ArticleComputational and structural biotechnology journal2023
Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 14 citations in OpenAlex.
- Flavonoids as Structural Probes Reveal Conformationally Dependent Ligand Recognition in the SARS-CoV-2 JN.1 Spike Protein.International journal of molecular sciences · 2026Article
- PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural ensembles.Nucleic acids research · 2026Article
- EMoMiS: A pipeline for epitope-based molecular mimicry search in protein structures with potential applications to SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- Eigenvalue Ratios Reveal Shared Binding Pocket Shapes in RNA and Protein Structures.Computational and structural biotechnology journal · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- Natural Fatty Acids as Dual ACE2-Inflammatory Modulators: Integrated Computational Framework for Pandemic Preparedness.International journal of molecular sciences · 2025Article
- Complete genome sequence analysis of Sarbecovirus (severe acute respiratory syndrome-related coronaviruses) from Zimbabwean insectivorous bats.BMC genomics · 2025Article
- Broad-spectrum inhibition of SARS-CoV-2 variants by dibutyl phthalate through allosteric disruption of Spike-ACE2 interface.Frontiers in microbiology · 2025Article
- Article
- Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking.International journal of molecular sciences · 2024Article
- Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein.The journal of physical chemistry. B · 2023Article
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Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for viral infection. The interaction of its receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2) protein is required for the virus to enter the host cell. We identified RBD binding sites to block its function with inhibitors by combining the protein structural flexibility with machine learning analysis. Molecular dynamics simulations were performed on unbound or ACE2-bound RBD conformations. Pockets estimation, tracking and druggability prediction were performed on a large sample of simulated RBD conformations. Recurrent druggable binding sites and their key residues were identified by clustering pockets based on their residue similarity. This protocol successfully identified three druggable sites and their key residues, aiming to target with inhibitors for preventing ACE2 interaction. One site features key residues for direct ACE2 interaction, highlighted using energetic computations, but can be affected by several mutations of the variants of concern. Two highly druggable sites, located between the spike protein monomers interface are promising. One weakly impacted by only one Omicron mutation, could contribute to stabilizing the spike protein in its closed state. The other, currently not affected by mutations, could avoid the activation of the spike protein trimer.
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