Comparative analysis of backbone atom cross-correlation matrices and folding dynamics of amyloid fibril and its complexes with novel biosurfactants isolated from Bacillus strain: a binding free energy calculation (mM-PBSA) and MD simulation approach DOI
Rohit Pritam Das, Santosh Kumar Behera, Banishree Sahoo

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 16

Published: Dec. 28, 2024

In the relentless pursuit of unraveling intricate pathophysiology Alzheimer's disease (AD), amyloid β (Aβ) proteins emerge as focal points due to their pivotal role in progression. The pathological hallmark AD involves aberrant aggregation Aβ peptides into fibrils, precipitating a cascade neurodegenerative events culminating cognitive decline and neuronal loss. This study adopts computational framework investigate potential therapeutic efficacy novel biosurfactants (BS) mitigating fibril formation. Initial analyses encompassing sequence alignment, structural elucidation, functional characterization reveal distinctive attributes peptide identified BS candidates. Quantum chemical calculations, using ORCA Program (v4.0) employed Density Functional Theory (DFT), specifically Becke 3-parameter Lee-Yang-Parr (B3LYP) method, electronic structure energetics isolates. Molecular docking through AutoDock Vina (version 1.1.2) employing advanced algorithms elucidates binding affinities interaction energies between fibrils molecules. observed energy −7.0 kcal/mol for BG2A −6.6 BG2B, underscoring robustness stability formed complexes. mechanism docked complexes was predicted molecular dynamics (MD) simulations GROMACS 2021.3 Charmm36 force field, capture complex over 100 nanoseconds. Analysis via RMSD, RMSF, Rg, PCA, SASA offers insights Aβ-BS dynamics. These promising results highlight BG2B candidates against AD. However, rigorous preclinical clinical validation is crucial ascertain safety, efficacy, translational relevance.

Language: Английский

Design, synthesis, molecular docking, DFT analysis, dynamics simulation and cytotoxicity evaluation of coumarin derivatives as acetylcholinesterase (AChE) inhibitors against alzheimer's disease DOI

Shivangi Rai,

Vishal Singh, Iqrar Ahmad

et al.

Journal of Molecular Structure, Journal Year: 2025, Volume and Issue: unknown, P. 141436 - 141436

Published: Jan. 1, 2025

Language: Английский

Citations

0
Mapping knowledge landscapes and emerging trends in artificial intelligence for antimicrobial resistance: bibliometric and visualization analysis DOI Creative Commons
Zhongli Wang, Gaopei Zhu,

Shixue Li

et al.

Frontiers in Medicine, Journal Year: 2025, Volume and Issue: 12

Published: Jan. 28, 2025

Objective To systematically map the knowledge landscape and development trends in artificial intelligence (AI) applications for antimicrobial resistance (AMR) research through bibliometric analysis, providing evidence-based insights to guide future directions inform strategic decision-making this dynamic field. Methods A comprehensive analysis was performed using Web of Science Core Collection database publications from 2014 2024. The integrated multiple approaches: VOSviewer visualization collaboration networks clusters, CiteSpace temporal evolution quantitative publication metrics. Key indicators including co-authorship patterns, keyword co-occurrence, citation impact were analyzed delineate patterns domain. Results collection 2,408 analyzed, demonstrating significant annual growth with increasing 4 549 2023 (22.7% total output). United States (707), China (581), India (233) leading contributors international collaborations. Chinese Academy Sciences (53), Harvard Medical School (43), University California San Diego (26) identified as top contributing institutions. Citation highlighted two major breakthroughs: AlphaFold’s protein structure prediction (6,811 citations) deep learning approaches antibiotic discovery (4,784 citations). Keyword six enduring clusters 2024: sepsis, neural networks, resistance, peptides, drug repurposing, molecular docking, sustained integration AI therapy development. Recent show application technologies traditional approaches, particularly MALDI-TOF MS pathogen identification graph large-scale screening. Conclusion This shows importance enhancing progress drugs especially toward fight against AMR. From fast, efficient predictive performance methods, current capabilities have revealed observable potential be proactive combating ever-growing challenge AMR worldwide. study serves not only an trends, but also, especially, offers a approach further investigations.

Language: Английский

Citations

0
Targeting EGFR by Newer 1-(3,5-Bis((E)-4-hydroxy-3-methoxystyryl)-1H-pyrazol-1-yl)-2-((substituted phenyl)amino)ethan-1-one Analogues for the Treatment of Cancer: Synthesis, In-vitro and In-silico Studies DOI

Menshawy A. Mohamed,

Abuzer Ali, Amena Ali

et al.

Journal of Molecular Structure, Journal Year: 2024, Volume and Issue: 1315, P. 138826 - 138826

Published: June 3, 2024

Language: Английский

Citations

1
An Insightful Overview of Microbial Biosurfactant: A Promising Next‐Generation Biomolecule for Sustainable Future DOI

Athira Thundiparambil Venu,

Jasna Vijayan, A. A. Mohamed Hatha

et al.

