Three-dimensional quantitative structure activity relationship (3D QSAR) analysis was carried out on a et of 56 N,N'-diarylsquaramides, N,N'-diarylureas and diaminocyclobutenediones in order to understand their antagonistic activities against CXCR2. The studies included comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Models with good ...

Novel anthracenone derivatives were designed through in silico studies including 3D QSAR, pharmacophore mapping, and molecular docking approaches. Tubulin protein was explored for the residues imperative for activity by analyzing the binding pattern of colchicine and selected compounds of anthracenone derivatives in the active domain. The docking methodology applied in the study was first valid...

We have carried out a computational structure-based design of new potent pyrrolidine carboxamide (PCAMs) inhibitors of enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (MTb). Three-dimensional (3D) models of InhA-PCAMx complexes were prepared by in situ modification of the crystal structure of InhA-PCAM1 (Protein Data Bank (PDB) entry code: 4U0J), the reference compound...

Stereochemistry is an important determinant of a molecule's biological activity. Stereoisomers can have different degrees of efficacy or even opposing effects when interacting with a target protein. Stereochemistry is a molecular property difficult to represent in 2D-QSAR as it is an inherently three-dimensional phenomenon. A major drawback of most proposed descriptors for 3D-QSAR that encode s...

The 3VHE protein is considered as a potential target for the treatment of prostate cancer. In order to find new inhibitors, pharmacophore models based on molecular structure rhodanine derivatives and three-dimensional quantitative structure-activity relationship model (3D-QSAR) have been developed validated by different methods. 3D-QSAR was evaluated its predictive performance diverse test set ...

Receptors A2A have an important role in the regulation of mood and motor activity; the available evidence has provided the basis for the formulation of a theory according to which selective A2A adenosine receptor antagonists can be useful for the treatment of Parkinson’s Disease. To explore the binding properties of some adenosine-like antagonists, we have employed two different approaches: (1)...

The recently introduced non-stochastic and stochastic bond-based linear indices are been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. These improved modified descriptors are applied to several well-known data sets to validate each one of them. Particularly, Cramer's steroid data set has become a benchmark fo...

Alignment or superposition of multiple flexible ligands in 3D is a key step in rational ligand-based drug design, pharmacophore elucidation and 3D QSAR analysis. We have recently introduced Atomic Property Fields methodology, which utilizes continuous Gaussian-based multicomponent potentials to represent the distributions of physico-chemical atomic properties. Calculation of APF pseudo-energy p...

Fructose 1,6-bisphosphatase (FBPase) has been identified as a drug discovery target for lowering glucose in type 2 diabetes mellitus. In this study, a large series of 105 FBPase inhibitors were studied using a combinational method by 3D-QSAR, molecular docking and molecular dynamics simulations for a further improvement in potency. The optimal 3D models exhibit high statistical significance of ...