Nanoinformatics and nanomodeling: Recent developments in computational nanodrug design and delivery systems

Ahmad, Shaban; Khan, Fatima Nazish; Ramlal, Ayyagari; Begum, Shahanaz; Qazi, Sahar; Raza, Khalid

doi:10.1016/b978-0-323-91182-5.00001-2

Cited by 10 publications

(4 citation statements)

References 65 publications

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“…To address these challenges, efforts are underway to identify data gaps and prioritize research needs for specific nanomaterials and physicochemical properties. This includes efforts to develop and implement new experimental methods and protocols for collecting data on nanomaterials, as well as improving data sharing and collaboration across different sectors and regions …”

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

confidence: 99%

“…Nano-QSAR, or quantitative structure–activity relationship modeling to nanomaterials, represents a burgeoning research field focused on predicting the toxicological effects of nanomaterials on biological systems based on their physicochemical properties . This approach is especially pertinent in the context of nanomaterials used in agriculture, where direct contact with soil, plants, animals, and humans raises concerns about potential adverse health effects .…”

Section: Introductionmentioning

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: Introductionmentioning

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

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“…The reasons for this limited success are multifaceted. Firstly, the molecular diversity of lung cancer means that a single-target drug may only be effective for a subset of patients whose tumours harbour the specific target [ 11 , 12 , 13 , 14 , 15 ]. In essence, these drugs often fail to account for the heterogeneous nature of the disease.…”

Section: Introductionmentioning

confidence: 99%

Delineated 3-1-BenCarMethInYlPro-Phosphonic Acid’s Adroit Activity against Lung Cancer through Multitargeted Docking, MM\GBSA, QM-DFT and Multiscale Simulations

Hakami,

Hazazi,

Albloui

et al. 2024

IJMS

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Lung cancer is a pervasive and challenging disease with limited treatment options, with global health challenges often present with complex molecular profiles necessitating the exploration of innovative therapeutic strategies. Single-target drugs have shown limited success due to the heterogeneity of this disease. Multitargeted drug designing is imperative to combat this complexity by simultaneously targeting multiple target proteins and pathways, which can enhance treatment efficacy and overcome resistance by addressing the dynamic nature of the disease and stopping tumour growth and spread. In this study, we performed the molecular docking studies of Drug Bank compounds with a multitargeted approach against crucial proteins of lung cancer such as heat shock protein 5 (BIP/GRP78) ATPase, myosin 9B RhoGAP, EYA2 phosphatase inhibitor, RSK4 N-terminal kinase, and collapsin response mediator protein-1 (CRMP-1) using HTVS, SP with XP algorithms, and poses were filtered using MM\GBSA which identified [3-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Propyl-]-Phosphonic Acid (3-1-BenCarMethIn YlPro-Phosphonic Acid) (DB02504) as multitargeted drug candidate with docking and MM\GBSA score ranges from −5.83 to −10.66 and −7.56 to −50.14 Kcal/mol, respectively. Further, the pharmacokinetic and QM-based DFT studies have shown complete acceptance results, and interaction fingerprinting reveals that ILE, GLY, VAL, TYR, LEU, and GLN were among the most interacting residues. The 100 ns MD simulation in the SPC water model with NPT ensemble showed stable performance with deviation and fluctuations <2 Å with huge interactions, making it a promising multitargeted drug candidate; however, experimental studies are needed before use.

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“…Ras and related G proteins are relied upon for more broad applications to different compounds that catalyze phosphoryl )-PO)3(2-(, including kinases and phosphatases. [13][14][15][16] To comprehend the molecular mechanisms of hidden bortezomib obstruction, we should recognize the potential objective genes differentially expressed in bortezomib-safe leukemia cells versus organ controls. [17][18][19][20] In this study, we extricate the short sequence repeats )SSRs( to comprehend this issue and focus on the medication component with new methodologies.…”

mentioning

confidence: 99%

Ras-related associated with diabetes genes for biomarker-based therapeutics in cancer

Hakami

2024

SMJ

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Objectives: To compare Ras-related associated with diabetes )RRAD( across different species and to identify specific biomarkers for cancer therapy. Methods:The study involves comparing the coding sequences, genes, messenger ribonucleic acid )RNA(, non-coding RNA, open reading frame, short-and long-sequence repeats, and transcription factors of RRAD genes from 82 species. Various tools and software are employed for these comparisons, and evolutionary analysis was carried out to understand the gene's evolutionary history. The data are classified based on forward and reverse sequences.Results: Our analysis indicates that ACTG1 may function as a downstream effector of RRAD, offering potential avenues for diabetes and cancer treatments. By collecting RRAD sequences from 82 species Original Articleand carrying out comparative genomics, this study provides diverse strategies for developing biomarkerbased therapeutics. Furthermore, it suggests using RRAD in other organisms as a model for studying the knockdown effects of specific sequence sets. The study presents RRAD sequences from 82 organisms across different families, contributing to a diverse knowledge base for identifying drug-designing biomarkers. Conclusion:This research offers insights into the potential of RRAD as a therapeutic target in various organisms and highlights the importance of biomarker identification in drug development.

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Nanoinformatics and nanomodeling: Recent developments in computational nanodrug design and delivery systems

Cited by 10 publications

References 65 publications

Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials

Harmonization Risks and Rewards: Nano-QSAR for Agricultural Nanomaterials

Delineated 3-1-BenCarMethInYlPro-Phosphonic Acid’s Adroit Activity against Lung Cancer through Multitargeted Docking, MM\GBSA, QM-DFT and Multiscale Simulations

Ras-related associated with diabetes genes for biomarker-based therapeutics in cancer

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