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Structural and energetic features of the dimerization of the main proteinase of SARS-CoV-2 using molecular dynamic simulations.
Zhang, Yunju; Zheng, Liangzhen; Yang, Yanmei; Qu, Yuanyuan; Li, Yong-Qiang; Zhao, Mingwen; Mu, Yuguang; Li, Weifeng.
  • Zhang Y; School of Physics, Shandong University, Jinan, Shandong, 250100, China.
  • Zheng L; Tencent AI Lab, Shenzhen, Guangdong, 518000, China.
  • Yang Y; College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014, China.
  • Qu Y; School of Physics, Shandong University, Jinan, Shandong, 250100, China.
  • Li YQ; School of Physics, Shandong University, Jinan, Shandong, 250100, China.
  • Zhao M; School of Physics, Shandong University, Jinan, Shandong, 250100, China.
  • Mu Y; School of Biological Sciences, Nanyang Technological University, Singapore, 637650, Singapore. ygmu@ntu.edu.sg.
  • Li W; School of Physics, Shandong University, Jinan, Shandong, 250100, China.
Phys Chem Chem Phys ; 24(7): 4324-4333, 2022 Feb 16.
Article in English | MEDLINE | ID: covidwho-1671657
ABSTRACT
The COVID-19 pandemic caused by SARS-CoV-2 has been declared a global health crisis. The development of anti-SARS-CoV-2 drugs heavily depends on the systematic study of the critical biological processes of key proteins of coronavirus among which the main proteinase (Mpro) dimerization is a key step for virus maturation. Because inhibiting the Mpro dimerization can efficiently suppress virus maturation, the key residues that mediate dimerization can be treated as targets of drug and antibody developments. In this work, the structure and energy features of the Mpro dimer of SARS-CoV-2 and SARS-CoV were studied using molecular dynamics (MD) simulations. The free energy calculations using the Generalized Born (GB) model showed that the dimerization free energy of the SARS-CoV-2 Mpro dimer (-107.5 ± 10.89 kcal mol-1) is larger than that of the SARS-CoV Mpro dimer (-92.83 ± 9.81 kcal mol-1), indicating a more stable and possibly a quicker formation of the Mpro dimer of SARS-CoV-2. In addition, the energy decomposition of each residue revealed 11 key attractive residues. Furthermore, Thr285Ala weakens the steric hindrance between the two protomers of SARS-CoV-2 that can form more intimate interactions. It is interesting to find 11 repulsive residues which effectively inhibit the dimerization process. At the interface of the Mpro dimer, we detected three regions that are rich in interfacial water which stabilize the SARS-CoV-2 Mpro dimer by forming hydrogen bonds with two protomers. The key residues and rich water regions provide important targets for the future design of anti-SARS-CoV-2 drugs through inhibiting Mpro dimerization.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Coronavirus 3C Proteases / SARS-CoV-2 Type of study: Systematic review/Meta Analysis Limits: Humans Language: English Journal: Phys Chem Chem Phys Journal subject: Biophysics / Chemistry Year: 2022 Document Type: Article Affiliation country: D1cp04630f

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Coronavirus 3C Proteases / SARS-CoV-2 Type of study: Systematic review/Meta Analysis Limits: Humans Language: English Journal: Phys Chem Chem Phys Journal subject: Biophysics / Chemistry Year: 2022 Document Type: Article Affiliation country: D1cp04630f