In-silico investigation of phenolic compounds from leaves of Phillyrea angustifolia L. as a potential inhibitor against the SARS-CoV-2 main protease (Mpro PDB ID:5R83) using a virtual screening method

Boufissiou, Ahmed; Abdalla, Mohnad; Sharaf, Mohamed; Al‐Resayes, Saud I.; Kadi, Imededdine; Alam, Mahboob; Yagi, Sakina; Azam, Mohammad; Yousfi, Mohamed

doi:10.1016/j.jscs.2022.101473

Cited by 18 publications

(7 citation statements)

References 41 publications

(36 reference statements)

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“…Chemical treatments have always been popular because of their immediate action against the ailment they are meant to treat ( Moon and Alam, 2020 ). Herbal medications also have been chastised for their sluggish action on the human body ( Abdalla et al, 2021 , Boufissiou et al, 2022 ). Additionally, herbal medications have a big advantage in terms of their benign nature, which means they are far less likely to harm humans.…”

Section: Introductionmentioning

confidence: 99%

1,4,9,9-tetramethyloctahydro-4,7-(epoxymethano)azulen-5(1H)-one, a natural product as a potential inhibitor of COVID-19: Extraction, crystal structure, and virtual screening approach

Bakri

Mohamed

Kandasamy

et al. 2023

Journal of King Saud University - Science

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Section: Introductionmentioning

confidence: 99%

1,4,9,9-tetramethyloctahydro-4,7-(epoxymethano)azulen-5(1H)-one, a natural product as a potential inhibitor of COVID-19: Extraction, crystal structure, and virtual screening approach

Bakri

Mohamed

Kandasamy

et al. 2023

Journal of King Saud University - Science

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“…C-5 and C-8 were put through molecular dynamics (MD) simulations to ascertain the stability of the ligand-protein interactions, which served to further establish their potential as therapeutic leads (62). Additionally, research was done to evaluate the pharmacokinetics, drug-likeness, and quantitative structure-activity relationship (QSAR) of these compounds (63). The findings revealed that C-5 had the best pharmacokinetic and drug-like characteristics, making it a good candidate for further development and optimization as a medication to treat COVID-19 (64).…”

Section: Computational Methods For Sars-cov-2 Protease Inhibitor Iden...mentioning

confidence: 99%

A Molecular Modeling and Molecular Dynamics Simulations Investigation of the Potential Therapeutic Applications of Main Protease Inhibitors for SARS-CoV-2

Mushebenge,

Ugbaja,

Mbatha

et al. 2023

Preprint

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A major public health emergency has been created by the COVID-19 pandemic, which is brought on by the SARS-CoV-2 virus. Due to its crucial function in viral replication, the primary protease (Mpro) of the virus is a prime target for therapeutic research. In this study, we used molecular modeling and molecular dynamics simulations to examine the potential therapeutic uses of Mpro inhibitors for the treatment of COVID-19. Using induced fit docking and molecular dynamics simulations, we confirmed the top compounds after screening a library of compounds for their ability to bind to Mpro. Simulation interaction diagrams were used to investigate protein-ligand interactions, and MM-GBSA was used to determine binding energies. The Swiss ADME server was used to predict ADME properties. According to our findings, numerous substances are strong COVID-19 medication candidates since they have excellent ADME features and high binding affinities. This work serves as a foundation for additional experimental research and drug development initiatives aimed at Mpro.

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“…The crystal structure of COVID-19 main protease (PDB 6LU7) in complex with an inhibitor N3 was also used. All proteins were preprocessed than targeted for molecular binding with the compound as previously described [30][31][32]. Preprocessing includes removing water molecules and adding polar hydrogen and Coleman charges [33,34].…”

Section: In Silico Molecular Docking Druggability and Pharmacokineticsmentioning

confidence: 99%

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

et al. 2023

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In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C 5 H 7 N 2 )(C 5 H 8 N 2 )[AsO 4 ]·H 2 O ((4-APH)(4-APH 2 )[AsO 4 ]·H 2 O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values. Supplementary Information The online version contains supplementary material available at 10.1007/s42250-023-00620-8.

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In-silico investigation of phenolic compounds from leaves of Phillyrea angustifolia L. as a potential inhibitor against the SARS-CoV-2 main protease (Mpro PDB ID:5R83) using a virtual screening method

Cited by 18 publications

References 41 publications

1,4,9,9-tetramethyloctahydro-4,7-(epoxymethano)azulen-5(1H)-one, a natural product as a potential inhibitor of COVID-19: Extraction, crystal structure, and virtual screening approach

1,4,9,9-tetramethyloctahydro-4,7-(epoxymethano)azulen-5(1H)-one, a natural product as a potential inhibitor of COVID-19: Extraction, crystal structure, and virtual screening approach

A Molecular Modeling and Molecular Dynamics Simulations Investigation of the Potential Therapeutic Applications of Main Protease Inhibitors for SARS-CoV-2

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

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