MOLECULAR DOCKING STUDIES FOR THE COMPARATIVE ANALYSIS OF DIFFERENT BIOMOLECULES TO TARGET HYPOXIA INDUCIBLE FACTOR-1α

Jha, Niraj Kumar; Kumar, Pravir

doi:10.22159/ijap.2017v9i4.19505

Cited by 8 publications

(4 citation statements)

References 16 publications

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“…The same was also revealed by CanSAR Black, and both mutations are of moderate severity. Low levels of CCN6 expression were observed in metastasizing breast cancer cell lines, suggesting that this gene may function as a tumor suppressor [36].…”

Section: Survival Analysis In Coad Patientsmentioning

confidence: 99%

Prediction of High-Risk NSSNPS Associated With Wisp3 Gene Expression: An in Silico Study

M. S.,

DINESH,

SHARMA

2023

Int J App Pharm

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Objective: The primary aim of this investigation is to comprehensively examine the detrimental effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on the WISP3 gene. This objective will be accomplished through intricate evaluations encompassing protein stability prediction, amino acid conservation analysis, investigation of protein-protein interactions (PPI), scrutiny of post-translational modifications (PTM), and the utilization of bioinformatics tools to forecast the potential association between nsSNPs and various diseases. By implementing these sophisticated methodologies, we aim to unveil the intricate mechanisms by which harmful nsSNPs influence the functionality and pathological implications of the WISP3 gene. Methods: Retrieved rsIDs of SNPs from the dbSNP database and filtered using 5 in silico programs. Selected nsSNPs were subjected to further analysis i.e., protein stability and conservation analysis, solvent accessibility analysis, PPI and PTM analysis, prediction and evaluation of both native and mutant protein, and identification of cancer association and gene expression analysis. Results: The study found that seven (C122Y, C145Y, C52Y, C78R, C75G, N233K, and R245I) of the nsSNPs are potentially vulnerable due to their higher conservancy and ability to reduce protein stability. Two (D271N and Q56H) of the nsSNPs from the initial screening were found to be associated with colon adenocarcinoma. Conclusion: The study's findings could help researchers design experiments to validate the predictions and develop potential treatments for diseases associated with the WISP3 gene.

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Section: Survival Analysis In Coad Patientsmentioning

confidence: 99%

Prediction of High-Risk NSSNPS Associated With Wisp3 Gene Expression: An in Silico Study

M. S.,

DINESH,

SHARMA

2023

Int J App Pharm

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“…Validation of generated model using Golbraikh-Tropsha acceptance criteria, k-fold cross validation, leave one out, viii. Applicability domain analysis using Euclidean distance and Mahalanobis distance [80][81].…”

Section: Future Scopementioning

confidence: 99%

Computational Approaches Related to Drug Disposition

Saha¹,

Pal

2021

Int J Pharm Pharm Sci

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Drug disposition connects with the movement of drug molecules inside the body after administration irrespective with the route of administration. After entering the system, drug molecule and internal body systems comes under various pharmacokinetic interactions followed by observation of suitable biological activity. In this exhaustive process, physicochemical nature of the chemical substance and physiological nature of system makes this movement competitive. In this view, pharmacokinetic and toxic properties of the molecule regulates the destination of the molecule. Various computational processes are available for in silico pharmacokinetic assessment of drug molecule after absorption through biological membrane, distributed throughout the system based on the percent ionization or partition coefficient factors followed by biologically transformed into an another entity in presence of microsomal enzymes and finally excrete out from system using various cellular transport systems as well as related cellular toxicity behavior. In this chapter, we ensemble all the possible information related with the drug movement and related computational tools to understand the possible chemical and pathophysiological changes. Here detailed knowledge on database expedition, establishment of pharmacophore model, homology modelling based on sequence similarity, molecular docking study (rigid and flexible docking) and QSAR/QSPR study (with detailed process and available softwares) are provided. These diversely united informations actually helps a researcher to understand the factual movement of a drug molecule inside the system.

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“…In silico screening was performed using Vina and AutoDock 4.2 docking program [13][14][15][16][17]. The ligands were allowed to have flexible rotational bonds, while the protein was kept rigid.…”

Section: Vina and Autodock 42mentioning

confidence: 99%

In Silico Identification of Apobec3b Small Molecule Inhibitors From DTP-Nci Libraries

Mohamed

Jusril

Adenan³

et al. 2021

Int J App Pharm

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Objective: APOBEC3B (A3B) enzyme causes C-to-T or C-to-G somatic alteration in the cancer genome, leading to the evolution of a broad spectrum of human cancers. The present study aims to identify A3B small molecule inhibitors using a top-down approach via pharmacoinformatic virtual screening. Methods: Virtual screening of 2951 drug-alike molecules with diversified structures from the National Cancer Institute Development Therapeutics Program (DTP-NCI) compounds library was performed using GOLD and AutoDock Vina docking programs against the 3D structure of A3B (PDB ID: 5TD5). Results: Amongst the docked compounds, Nordracorubin, NSC641233 and Raloxifene hydrochloride showed the most potent binding affinities towards A3B on both Autodock/Vina and GOLD. Several significant similarities were observed between A3B and the three hits, including hydrogen bonds and pi-pi stacking. The three compounds also exhibited interaction with the centralized zinc cofactor and amino acid residues that directly contribute the deaminase activity of A3B enzyme. Conclusion: We hypothesize that the findings from this study could significantly shorten the quest for novel molecules against the A3B after confirmation with subsequent in vitro and in vivo studies in the near future.

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MOLECULAR DOCKING STUDIES FOR THE COMPARATIVE ANALYSIS OF DIFFERENT BIOMOLECULES TO TARGET HYPOXIA INDUCIBLE FACTOR-1α

Cited by 8 publications

References 16 publications

Prediction of High-Risk NSSNPS Associated With Wisp3 Gene Expression: An in Silico Study

Prediction of High-Risk NSSNPS Associated With Wisp3 Gene Expression: An in Silico Study

Computational Approaches Related to Drug Disposition

In Silico Identification of Apobec3b Small Molecule Inhibitors From DTP-Nci Libraries

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