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Amino acid mutations are enriched in the spike protein of SARS-CoV-2, which plays a crucial role in cell infection. However, the impact of these mutations on protein structure and function is unclear. Understanding the pathophysiology and pandemic features of these SARS-CoV-2 variants requires knowledge of the spike protein structures. Here, we obtained the spike protein structures of 10 main globally endemic SARS-CoV-2 strains using AlphaFold2. The clustering analysis based on structural similarity revealed the unique features of the mainly pandemic SARS-CoV-2 Delta variants, indicating that structural clusters can reflect the current characteristics of the epidemic more accurately than those based on the protein sequence. The analysis of the binding affinities of ACE2-RBD, antibody-NTD, and antibody-RBD complexes in the different variants revealed that the recognition of antibodies against S1 NTD and RBD was decreased in the variants, especially the Delta variant compared with the original strain, which may induce the immune evasion of SARS-CoV-2 variants. Furthermore, by virtual screening the ZINC database against a high-accuracy predicted structure of Delta spike protein and experimental validation, we identified multiple compounds that target S1 NTD and RBD, which might contribute towards the development of clinical anti-SARS-CoV-2 medicines. Our findings provided a basic foundation for future in vitro and in vivo investigations that might speed up the development of potential therapies for the SARS-CoV-2 variants.<\/jats:p>","DOI":"10.34133\/2022\/9781758","type":"journal-article","created":{"date-parts":[[2022,2,1]],"date-time":"2022-02-01T18:45:15Z","timestamp":1643741115000},"source":"Crossref","is-referenced-by-count":27,"title":["Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants"],"prefix":"10.34133","volume":"2022","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8648-5560","authenticated-orcid":false,"given":"Qiangzhen","family":"Yang","sequence":"first","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuemin","family":"Jian","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali Alamdar Shah","family":"Syed","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aamir","family":"Fahira","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenxiang","family":"Zheng","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijia","family":"Zhu","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Wang","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinmai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanqin","family":"Wen","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiqiang","family":"Li","sequence":"additional","affiliation":[{"name":"Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao 266003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dun","family":"Pan","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Lu","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuo","family":"Wang","sequence":"additional","affiliation":[{"name":"Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, 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Naujokat, \u201cStructural features of coronavirus SARS-CoV-2 spike protein: targets for vaccination,\u201d Life Sciences, vol. 257, article 118056, 2020","journal-title":"Life Sciences"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.02.058"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-00459-7"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-021-00495-9"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.037"},{"key":"e_1_3_4_10_2","article-title":"Phylogenetic and phylodynamic analyses of SARS-CoV-2","volume":"287","author":"Nie Q.","year":"2020","unstructured":"Q. Nie, X. Li, W. Chen, D. Liu, Y. Chen, H. Li, D. Li, M. Tian, W. Tan, and J. Zai, \u201cPhylogenetic and phylodynamic analyses of SARS-CoV-2,\u201d Virus Research, vol. 287, article 198098, 2020","journal-title":"Virus Research"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2020.12.024"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2021.05.022"},{"issue":"4","key":"e_1_3_4_13_2","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1016\/j.jinf.2021.01.007","article-title":"Introduction