Molecular Simulation of a Series of Benzothiazole PI3K α Inhibitors: Probing the Relationship Between Structural Features, Anti-tumor Potency and Selectivity

The phosphatidylinositol 3-kinase α (PI3Kα) was genetically validated as a promising therapeutic target for developing novel anticancer drugs. In order to explore the structure-activity correlation of benzothiazole series as inhibitors of PI3Kα, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) were performed on 61 promising molecules to build 3D-QSAR models based on … Continued

Development of Multiple QSAR Models for Consensus Predictions and Unified Mechanistic Interpretations of the Free-radical Scavenging Activities of Chromone Derivatives

Antioxidants are important defenders of the human body against nocive free radicals, which are the causative agents of most life-threatening diseases. The immense biomedicinal utility of antioxidants necessitates the development and design of new synthetic antioxidant molecules. The present report deals with the modeling of a series of chromone derivatives, which was done to provide … Continued

Insights into ET(A) Subtype Selectivity of Benzodiazepine Endothelin Receptor Antagonists by 3D-QSAR Approaches

ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin receptor were selected to establish the 3D-QSAR models using CoMFA and CoMSIA approaches. These … Continued

Insights into the Permeability of Drugs and Drug-like Molecules from MI-QSAR and HQSAR Studies

Membrane-interaction QSAR (MI-QSAR) and Holographic QSAR (HQSAR) analyses have been performed on a diverse set of drugs and drug-like molecules. MI-QSAR combines a set of membrane-solute interaction properties calculated during molecular dynamics simulation with the set of classical solute descriptors to predict the biological behavior of drugs and drug-like molecules. HQSAR is a technique which … Continued

Studies of H4R Antagonists Using 3D-QSAR, Molecular Docking, and Molecular Dynamics

Three-dimensional quantitative structure-activity relationship studies were performed on a series of 88 histamine receptor 4 (H4R) antagonists in an attempt to elucidate the 3D structural features required for activity. Several in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), molecular docking, and molecular dynamics (MD), were carried out. The … Continued

Molecular Docking and 3D-QSAR Study on 4-(1H-indazol-4-yl)phenylamino and Aminopyrazolopyridine Urea Derivatives as Kinase Insert Domain Receptor (KDR) Inhibitors

Vascular endothselial growth factor (VEGF) and its receptor tyrosine kinase VEGFR-2 or kinase insert domain receptor (KDR) have been identified as new promising targets for the design of novel anticancer agents. It is reported that 4-(1H-indazol-4-yl)phenylamino and aminopyrazolopyridine urea derivatives exhibit potent inhibitory activities toward KDR. To investigate how their chemical structures relate to the … Continued

Multiple Receptor Conformation Docking and Dock Pose Clustering as Tool for CoMFA and CoMSIA Analysis, a Case Study on HIV-1 Protease Inhibitors

Multiple receptors conformation docking (MRCD) and clustering of dock poses allows seamless incorporation of receptor binding conformation of the molecules on wide range of ligands with varied structural scaffold. The accuracy of the approach was tested on a set of 120 cyclic urea molecules having HIV-1 protease inhibitory activity using 12 high resolution X-ray crystal … Continued

Developing Consensus 3D-QSAR and Pharmacophore Models for Several β-secretase, Farnesyl Transferase, and Histone Deacetylase Inhibitors

Three consensus 3D-QSAR (c-3D-QSAR) models were built for 38, 34, and 78 inhibitors of β-secretase, histone deacetylase, and farnesyltransferase, respectively. To build an individual 3D-QSAR model, the structures of an inhibitor series are aligned through docking of a protein receptor into the active site using the program GOLD. CoMFA, CoMSIA, and Catalyst are then performed … Continued

Identification of Novel 5-hydroxy-1H-indole-3-carboxylates with Anti-HBV Activities Based on 3D-QSAR Studies

Infection with hepatitis B virus (HBV) is a major cause of liver diseases such as cirrhosis and hepatocellular carcinoma. In our previous studies, we identified indole derivatives that have anti-HBV activities. In this study, we optimize a series of 5-hydroxy-1H-indole-3-carboxylates, which exhibited potent anti-HBV activities, using three-dimensional quantitative structure-activity relationship (3D QSAR) studies with comparative … Continued

3,4,5-trisubstituted-1,2,4-4H-triazoles as WT and Y188L Mutant HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors: Docking-based CoMFA and CoMSIA Analyses

3,4,5-Trisubstituted-1,2,4-4H-triazoles (TTs) have recently been identified as a new class of potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. Two series of triazoles have been studied, one of which was also screened against the Y188L mutant. A computational strategy based on molecular docking studies followed by comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices … Continued

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