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Jaber AA, Chowdhury ZM, Bhattacharjee A, Mourin M, Keya CA, Bhuyan ZA. Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing. Genomics Inform 2021; 19:e48. [PMID: 35172476 PMCID: PMC8752979 DOI: 10.5808/gi.21040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/05/2021] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes small envelope protein (E) that plays a major role in viral assembly, release, pathogenesis, and host inflammation. Previous studies demonstrated that pyrazine ring containing amiloride analogs inhibit this protein in different types of coronavirus including SARS-CoV-1 small envelope protein E (SARS-CoV-1 E). SARS-CoV-1 E has 93.42% sequence identity with SARS-CoV-2 E and shared a conserved domain NS3/small envelope protein (NS3_envE). Amiloride analog hexamethylene amiloride (HMA) can inhibit SARS-CoV-1 E. Therefore, we performed molecular docking and dynamics simulations to explore whether amiloride analogs are effective in inhibiting SARS-CoV-2 E. To do so, SARS-CoV-1 E and SARS-CoV-2 E proteins were taken as receptors while HMA and 3-amino-5-(azepan-1-yl)-N-(diaminomethylidene)-6-pyrimidin-5-ylpyrazine-2-carboxamide (3A5NP2C) were selected as ligands. Molecular docking simulation showed higher binding affinity scores of HMA and 3A5NP2C for SARS-CoV-2 E than SARS-CoV-1 E. Moreover, HMA and 3A5NP2C engaged more amino acids in SARS-CoV-2 E. Molecular dynamics simulation for 1 μs (1,000 ns) revealed that these ligands could alter the native structure of the proteins and their flexibility. Our study suggests that suitable amiloride analogs might yield a prospective drug against coronavirus disease 2019.
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Affiliation(s)
- Abdullah All Jaber
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh.,Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Arittra Bhattacharjee
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh.,Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Muntahi Mourin
- Department of Microbiology, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
| | - Zaied Ahmed Bhuyan
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
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