of the South African SARS-CoV-2 variant 501Y.V2 into the UK","volume":"82","author":"Tang J. W.","year":"2021","unstructured":"J. W. Tang, O. T. R. Toovey, K. N. Harvey, and D. S. C. Hui, \u201cIntroduction of the South African SARS-CoV-2 variant 501Y.V2 into the UK,\u201d The Journal of Infection, vol. 82, no. 4, pp. e8\u2013e10, 2021","journal-title":"The Journal of Infection"},{"issue":"30","key":"e_1_3_4_14_2","doi-asserted-by":"crossref","first-page":"4013","DOI":"10.1016\/j.vaccine.2021.05.099","article-title":"Evaluation of post-introduction COVID-19 vaccine effectiveness: summary of interim guidance of the World Health Organization","volume":"39","author":"Patel M. K.","year":"2021","unstructured":"M. K. Patel, I. Bergeri, J. S. Bresee, B. J. Cowling, N. S. Crowcroft, K. Fahmy, S. Hirve, G. Kang, M. A. Katz, C. F. Lanata, M. L'Azou Jackson, S. Joshi, M. Lipsitch, J. M. Mwenda, F. Nogareda, W. A. Orenstein, J. R. Ortiz, R. Pebody, S. J. Schrag, P. G. Smith, P. Srikantiah, L. Subissi, M. Valenciano, D. W. Vaughn, J. R. Verani, A. Wilder-Smith, and D. R. Feikin, \u201cEvaluation of post-introduction COVID-19 vaccine effectiveness: summary of interim guidance of the World Health Organization,\u201d Vaccine, vol. 39, no. 30, pp. 4013\u20134024, 2021","journal-title":"Vaccine"},{"issue":"1","key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/s12985-021-01633-w","article-title":"Evolutionary trajectory of SARS-CoV-2 and emerging variants","volume":"18","author":"Singh J.","year":"2021","unstructured":"J. Singh, P. Pandit, A. G. McArthur, A. Banerjee, and K. Mossman, \u201cEvolutionary trajectory of SARS-CoV-2 and emerging variants,\u201d Virology Journal, vol. 18, no. 1, p. 166, 2021","journal-title":"Virology Journal"},{"issue":"6","key":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/s41577-021-00556-5","article-title":"Will SARS-CoV-2 variants of concern affect the promise of vaccines?","volume":"21","author":"Gupta R. K.","year":"2021","unstructured":"R. K. Gupta, \u201cWill SARS-CoV-2 variants of concern affect the promise of vaccines?,\u201d Nature Reviews. Immunology, vol. 21, no. 6, pp. 340\u2013341, 2021","journal-title":"Nature Reviews. Immunology"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2021.2088"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1080\/14760584.2021.1903879"},{"issue":"7","key":"e_1_3_4_19_2","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1056\/NEJMoa2108891","article-title":"Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant","volume":"385","author":"Lopez Bernal J.","year":"2021","unstructured":"J. Lopez Bernal, N. Andrews, C. Gower, E. Gallagher, R. Simmons, S. Thelwall, J. Stowe, E. Tessier, N. Groves, G. Dabrera, R. Myers, C. N. J. Campbell, G. Amirthalingam, M. Edmunds, M. Zambon, K. E. Brown, S. Hopkins, M. Chand, and M. Ramsay, \u201cEffectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant,\u201d The New England Journal of Medicine, vol. 385, no. 7, pp. 585\u2013594, 2021","journal-title":"The New England Journal of Medicine"},{"issue":"1","key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/s41577-021-00662-4","article-title":"SARS-CoV-2 breakthrough infections in vaccinated individuals: measurement, causes and impact","volume":"20","author":"Lipsitch M.","year":"2022","unstructured":"M. Lipsitch, F. Krammer, G. Regev-Yochay, Y. Lustig, and R. D. Balicer, \u201cSARS-CoV-2 breakthrough infections in vaccinated individuals: measurement, causes and impact,\u201d Nature Reviews. Immunology, vol. 20, no. 1, pp. 57\u201365, 2022","journal-title":"Nature Reviews. Immunology"},{"issue":"1","key":"e_1_3_4_21_2","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/s41392-021-00835-6","article-title":"Azvudine is a thymus-homing anti-SARS-CoV-2 drug effective in treating COVID-19 patients","volume":"6","author":"Zhang J.-L.","year":"2021","unstructured":"J.