Identification of novel inhibitor against endonuclease subunit of Influenza pH1N1 polymerase: A combined molecular docking, molecular dynamics, MMPBSA, QMMM and ADME studies to combat influenza A viruses

Mohseni, S.; Nasri, Fariborz; Davari, Kambiz; Mirzaie, Sako; Moradzadegan, Atousa; Abdi, Fatemeh; Farzaneh, Farhad

doi:10.1016/j.compbiolchem.2018.08.005

Cited by 10 publications

(2 citation statements)

References 56 publications

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“…The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA), developed by Koll-man and Case, is a method for precisely determining the extent of ligand-protein interaction [ 33 , 34 ].To the calculation of binding free energy of docked system (drugs-spike protein complex) by MMPBSA, the molecular mechanics energies (EMM) and continuum solvent Poisson–Boltzmann (PB) model for polar salvation and solvent-accessible surface area (SA) for nonpolar salvation were considered. The following equation was used to calculate the system's overall free energy [35] :

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Section: Resultsmentioning

confidence: 99%

Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry

Farhadian

Heidari-Soureshjani

Hashemi-Shahraki

et al. 2022

Journal of Molecular Structure

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Although COVID-19 emerged as a major concern to public health around the world, no licensed medication has been found as of yet to efficiently stop the virus spread and treat the infection. The SARS-CoV-2 entry into the host cell is driven by the direct interaction of the S1 domain with the ACE-2 receptor followed by conformational changes in the S2 domain, as a result of which fusion peptide is inserted into the target cell membrane, and the fusion process is mediated by the specific interactions between the heptad repeats 1 and 2 (HR1 and HR2) that form the six-helical bundle. Since blocking this interaction between HRs stops virus fusion and prevents its subsequent replication, the HRs inhibitors can be used as anti-COVID drugs. The initial drug selection is based on existing molecular databases to screen for molecules that may have a therapeutic effect on coronavirus. Based on these premises, we chose two approved drugs to investigate their interactions with the HRs (based on docking methods). To this end, molecular dynamics simulations and molecular docking were carried out to investigate the changes in the structure of the SARS-CoV-2 spike protein. Our results revealed, cefpiramide has the highest affinity to S protein, thereby revealing its potential to become an anti-COVID-19 clinical medicine. Therefore, this study offers new ways to re-use existing drugs to combat SARS-CoV-2 infection.

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…”

Section: Resultsmentioning

confidence: 99%

Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry

Farhadian

Heidari-Soureshjani

Hashemi-Shahraki

et al. 2022

Journal of Molecular Structure

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“…It was also tested against the I38T-mutant enzyme and proved able to inhibit the mutant enzyme with high efficiency. The same compound illustrated exceptional theoretical ADME properties and is therefore suitable to serve as a primer for further in vivo and in vitro experiments with the ultimate aim of validating these promising but theoretical characteristics [ 34 ].…”

Section: Influenza Virus Rna-dependent Rna Polymerase Pa N-terminal E...mentioning

confidence: 99%

Targeting Metalloenzymes: The “Achilles’ Heel” of Viruses and Parasites

Moianos,

Prifti,

Makri

et al. 2023

Pharmaceuticals

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Metalloenzymes are central to the regulation of a wide range of essential viral and parasitic functions, including protein degradation, nucleic acid modification, and many others. Given the impact of infectious diseases on human health, inhibiting metalloenzymes offers an attractive approach to disease therapy. Metal-chelating agents have been expansively studied as antivirals and antiparasitics, resulting in important classes of metal-dependent enzyme inhibitors. This review provides the recent advances in targeting the metalloenzymes of viruses and parasites that impose a significant burden on global public health, including influenza A and B, hepatitis B and C, and human immunodeficiency viruses as well as Trypanosoma brucei and Trypanosoma cruzi.

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Ligand and structure-based virtual screening approaches in drug discovery: minireview

da Rocha,

de Sousa,

da Silva Mendes

et al. 2024

Mol Divers

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Identification of novel inhibitor against endonuclease subunit of Influenza pH1N1 polymerase: A combined molecular docking, molecular dynamics, MMPBSA, QMMM and ADME studies to combat influenza A viruses

Cited by 10 publications

References 56 publications

Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry

Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry

Targeting Metalloenzymes: The “Achilles’ Heel” of Viruses and Parasites

Ligand and structure-based virtual screening approaches in drug discovery: minireview

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