- Title
- Novel dynamic residue network analysis approaches to study allosteric modulation: SARS-CoV-2 Mpro and its evolutionary mutations as a case study
- Creator
- Sheik Amamuddy, Olivier
- Creator
- Boateng, Rita A
- Creator
- Barozi, Victor
- Creator
- Nyamai, Dorothy W
- Creator
- Tastan Bishop, Özlem
- Subject
- To be catalogued
- Date Issued
- 2021
- Date
- 2021
- Type
- text
- Type
- article
- Identifier
- http://hdl.handle.net/10962/476596
- Identifier
- vital:77940
- Identifier
- xlink:href="https://doi.org/10.1016/j.csbj.2021.11.016"
- Description
- The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of mutations is a relatively unexplored field. Here, we established novel in silico approaches and applied them to SARS-CoV-2 main protease (Mpro) as a case study. First, we identified six potential allosteric modulators. Then, we focused on understanding the allosteric effects of these modulators on each of its protomers. We introduced a new combinatorial approach and dynamic residue network (DRN) analysis algorithms to examine patterns of change and conservation of critical nodes, according to five independent criteria of network centrality. We observed highly conserved network hubs for each averaged DRN metric on the basis of their existence in both protomers in the absence and presence of all ligands (persistent hubs). We also detected ligand specific signal changes. Using eigencentrality (EC) persistent hubs and ligand introduced hubs we identified a residue communication path connecting the allosteric binding site to the catalytic site. Finally, we examined the effects of the mutations on the behavior of the protein in the presence of selected potential allosteric modulators and investigated the ligand stability. One crucial outcome was to show that EC centrality hubs form an allosteric communication path between the allosteric ligand binding site to the active site going through the interface residues of domains I and II; and this path was either weakened or lost in the presence of some of the mutations. Overall, the results revealed crucial aspects that need to be considered in rational computational drug discovery.
- Format
- computer
- Format
- online resource
- Format
- application/pdf
- Format
- 1 online resource (25 pages)
- Format
- Publisher
- Elsevier
- Language
- English
- Relation
- Computational and Structural Biotechnology Journal
- Relation
- Amamuddy, O.S., Boateng, R.A., Barozi, V., Nyamai, D.W. and Bishop, Ö.T., 2021. Novel dynamic residue network analysis approaches to study allosteric modulation: SARS-CoV-2 Mpro and its evolutionary mutations as a case study. Computational and Structural Biotechnology Journal, 19, pp.6431-6455
- Relation
- Computational and Structural Biotechnology Journal volume 19 p. 6341 2021 2001-0370
- Rights
- Publisher
- Rights
- Use of this resource is governed by the terms and conditions of the Elsevier Terms and Conditions Statement (https://www.elsevier.com/legal/elsevier-website-terms-and-conditions)
- Rights
- Open Access
- Hits: 32
- Visitors: 33
- Downloads: 4
Collections
Sheik Amamuddy, Olivier (Dr)
Tastan Bishop, Ozlem (Prof)
SDG 03. Good Health and Well-Being
RU Department of Biochemistry, Microbiology and Bioinformatics
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