-L. Zhang, Y. H. Li, L. L. Wang, H. Q. Liu, S. Y. Lu, Y. Liu, K. Li, B. Liu, S. Y. Li, F. M. Shao, K. Wang, N. Sheng, R. Li, J. J. Cui, P. C. Sun, C. X. Ma, B. Zhu, Z. Wang, Y. H. Wan, S. S. Yu, Y. Che, C. Y. Wang, C. Wang, Q. Zhang, L. M. Zhao, X. Z. Peng, Z. Cheng, J. B. Chang, and J. D. Jiang, \u201cAzvudine is a thymus-homing anti-SARS-CoV-2 drug effective in treating COVID-19 patients,\u201d Signal Transduction and Targeted Therapy, vol. 6, no. 1, p. 414, 2021","journal-title":"Signal Transduction and Targeted Therapy"},{"issue":"11","key":"e_1_3_4_22_2","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1038\/s41422-021-00570-1","article-title":"Design and development of an oral remdesivir derivative VV116 against SARS- CoV-2","volume":"31","author":"Xie Y.","year":"2021","unstructured":"Y. Xie, W. Yin, Y. Zhang, W. Shang, Z. Wang, X. Luan, G. Tian, H. A. Aisa, Y. Xu, G. Xiao, J. Li, H. Jiang, S. Zhang, L. Zhang, H. E. Xu, and J. Shen, \u201cDesign and development of an oral remdesivir derivative VV116 against SARS- CoV-2,\u201d Cell Research, vol. 31, no. 11, pp. 1212\u20131214, 2021","journal-title":"Cell Research"},{"issue":"1","key":"e_1_3_4_23_2","article-title":"'nAb' the self-reactive activity in the COVID-19 combat","volume":"6","author":"Madhusudhanan N.","year":"2021","unstructured":"N. Madhusudhanan, M. Lenin, and M. Alagarraju, \u201c'nAb' the self-reactive activity in the COVID-19 combat,\u201d Therapy, vol. 6, no. 1, 2021","journal-title":"Therapy"},{"key":"e_1_3_4_24_2","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofab466.719","article-title":"520. Pharmacokinetic and safety phase 1 study and microneutralization assay results with BRII-196\/BRII-198, a novel antibody cocktail active against a wide range of SARS-CoV-2 variants","volume":"8","author":"Margolis D. A.","year":"2021","unstructured":"D. A. Margolis, F. Zhang, X. Hao, Y. Li, M. Wang, C. Li, Y. Zhang, J. Ma, Y. Ji, and Q. Zhu, \u201c520. Pharmacokinetic and safety phase 1 study and microneutralization assay results with BRII-196\/BRII-198, a novel antibody cocktail active against a wide range of SARS-CoV-2 variants,\u201d Open Forum Infectious Diseases, vol. 8, Supplement_1, 2021","journal-title":"Open Forum Infectious Diseases"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2380-z"},{"issue":"5","key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1002\/prot.26042","article-title":"Human SARS CoV-2 spike protein mutations","volume":"89","author":"Guruprasad L.","year":"2021","unstructured":"L. Guruprasad, \u201cHuman SARS CoV-2 spike protein mutations,\u201d Proteins, vol. 89, no. 5, pp. 569\u2013576, 2021","journal-title":"Proteins"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-021-00573-0"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.61312","article-title":"Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants","volume":"9","author":"Weisblum Y.","year":"2020","unstructured":"Y. Weisblum, F. Schmidt, F. Zhang, J. DaSilva, D. Poston, J. C. C. Lorenzi, F. Muecksch, M. Rutkowska, H. H. Hoffmann, E. Michailidis, C. Gaebler, M. Agudelo, A. Cho, Z. Wang, A. Gazumyan, M. Cipolla, L. Luchsinger, C. D. Hillyer, M. Caskey, D. F. Robbiani, C. M. Rice, M. C. Nussenzweig, T. Hatziioannou, and P. D. Bieniasz, \u201cEscape from neutralizing antibodies by SARS-CoV-2 spike protein variants,\u201d eLife, vol. 9, 2020","journal-title":"eLife"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03398-2"},{"issue":"3","key":"e_1_3_4_30_2","article-title":"_In vivo_ characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential","volume":"37","author":"Lam B.","year":"2021","unstructured":"B. Lam, Y. J. Kung, J. Lin, S. H. Tseng, Y. C. Tsai, L. He, G. Castiglione, E. Egbert, E. J. Duh, E. M. Bloch, A. A. R. Tobian, A. M. Milstone, R. B. S. Roden, T. C. Wu, and C. F. Hung, \u201c_In vivo_ characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential,\u201d Cell Reports, vol. 37, no. 3, article 109838, 2021","journal-title":"Cell Reports"},{"issue":"48","key":"e_1_3_4_31_2","first-page":"30132","article-title":"The SARS-CoV-2 B.1.618 variant slightly alters the spike RBD-ACE2 binding affinity and is an antibody escaping variant: a computational structural perspective","volume":"11","author":"Khan A.","year":"2021","unstructured":"A. Khan, J. Gui, W. Ahmad, I. Haq, M. Shahid, A. A. Khan, A. Shah, A. Khan, L. Ali, Z. Anwar, M. Safdar, J. Abubaker, N. N. Uddin, L. Cao, D. Q. Wei, and A. 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