Induced fit docking, pharmacophore modeling, and molecular dynamic simulations on thiazolidinedione derivatives to explore key interactions with Tyr48 in polyol pathway

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• 作者：Manga Vijjulatha (1)
  Yamini Lingala (1)
  RaviRaja Tejaswi Merugu (1)
  
  1. Molecular Modeling and Medicinal Chemistry Group ; Dept. of Chemistry ; University College of Science ; Osmania University ; Hyderabad ; 500-007 ; India
  
• 关键词：ALR ; aldose reductase ; Diabetes mellitus ; IFD ; induced fit docking ; MD ; molecular dynamics ; Pharmacophore modeling ; PLS ; Partial least square analysis ; Polyol pathway
• 刊名：Journal of Molecular Modeling
• 出版年：2014
• 出版时间：July 2014
• 年：2014
• 卷：20
• 期：7
• 全文大小：2,635 KB
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• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Computer Applications in Chemistry
  Biomedicine
  Molecular Medicine
  Health Informatics and Administration
  Life Sciences
  Computer Application in Life Sciences
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：0948-5023

文摘

To obtain a scientific thought and expedition to explore key interactions with Tyr48 in aldose reductase (ALR), combined study of pharmacophore modeling, induced fit docking, and dynamics studies were performed on ALR. A stereo chemically and energetically valid model of ALR-NADP+ complex was developed using homology modeling technique. Statistically a significant five point pharmacophore model was designed on a set of 54 thiazolidinedione derivatives with good external and internal predictive ability. Rigid and induced fit docking protocols were applied on ALR protein for both with and without NADP+ cofactor to identify a suitable binding mode that facilitates the key hydrogen bond interactions with Tyr48. Docking of thiazolidinedione derivatives into ALR-NADP+ complex gave more promising results by reducing false positive binding of inhibitors into the co-factor binding site. Structural changes within Try48 and Asp43 during the binding process in enzyme inhibitor complex were analyzed using molecular dynamics (MD) simulations. The results obtained from dynamic simulations emphasized the role of Tyr48 in maintaining inter or intra molecular hydrogen bond interaction with the protein or inhibitor respectively. New molecules were designed and checked for their binding interactions and showed improved results compared to existing thiazolidinediones derivatives. Hence, these combined protocols will be helpful and cooperative to design and optimize molecules with better inhibitory activity against the biologically active target. Figure Homology modeling, induced fit docking, dynamics, and pharmacophore modeling on thiazolidinone derivatives to explore the catalytic role of Tyr48 in polyol pathway. Role of Tyr48, the key amino acid in polyol pathway was exemplified in a pictographic representation to give evidence for the results obtained in molecular modeling studies