ArticleMolecules (Basel, Switzerland)2021
Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Consensus scoring-guided virtual screening identifies potent anti-saprolegniasis compounds targeting a P450 fusion protein.Frontiers in microbiology · 2025Article
- Approaching Pharmacological Space: Events and Components.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses.Viruses · 2024Article
- Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics.International journal of molecular sciences · 2023Review
- A review onExploration of targeted anti-tumor therapy · 2023Review
- Ensemble of structure and ligand-based classification models for hERG liability profiling.Frontiers in pharmacology · 2023Article
- Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening.Molecules (Basel, Switzerland) · 2022Review
- Exscalate4CoV: Innovative High Performing Computing (HPC) Strategies to Tackle Pandemic Crisis.International journal of molecular sciences · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel.International journal of molecular sciences · 2022Article
- Characterization of raloxifene as a potential pharmacological agent against SARS-CoV-2 and its variants.Cell death & disease · 2022Article
- Natural Compounds Inhibit SARS-CoV-2 nsp13 Unwinding and ATPase Enzyme Activities.ACS pharmacology & translational science · 2022Article
- Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics.Molecules (Basel, Switzerland) · 2021Article
- Virus structure and structure-based antivirals.Current opinion in virology · 2021Review
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Authors and funding
11 authors.
Funding
Abstract
The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.
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