Journal of Basic Microbiology, Journal Year: 2024, Volume and Issue: 64(9)

Published: June 27, 2024

ABSTRACT Microbial biosurfactant is an emerging vital biomolecule of the 21st century. They are amphiphilic compounds produced by microorganisms and possess unique properties to reduce surface tension activity. The use microbial surfactants spans most industrial fields due their biodegradability, less toxicity, being environmentally safe, synthesized from renewable sources. These would be highly efficient eco‐friendly alternatives petroleum‐derived that open up new approaches research on production biosurfactants. In upcoming era, biobased will become a dominating multifunctional compound in world market. Research biosurfactants ranges search for novel can produce molecules, structural physiochemical characterization biosurfactants, fermentation process enhanced large‐scale productivity green applications. main goal this review provide overview recent state knowledge trends about microbially derived surfactants, various aspects production, definition, properties, characteristics, diverse advances, This lead long way as globally successful biomolecules current

Language: Английский

Citations

1
Harnessing Microbial Potential: Exploiting Heavy Oil-Laden Soil Microbiota for Sustainable Production of High-Yield Rhamnolipids from Waste Cooking Oil DOI Creative Commons

Siyabonga Nkosi,

John Onolame Unuofin,

Olubusola Ayoola Odeniyi

et al.

Biocatalysis and Agricultural Biotechnology, Journal Year: 2024, Volume and Issue: unknown, P. 103371 - 103371

Published: Sept. 1, 2024

Language: Английский

Citations

1
Design, Synthesis, and Evaluation of Quinoline‐1,2,3‐Triazole Hybrids as CYP51 Inhibitors: In Silico Study and In Vitro Antimicrobial Assessment DOI
Bhadreshkumar K. Chabhadiya, Hem N. Naik,

Bhavika A. Mohite

et al.

ChemistrySelect, Journal Year: 2024, Volume and Issue: 9(36)

Published: Sept. 1, 2024

Abstract Novel Quinoline‐triazole hybrid derivatives ( 9 a – l ) were designed and synthesized via click reaction methodology to develop lead compounds with good antibacterial antifungal potency. Synthetic have been characterized using 1 H NMR, 13 C mass spectrum analysis. In‐vitro activity against two gram‐positive gram‐negative strains in‐vitro three different performed for the compounds. Compounds , d i exhibited potent inhibition S. aureus ranging from MIC=12.5–50 μg/mL, c e f j C. albicans fungal MFC=250–500 μg/mL. Molecular docking study of Sterol 14α‐demethylase (CYP51) protein (PDB ID:5TZ1) tyrosyl‐tRNA synthetase ID: 1JIJ) was understand mechanism action through which these work. In silico studies Hybrid demonstrated strong hydrogen bonding π–π interactions Tyr64, Phe233, Phe228 in line co‐crystals SB‐239629 VT1161 exhibiting favorable that inhibits both bacterial strains.

Language: Английский

Citations

1
Study on the effects of endogenous polyphenols on the structure, physicochemical properties and in vitro digestive characteristics of Euryales Semen starch based on multi-spectroscopies, enzyme kinetics, molecular docking and molecular dynamics simulation DOI
Miao Yu, Cheng Qu, Dishuai Li

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 282, P. 137245 - 137245

Published: Nov. 5, 2024

Language: Английский

Citations

0
Comparative analysis of backbone atom cross-correlation matrices and folding dynamics of amyloid fibril and its complexes with novel biosurfactants isolated from Bacillus strain: a binding free energy calculation (mM-PBSA) and MD simulation approach DOI
Rohit Pritam Das, Santosh Kumar Behera, Banishree Sahoo

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 16

Published: Dec. 28, 2024

In the relentless pursuit of unraveling intricate pathophysiology Alzheimer's disease (AD), amyloid β (Aβ) proteins emerge as focal points due to their pivotal role in progression. The pathological hallmark AD involves aberrant aggregation Aβ peptides into fibrils, precipitating a cascade neurodegenerative events culminating cognitive decline and neuronal loss. This study adopts computational framework investigate potential therapeutic efficacy novel biosurfactants (BS) mitigating fibril formation. Initial analyses encompassing sequence alignment, structural elucidation, functional characterization reveal distinctive attributes peptide identified BS candidates. Quantum chemical calculations, using ORCA Program (v4.0) employed Density Functional Theory (DFT), specifically Becke 3-parameter Lee-Yang-Parr (B3LYP) method, electronic structure energetics isolates. Molecular docking through AutoDock Vina (version 1.1.2) employing advanced algorithms elucidates binding affinities interaction energies between fibrils molecules. observed energy −7.0 kcal/mol for BG2A −6.6 BG2B, underscoring robustness stability formed complexes. mechanism docked complexes was predicted molecular dynamics (MD) simulations GROMACS 2021.3 Charmm36 force field, capture complex over 100 nanoseconds. Analysis via RMSD, RMSF, Rg, PCA, SASA offers insights Aβ-BS dynamics. These promising results highlight BG2B candidates against AD. However, rigorous preclinical clinical validation is crucial ascertain safety, efficacy, translational relevance.

Language: Английский

Citations

0