Computational screening of phytochemicals for anti-bacterial drug discovery

Turabi, Khadija Shahab; Sannakki, Janhavi Avinash; Aich, Jyotirmoi; Garse, Samiksha; Iyer, Deepak; Devarajan, Shine

doi:10.1016/b978-0-323-90593-0.00011-3

Cited by 3 publications

(3 citation statements)

References 84 publications

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“…Quantitative structure–activity relationship is a computational method used to predict the biological activity of chemical compounds based on their structural features . Grounded in the principle that the biological activity of a chemical compound correlates with its quantifiable physicochemical properties, QSAR utilizes mathematical models widely across drug discovery, chemical risk assessment, and environmental monitoring . Nano-QSAR, an extension of this approach, focuses on predicting the biological activities of nanoparticles by scrutinizing their physicochemical properties .…”

Section: Quantitative Structure–activity Relationship For Nanomateria...mentioning

confidence: 99%

“…50 Grounded in the principle that the biological activity of a chemical compound correlates with its quantifiable physicochemical properties, QSAR utilizes mathematical models widely across drug discovery, chemical risk assessment, and environmental monitoring. 51 Nano-QSAR, an extension of this approach, focuses on predicting the biological activities of nanoparticles by scrutinizing their physicochemical properties. 6 This involves the development of both knowledge based expert systems and statistically driven mathematical models that relate the properties of nanomaterials to their biological activities, such as toxicity, uptake, and transport in living systems.…”

Section: Quantitative Structure−activity Relationship For Nanomateria...mentioning

confidence: 99%

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Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials

Singh,

Shelar,

Rai

et al. 2024

J. Agric. Food Chem.

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This comprehensive review explores the emerging landscape of Nano-QSAR (quantitative structure−activity relationship) for assessing the risk and potency of nanomaterials in agricultural settings. The paper begins with an introduction to Nano-QSAR, providing background and rationale, and explicitly states the hypotheses guiding the review. The study navigates through various dimensions of nanomaterial applications in agriculture, encompassing their diverse properties, types, and associated challenges. Delving into the principles of QSAR in nanotoxicology, this article elucidates its application in evaluating the safety of nanomaterials, while addressing the unique limitations posed by these materials. The narrative then transitions to the progression of Nano-QSAR in the context of agricultural nanomaterials, exemplified by insightful case studies that highlight both the strengths and the limitations inherent in this methodology. Emerging prospects and hurdles tied to Nano-QSAR in agriculture are rigorously examined, casting light on important pathways forward, existing constraints, and avenues for research enhancement. Culminating in a synthesis of key insights, the review underscores the significance of Nano-QSAR in shaping the future of nanoenabled agriculture. It provides strategic guidance to steer forthcoming research endeavors in this dynamic field.

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Section: Quantitative Structure–activity Relationship For Nanomateria...mentioning

confidence: 99%

Section: Quantitative Structure−activity Relationship For Nanomateria...mentioning

confidence: 99%

Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials

Singh,

Shelar,

Rai

et al. 2024

J. Agric. Food Chem.

View full text Add to dashboard Cite

show abstract

“…This was carried out to determine the stability of ligand(s) at the active site of the target [42]. The ligand topology was generated using the Swiss Param web server [47] and target topology generated using the CHARMM27 forcefield. The ligand and target were merged to form the complex; then, triclinic water boxes with a distance of 1nm and a transferable intermolecular potential (TIP) 3-point water model were deployed for the solvation of the complexes.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

In Silico Design of Potential Small-Molecule Antibiotic Adjuvants against Salmonella typhimurium Ortho Acetyl Sulphydrylase Synthase to Address Antimicrobial Resistance

