Structural and dynamics insights into the GBA variants associated with Parkinson’s disease

Mahmood, Arif; Samad, Abdus; Bano, Shazia; Umair, Muhammad; Ajmal, Amar; Ilyas, Iqra; Shah, Abid Ali; Li, Ping; Hu, Junjie

doi:10.1080/07391102.2023.2233617

Cited by 4 publications

(2 citation statements)

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“…The fundamental elements of protein–ligand interactions can be studied well with the use of MD simulations. They expand our understanding of the molecular mechanisms behind protein–ligand interaction, enhance docking predictions, rank ligand candidates, and coordinate subsequent optimization efforts 68 – 70 . According to MMGBSA analyses and MD simulations, these compounds were stable as effective inhibitors within the binding pocket of protein.…”

Section: Discussionmentioning

confidence: 99%

Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila

Aslam,

Aljawdah,

Murshed

et al. 2024

Sci Rep

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Waddlia chondrophila is a possible cause of fetal death in humans. This Chlamydia-related bacterium is an emergent pathogen that causes human miscarriages and ruminant abortions, which results in financial losses. Despite the years of efforts, the underlying mechanism behind the pathogenesis of W. chondrophila is little known which hindered the development of novel treatment options. In the framework of current study, computational approaches were used to identify novel inhibitors (phytocompounds) and drug targets against W. chondrophila. At first, RNA polymerase sigma factor SigA and 3-deoxy-d-manno-octulosonic acid transferase were identified through subtractive proteomics pipeline. Afterwards, extensive docking and simulation analyses were conducted to optimize potentially novel phytocompounds by assessing their binding affinity to target proteins. A 100ns molecular dynamics simulation well complimented the compound's binding affinity and indicated strong stability of predicted compounds at the docked site. The calculation of binding free energies with MMGBSA corroborated the significant binding affinity between phytocompounds and target protein binding sites. The proposed phytocompounds may be a viable treatment option for patients infected with W. chondrophila; however, further research is required to ensure their safety.

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Section: Discussionmentioning

confidence: 99%

Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila

Aslam,

Aljawdah,

Murshed

et al. 2024

Sci Rep

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show abstract

“…A Langevin thermostat was used to keep the temperature constant at 300 K, and a Berendsen barostat was used to keep the pressure constant at 1.0 bar. Each system was optimized using a two-step energy minimization process that involved conjugate gradient and steepest descent algorithms [ 25 ]. We employed the AMBER-22 Particle Mesh Ewald (PME) method to calculate the long-range electrostatic interaction.…”

Section: Methodsmentioning

confidence: 99%

In vivo analgesic, anti-inflammatory and molecular docking studies of S-naproxen derivatives

Muhammad,

Khan,

Seraj

et al. 2024

Heliyon

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Structure-based virtual screening and molecular docking approaches to identify potential inhibitors against KIF2C to combat glioma

Hussein,

Saka,

Baeesa

et al. 2023

Journal of Biomolecular Structure and Dynamics

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Structural and dynamics insights into the GBA variants associated with Parkinson’s disease

Cited by 4 publications

References 50 publications

Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila

Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila

In vivo analgesic, anti-inflammatory and molecular docking studies of S-naproxen derivatives

Structure-based virtual screening and molecular docking approaches to identify potential inhibitors against KIF2C to combat glioma

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