Rational approaches to discover SARS-CoV-2/ACE2 interaction inhibitors: Pharmacophore-based virtual screening, molecular docking, molecular dynamics and binding free energy studies

Yazdani, Mohsen; Jafari, Ameneh; Mahdian, Soodeh; Namazi, Mohsen; Gharaghani, Sajjad

doi:10.1016/j.molliq.2023.121345

Cited by 5 publications

(2 citation statements)

References 49 publications

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“…The combination of the 3D-RISM with bioinformatics tools assumes the use of extensive data sets. Despite recent progress in virtual screening and machine learning for virus-ligand complexes (see, for instance, [114][115][116][117]), information about the actual conformation of hydrated virus complexes is rather limited so far. However, we can make the following statement based on our own results [5,37,40] and comparative analysis of data from various computational methods [118] for proteins and solvated protein-ligand complexes.…”

Section: Discussionmentioning

confidence: 99%

The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands

Fedotova,

Chuev

2024

IJMS

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Viruses are the most numerous biological form living in any ecosystem. Viral diseases affect not only people but also representatives of fauna and flora. The latest pandemic has shown how important it is for the scientific community to respond quickly to the challenge, including critically assessing the viral threat and developing appropriate measures to counter this threat. Scientists around the world are making enormous efforts to solve these problems. In silico methods, which allow quite rapid obtention of, in many cases, accurate information in this field, are effective tools for the description of various aspects of virus activity, including virus–host cell interactions, and, thus, can provide a molecular insight into the mechanism of virus functioning. The three-dimensional reference interaction site model (3D-RISM) seems to be one of the most effective and inexpensive methods to compute hydrated viruses, since the method allows us to provide efficient calculations of hydrated viruses, remaining all molecular details of the liquid environment and virus structure. The pandemic challenge has resulted in a fast increase in the number of 3D-RISM calculations devoted to hydrated viruses. To provide readers with a summary of this literature, we present a systematic overview of the 3D-RISM calculations, covering the period since 2010. We discuss various biophysical aspects of the 3D-RISM results and demonstrate capabilities, limitations, achievements, and prospects of the method using examples of viruses such as influenza, hepatitis, and SARS-CoV-2 viruses.

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Section: Discussionmentioning

confidence: 99%

The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands

Fedotova,

Chuev

2024

IJMS

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“…Several specific anti-COVID-19 treatments are in development, including promising small interfering RNA (siRNA)-based therapies. 13 , 14 , 15 These siRNAs, utilizing the RNA interference (RNAi) machinery, degrade viral RNAs and can be swiftly adapted to target emerging variants. 10 , 16 There is significant interest in RNAi-based therapeutics for COVID-19, especially targeting the viral RNA-dependent RNA polymerase (RdRp), a key replication enzyme.…”

Section: Introductionmentioning

confidence: 99%

A novel multitargeted self-assembling peptide-siRNA complex for simultaneous inhibition of SARS-CoV-2-host cell interaction and replication

Tuttolomondo,

Pham,

Terp

et al. 2024

Molecular Therapy - Nucleic Acids

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SARS-CoV-2 Spike Protein: A Review of Structure, Function, Care, Vaccines, and Possible Inhibitors Designed by Molecular Modeling

Coelho,

Silva,

Gomes

et al. 2023

Engineering Materials

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Rational approaches to discover SARS-CoV-2/ACE2 interaction inhibitors: Pharmacophore-based virtual screening, molecular docking, molecular dynamics and binding free energy studies

Cited by 5 publications

References 49 publications

The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands

The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands

A novel multitargeted self-assembling peptide-siRNA complex for simultaneous inhibition of SARS-CoV-2-host cell interaction and replication

SARS-CoV-2 Spike Protein: A Review of Structure, Function, Care, Vaccines, and Possible Inhibitors Designed by Molecular Modeling

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