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Lin J, Anjum Huma F, Irfan A, Ali SS, Waheed Y, Mohammad A, Munir M, Khan A, Wei DQ. Structural plasticity of omicron BA.5 and BA.2.75 for enhanced ACE-dependent entry into cells. J Biomol Struct Dyn 2023; 41:10762-10773. [PMID: 36541923 DOI: 10.1080/07391102.2022.2158944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
The current study investigated the binding variations among the wilt type, Omicron sub-variants BA.2.75 and BA.5, using protein-protein docking, protein structural graphs (P SG), and molecular simulation methods. HADDOCK predicted docking scores and dissociation constant (KD) revealed tighter binding of these sub-variants in contrast to the WT. Further investigation revealed variations in the hub residues, protein sub-networks, and GlobalMetapath in these variants as compared to the WT. A very unusual dynamic for BA.2.75 and BA.5 was observed, and secondary structure transition can also be witnessed in the loops (44-505). The results show that the flexibility of these three loops is increased by the mutations as an allosteric effect and thus enhances the chances of bonding with the nearby residues to connect and form a stable connection. Furthermore, the additional hydrogen bonding contacts steer the robust binding of these variants in contrast to the wild type. The total binding free energy for the wild type was calculated to be -61.38 kcal/mol, while for BA.2.75 and BA.5 variants the T BE was calculated to be -70.42 kcal/mol and 69.78 kcal/mol, respectively. We observed that the binding of BA.2.75 is steered by the electrostatic interactions while the BA.5 additional contacts are due to the vdW (Van der Waal) energy. From these findings, it can be observed the Spike (S) protein is undergoing structural adjustments to bind efficiently to the hACE2 (human angiotensin-converting enzyme 2) receptor and, in turn, increase entry to the host cells. The current study will aid the development of structure-based drugs against these variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Junqi Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | - Aiza Irfan
- Rawalpindi Medical University, Punjab, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation & Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
- Peng Cheng Laboratory, Nashan District, Shenzhen, Guangdong, P.R China
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