Enzyme Inhibitory Activities of Extracts and Carpachromene from the Stem of Ficus benghalensis

Ibrahim, Muhammad; Muhammad, Naveed; Naz, Sumera; Wadood, Abdul; Khan, Bilal; Ali, Toseef; Muhammad, Saleem; Alshammari, Abdulrahman; Alharbi, Metab; Suleria, Hafiz Ansar Rasul

doi:10.1155/2022/7053655

Cited by 2 publications

(1 citation statement)

References 22 publications

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“…Over 9000 compounds documented in the drug-bank database were retrieved from the drug-bank database. All of the compounds in the drug-bank database were subjected to three-dimensional protonation using the MMFF94x force field and energy minimization using MOE software with an RMS gradient of 0.05 ( Rauf et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Computer-assisted drug repurposing for thymidylate kinase drug target in monkeypox virus

Ajmal

Mahmood

Hayat

et al. 2023

Front. Cell. Infect. Microbiol.

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IntroductionMonkeypox is a zoonotic disease caused by brick-shaped enveloped monkeypox (Mpox) virus that belongs to the family of ancient viruses known as Poxviridae. Subsequently, the viruses have been reported in various countries. The virus is transmitted by respiratory droplets, skin lesions, and infected body fluids. The infected patients experience fluid-filled blisters, maculopapular rash, myalgia, and fever. Due to the lack of effective drugs or vaccines, there is a need to identify the most potent and effective drugs to reduce the spread of monkeypox. The current study aimed to use computational methods to quickly identify potentially effective drugs against the Mpox virus.MethodsIn our study, the Mpox protein thymidylate kinase (A48R) was targeted because it is a unique drug target. We screened a library of 9000 FDA-approved compounds of the DrugBank database by using various in silico approaches, such as molecular docking and molecular dynamic (MD) simulation.ResultsBased on docking score and interaction analysis, compounds DB12380, DB13276, DB13276, DB11740, DB14675, DB11978, DB08526, DB06573, DB15796, DB08223, DB11736, DB16250, and DB16335 were predicted as the most potent. To examine the dynamic behavior and stability of the docked complexes, three compounds—DB16335, DB15796, and DB16250 —along with the Apo state were simulated for 300ns. The results revealed that compound DB16335 revealed the best docking score (-9.57 kcal/mol) against the Mpox protein thymidylate kinase.DiscussionAdditionally, during the 300 ns MD simulation period, thymidylate kinase DB16335 showed great stability. Further, in vitro and in vivo study is recommended for the final predicted compounds.

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Section: Methodsmentioning

confidence: 99%

Computer-assisted drug repurposing for thymidylate kinase drug target in monkeypox virus

Ajmal

Mahmood

Hayat

et al. 2023

Front. Cell. Infect. Microbiol.

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Identification of new potent NLRP3 inhibitors by multi-level in-silico approaches

Hayat,

Subramaniyan,

Alamri

et al. 2024

BMC Chemistry

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Nod-like receptor protein 3 (NLRP-3), is an intracellular sensor that is involved in inflammasome activation, and the aberrant expression of NLRP3 is responsible for diabetes mellitus, its complications, and many other inflammatory diseases. NLRP3 is considered a promising drug target for novel drug design. Here, a pharmacophore model was generated from the most potent inhibitor, and its validation was performed by the Gunner-Henry scoring method. The validated pharmacophore was used to screen selected compounds databases. As a result, 646 compounds were mapped on the pharmacophore model. After applying Lipinski's rule of five, 391 hits were obtained. All the hits were docked into the binding pocket of target protein. Based on docking scores and interactions with binding site residues, six compounds were selected potential hits. To check the stability of these compounds, 100 ns molecular dynamic (MD) simulations were performed. The RMSD, RMSF, DCCM and hydrogen bond analysis showed that all the six compounds formed stable complex with NLRP3. The binding free energy with the MM-PBSA approach suggested that electrostatic force, and van der Waals interactions, played a significant role in the binding pattern of these compounds. Thus, the outcomes of the current study could provide insights into the identification of new potential NLRP3 inflammasome inhibitors against diabetes and its related disorders.

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Enzyme Inhibitory Activities of Extracts and Carpachromene from the Stem of Ficus benghalensis

Cited by 2 publications

References 22 publications

Computer-assisted drug repurposing for thymidylate kinase drug target in monkeypox virus

Computer-assisted drug repurposing for thymidylate kinase drug target in monkeypox virus

Identification of new potent NLRP3 inhibitors by multi-level in-silico approaches

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