). Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin lactococcin G. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1784(3), 543–554. https://doi.org/10.1016/j.bbapap.2007.12.002
   PubMed Web of Science ®Google Scholar
• Sanches, P. R., Charlie-Silva, I., Braz, H. L., Bittar, C., Calmon, M. F., Rahal, P., & Cilli, E. M. (2021). Recent advances in SARS-CoV-2 Spike protein and RBD mutations comparison between new variants Alpha (B. 1.1. 7, United Kingdom), Beta (B. 1.351, South Africa), Gamma (P. 1, Brazil) and Delta (B. 1.617. 2, India). Journal of Virus Eradication, 7(3), 100054. https://doi.org/10.1016/j.jve.2021.100054
   PubMed Web of Science ®Google Scholar
• Schwede, T., Kopp, J., Guex, N., & Peitsch, M. C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31(13), 3381–3385. https://doi.org/10.1093/nar/gkg520
   PubMed Web of Science ®Google Scholar
• Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., & Li, F. (2020). Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America, 117(21), 11727–11734. https://doi.org/10.1073/pnas.2003138117
   PubMed Web of Science ®Google Scholar
• Sharma, P., Joshi, T., Mathpal, S., Joshi, T., Pundir, H., Chandra, S., & Tamta, S. (2022). Identification of natural inhibitors against Mpro of SARS-CoV-2 by molecular docking, molecular dynamics simulation, and MM/PBSA methods. Journal of Biomolecular Structure & Dynamics, 40(6), 2757–2768. https://doi.org/10.1080/07391102.2020.1842806
   PubMed Web of Science ®Google Scholar
• Sitthiyotha, T., & Chunsrivirot, S. (2020). Computational design of 25-mer peptide binders of SARS-CoV-2. The Journal of Physical Chemistry. B, 124(48), 10930–10942. https://doi.org/10.1021/acs.jpcb.0c07890
   PubMed Web of Science ®Google Scholar
• Souza, P. F., Mesquita, F. P., Amaral, J. L., Landim, P. G., Lima, K. R., Costa, M. B., Farias, I. R., Belém, M. O., Pinto, Y. O., Moreira, H. H., Magalhaes, I. C., Castelo-Branco, D. S., Montenegro, R. C., & de Andrade, C. R. (2022). The spike glycoproteins of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape. International Journal of Biological Macromolecules, 208, 105–125. https://doi.org/10.1016/j.ijbiomac.2022.03.058
   PubMed Web of Science ®Google Scholar
• Suárez, D., & Díaz, N. (2020). SARS-CoV-2 main protease: A molecular dynamics study. Journal of Chemical Information and Modeling, 60(12), 5815–5831. https://doi.org/10.1021/acs.jcim.0c00575
   PubMed Web of Science ®Google Scholar
• Sun, C., Xie, C., Bu, G. L., Zhong, L. Y., & Zeng, M. S. (2022). Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduction and Targeted Therapy, 7(1), 202. https://doi.org/10.1038/s41392-022-01039-2
   PubMed Web of Science ®Google Scholar
• Thevenet, P., Shen, Y., Maupetit, J., Guyon, F., Derreumaux, P., & Tuffery, P. (2012). PEP-FOLD: An updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Research, 40(W1), W288–W293. https://doi.org/10.1093/nar/gks419
   PubMed Web of Science ®Google Scholar
• Tian, D., Sun, Y., Xu, H., & Ye, Q. (2022). The emergence and epidemic characteristics of the highly mutated SARS‐CoV‐2 Omicron variant. Journal of Medical Virology, 94(6), 2376–2383. https://doi.org/10.1002/jmv.27643
   PubMed Web of Science ®Google Scholar
• Tsomaia, N. (2015). Peptide therapeutics: Targeting the undruggable space. European Journal of Medicinal Chemistry, 94, 459–470. https://doi.org/10.1016/j.ejmech.2015.01.014
   PubMed Web of Science ®Google Scholar
• Ullrich, S., Ekanayake, K. B., Otting, G., & Nitsche, C. (2022). Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Bioorganic & Medicinal Chemistry Letters, 62, 128629. https://doi.org/10.1016/j.bmcl.2022.128629
   PubMed Web of Science ®Google Scholar
• Vangeel, L., Chiu, W., De Jonghe, S., Maes, P., Slechten, B., Raymenants, J., André, E., Leyssen, P., Neyts, J., & Jochmans, D. (2022). Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern. Antiviral Research, 198, 105252. https://doi.org/10.1016/j.antiviral.2022.105252
   PubMed Web of Science ®Google Scholar
• Venugopal, H., Edwards, P. J., Schwalbe, M., Claridge, J. K., Libich, D. S., Stepper, J., Loo, T., Patchett, M. L., Norris, G. E., & Pascal, S. M. (2011). Structural, dynamic, and chemical characterization of a novel S-glycosylated bacteriocin. Biochemistry, 50(14), 2748–2755. https://doi.org/10.1021/bi200217u
   PubMed Web of Science ®Google Scholar
• Wang, S., Xu, X., Wei, C., Li, S., Zhao, J., Zheng, Y., Liu, X., Zeng, X., Yuan, W., & Peng, S. (2022). Molecular evolutionary characteristics of SARS‐CoV‐2 emerging in the United States. Journal of Medical Virology, 94(1), 310–317. https://doi.org/10.1002/jmv.27331
   PubMed Web of Science ®Google Scholar
• Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., Lu, G., Qiao, C., Hu, Y., Yuen, K.-Y., Wang, Q., Zhou, H., Yan, J., & Qi, J. (2020). Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell, 181(4), 894–904.e9. https://doi.org/10.1016/j.cell.2020.03.045
   PubMed Web of Science ®Google Scholar
• Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., Gaebler, C., Agudelo, M., Cho, A., Wang, Z., Gazumyan, A., Cipolla, M., Luchsinger, L., Hillyer, C. D., Caskey, M., … Bieniasz, P. D. (2020). Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife, 9, e61312. https://doi.org/10.7554/eLife.61312
   PubMed Web of Science ®Google Scholar
• WHO (2022). WHO Coronavirus (COVID-19) dashboard. https://covid19.who.int/
   Google Scholar
• Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., Rossouw, T., Boswell, M., Ueckermann, V., Meiring, S., von Gottberg, A., Cohen, C., Morris, L., Bhiman, J. N., & Moore, P. L. (2021). SARS-CoV-2 501Y. V2 escapes neutralization by South African COVID-19 donor plasma. Nature Medicine, 27(4), 622–625. https://doi.org/10.1038/s41591-021-01285-x
   PubMed Web of Science ®Google Scholar
• Xu, W., Wang, M., Yu, D., & Zhang, X. (2020). Variations in SARS-CoV-2 spike protein cell epitopes and glycosylation profiles during global transmission course of COVID-19. Frontiers in Immunology, 11, 565278. https://doi.org/10.3389/fimmu.2020.565278
   PubMed Web of Science ®Google Scholar
• Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A novel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/NEJMoa2001017
   PubMed Web of Science ®Google Scholar