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In-Silico Design of a Novel Tridecapeptide Targeting Spike Protein of SARS-CoV-2 Variants of Concern.
Rajpoot, Sajjan; Solanki, Kundan; Kumar, Ashutosh; Zhang, Kam Y J; Pullamsetti, Soni Savai; Savai, Rajkumar; Faisal, Syed M; Pan, Qiuwei; Baig, Mirza S.
  • Rajpoot S; Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552 India.
  • Solanki K; Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552 India.
  • Kumar A; Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa Japan.
  • Zhang KYJ; Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Tsurumi, Yokohama, Kanagawa Japan.
  • Pullamsetti SS; Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Hessen Germany.
  • Savai R; Institute for Lung Health (ILH), Justus-Liebig-University Giessen, 35392 Giessen, Hessen Germany.
  • Faisal SM; Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), 61231 Bad Nauheim, Hessen Germany.
  • Pan Q; Institute for Lung Health (ILH), Justus-Liebig-University Giessen, 35392 Giessen, Hessen Germany.
  • Baig MS; National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana India.
Int J Pept Res Ther ; 28(1): 28, 2022.
Article in English | MEDLINE | ID: covidwho-1568383
ABSTRACT
Several mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have increased the transmission and mortality rate of coronavirus disease-19 (COVID-19) across the globe. Although many vaccines have been developed, a large proportion of the global population remains at high risk of infection. The current study aims to develop an antiviral peptide capable of inhibiting the interaction of SARS-CoV-2 spike protein and its six major variants with the host cell angiotensin-converting enzyme 2 (ACE2) receptor. An in-silico approach was employed to design a therapeutic peptide inhibitor against the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 and its variants (B.1.1.7, B.1.351, P.1, B.1.617.1, B.1.617.2 and B.1.617.3). The binding specificity and affinity of our designed peptide inhibitor Mod13AApi (YADKYQKQYKDAY) with wild-type S-RBD and its six variants was confirmed by molecular docking using the HPEPDOCK tool, whereas complex stability was determined by the MD simulation study. The physicochemical and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of inhibitory peptides were determined using the ExPASy tool and pkCSM server. The docking results and its properties from our in-silico analysis present the Mod13AApi, a promising peptide for the rapid development of anti-coronavirus peptide-based antiviral therapy. Blockage of the binding of the spike protein of SARS-CoV-2 variants with ACE2 in the presence of the therapeutic peptide may prevent deadly SARS-CoV-2 variants entry into host cells. Therefore, the designed inhibitory peptide can be utilized as a promising therapeutic strategy to combat COVID-19, as evident from this in-silico study.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Vaccines / Variants Language: English Journal: Int J Pept Res Ther Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Topics: Vaccines / Variants Language: English Journal: Int J Pept Res Ther Year: 2022 Document Type: Article