Elebiju,

Oduselu,

Ogunnupebi

et al. 2024

Pharmaceuticals

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The inhibition of O-acetyl sulphydrylase synthase isoforms has been reported to represent a promising approach for the development of antibiotic adjuvants. This occurs via the organism developing an unpaired oxidative stress response, causing a reduction in antibiotic resistance in vegetative and swarm cell populations. This consequently increases the effectiveness of conventional antibiotics at lower doses. This study aimed to predict potential inhibitors of Salmonella typhimurium ortho acetyl sulphydrylase synthase (StOASS), which has lower binding energy than the cocrystalized ligand pyridoxal 5 phosphate (PLP), using a computer-aided drug design approach including pharmacophore modeling, virtual screening, and in silico ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) evaluation. The screening and molecular docking of 4254 compounds obtained from the PubChem database were carried out using AutoDock vina, while a post-screening analysis was carried out using Discovery Studio. The best three hits were compounds with the PubChem IDs 118614633, 135715279, and 155773276, possessing binding affinities of −9.1, −8.9, and −8.8 kcal/mol, respectively. The in silico ADMET prediction showed that the pharmacokinetic properties of the best hits were relatively good. The optimization of the best three hits via scaffold hopping gave rise to 187 compounds, and they were docked against StOASS; this revealed that lead compound 1 had the lowest binding energy (−9.3 kcal/mol) and performed better than its parent compound 155773276. Lead compound 1, with the best binding affinity, has a hydroxyl group in its structure and a change in the core heterocycle of its parent compound to benzimidazole, and pyrimidine introduces a synergistic effect and consequently increases the binding energy. The stability of the best hit and optimized compound at the StOASS active site was determined using RMSD, RMSF, radius of gyration, and SASA plots generated from a molecular dynamics simulation. The MD simulation results were also used to monitor how the introduction of new functional groups of optimized compounds contributes to the stability of ligands at the target active site. The improved binding affinity of these compounds compared to PLP and their toxicity profile, which is predicted to be mild, highlights them as good inhibitors of StOASS, and hence, possible antimicrobial adjuvants.

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Comparative Phytochemical Profiling and Biological Activities in the Flowers and Stalks of Tulbaghia violacea

Maleka,

Oyerinde,

Risenga

2024

Borneo J Pharm

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Tulbaghia violacea is indigenous to Southern Africa and has been used extensively in traditional medicine in this region. Extensive research has been documented on the bioactive compounds found in the leaves and roots but not in the flowers and stalks. Thus, this study assessed the phytochemical profile and biological activities in the flowers and stalks of T. violacea. Methanolic and aqueous extracts of the air and freeze-dried T. violacea were screened for phytochemicals, and then antioxidant and antibacterial assays were performed. Phytochemicals such as phenols, tannins, flavonoids, coumarins, and terpenoids are present in either of the tested plant parts. The flowers contain most of the phytochemicals being tested and a higher total phenolic, tannin, and proanthocyanidin content than the stalks. The flowers exhibit the strongest scavenging activity against 2,2-diphenylpicryhydrazyl radicals and metal oxidants. The hydrogen peroxide scavenging activities show that the aqueous flower extracts have a higher radical scavenging activity than stalks. In contrast, the methanolic stalk extracts have a higher antioxidant activity than the flowers. Antibacterial activity is only exhibited in the flowers, showing resistant and intermediate inhibition zones of Escherichia coli and Staphylococcus aureus growth, respectively. This study validates the use of T. violacea in traditional medicine, and these results are significant for conserving the species as specific plant parts can be harvested to treat specific ailments. This study suggests the potential application of T. violacea, particularly the flowers and stalks, in the pharmaceutical and cosmetic sectors.

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Computational screening of phytochemicals for anti-bacterial drug discovery

Cited by 3 publications

References 84 publications

Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials

Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials

In Silico Design of Potential Small-Molecule Antibiotic Adjuvants against Salmonella typhimurium Ortho Acetyl Sulphydrylase Synthase to Address Antimicrobial Resistance

Comparative Phytochemical Profiling and Biological Activities in the Flowers and Stalks of Tulbaghia violacea

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