Three-dimensional quantitative structure-activity relationship studies on c-Src inhibitors based on different docking methods.

c-Src kinase play an important role in cell growth and differentiation and its inhibitors can be useful for the treatment of various diseases, including cancer, osteoporosis, and metastatic bone disease. Three dimensional quantitative structure-activity relationship (3D-QSAR) studies were carried out on quinazolin derivatives inhibiting c-Src kinase. Molecular field analysis (MFA) models with four different alignment techniques, namely, GLIDE, GOLD, LIGANDFIT and Least squares based methods were developed. glide based MFA model showed better results (Leave one out cross validation correlation coefficient r(2)(cv) = 0.923 and non-cross validation correlation coefficient r(2)= 0.958) when compared with other models. These results help us to understand the nature of descriptors required for activity of these compounds and thereby provide guidelines to design novel and potent c-Src kinase inhibitors.

Quantitative structure activity relationship and pharmacophore studies of adenosine receptor A2B inhibitors.

Adenosine receptor A2B (ADoR A2B) is an important G protein-coupled receptor (GPCR) of the rhodopsin family, and plays a pivotal role in gastrointestinal, neurological and hypersensitive disorders. QSAR and pharmacophore studies were carried out using 63 ADoR A2B inhibitor molecules to characterize molecular features and structural requirements for biological interaction. QSAR modelling using genetic algorithm- partial least squares (G/PLS) method identified molecular shape, size electrophilicity and conformational flexibility as important descriptors for these compounds affinity to the receptor. Further analysis of pharmacophore model revealed hydrogen bond acceptor (HBA), hydrogen bond donor (HBD), hydrophobic aliphatic (HY-ala) and hydrophobic aromatic (HY-aro) as the crucial molecular features that predict binding affinity of these compounds to ADoR A2B. These observations provide important insights to the rationale development of novel and potent compounds against ADoR A2B.

Strategies for generating less toxic P-selectin inhibitors: pharmacophore modeling, virtual screening and counter pharmacophore screening to remove toxic hits.

This paper describes the generation of ligand-based as well as structure-based models and virtual screening of less toxic P-selectin receptor inhibitors. Ligand-based model, 3D-pharmacophore was generated using 27 quinoline salicylic acid compounds and is used to retrieve the actives of P-selectin. This model contains three hydrogen bond acceptors (HBA), two ring aromatics (RA) and one hydrophobic feature (HY). To remove the toxic hits from the screened molecules, a counter pharmacophore model was generated using inhibitors of dihydrooratate dehydrogenase (DHOD), an important enzyme involved in nucleic acid synthesis, whose inhibition leads to toxic effects. Structure-based models were generated by docking and scoring of inhibitors against P-selectin receptor, to remove the false positives committed by pharmacophore screening. The combination of these ligand-based and structure-based virtual screening models were used to screen a commercial database containing 538,000 compounds.

Virtual screening of cathepsin k inhibitors using docking and pharmacophore models.

Cathepsin K is a lysosomal cysteine protease that is highly and selectively expressed in osteoclasts, the cells which degrade bone during the continuous cycle of bone degradation and formation. Inhibition of cathepsin K represents a potential therapeutic approach for diseases characterized by excessive bone resorption such as osteoporosis. In order to elucidate the essential structural features for cathepsin K, a three-dimensional pharmacophore hypotheses were built on the basis of a set of known cathepsin K inhibitors selected from the literature using catalyst program. Several methods are used in validation of pharmacophore hypothesis were presented, and the fourth hypothesis (Hypo4) was considered to be the best pharmacophore hypothesis which has a correlation coefficient of 0.944 with training set and has high prediction of activity for a set of 30 test molecules with correlation of 0.909. The model (Hypo4) was then employed as 3D search query to screen the Maybridge database containing 59,000 compounds, to discover novel and highly potent ligands. For analyzing intermolecular interactions between protein and ligand, all the molecules were docked using Glide software. The result showed that the type and spatial location of chemical features encoded in the pharmacophore are in full agreement with the enzyme inhibitor interaction pattern identified from molecular docking.

Molecular cloning and sequencing of MHC class II beta 1 domain of turkey reveals high sequence identity with chicken.

We report the nucleotide sequences of turkey (Meleagris gallopavo) major histocompatibility complex (MHC) class II loci (beta 1 domain or exon 2 encoding the peptide-binding region). In the present investigation, three distinct sequences from the beta 1 domain of turkey MHC class II were isolated. A BLAST search and phylogenetic analysis revealed that turkey MHC sequences are most similar to chicken and peacock MHC. There was no strong evidence of recombination among the turkey MHC sequences or with other avian MHC, but diversity was high. The diversity in this peptide-binding region may be the result of point mutation and balancing selection or frequent gene conversion within turkey. However, more work and data are needed to understand the evolution of turkey and other avian MHC. Moreover, polymerase chain reaction-restriction fragment-length polymorphism analysis of exon 2 using the Hinf I restriction enzyme demonstrated three restriction patterns and a preliminary evidence of multiple beta loci in turkey. PCR-RFLP analysis of turkey MHC class II loci could be a promising method of MHC genotyping, when more sequences are available. Turkey MHC haplotypes identified earlier by RFLP analysis should be sequenced to standardize turkey MHC nomenclature and to develop DNA based method of haplotyping.

Differential expression of inducible nitric oxide synthase and cytokine mRNA in chicken lines divergent for cutaneous hypersensitivity response.

Phytohemagglutinin (PHA)-induced delayed-type hypersensitivity is an immunocompetent trait considered an indicator of cell-mediated immune or T-cell responses. Divergent selection was performed to generate high and low lines for response to PHA-P. Extreme-responder birds of the F2 generation in each line were used to study possible differences in macrophage activity and the associated functional genes. To evaluate macrophage activity, nitric oxide (NO) was estimated both systemically in serum and in in vitro monocyte culture. Semi-quantitative RT-PCR was used to detect the differential mRNA expression patterns of iNOS and MIP-1beta in monocyte culture, whereas T(H)1 cytokines (IL-2 and IFN-gamma) were studied in peripheral blood mononuclear cells (PBMC) at different time intervals after lipopolysaccharide (LPS) induction. The high line showed strong systemic, as well as in vitro NO production, compared to the low line, upon stimulation with NDV and LPS, similar to early and high iNOS mRNA expression. Following the pattern of iNOS gene expression, an early strong expression of cytokines with powerful iNOS-inducing action, such as IFN-gamma and the chemokine MIP-1beta, was observed in the high line. In contrast, for response to PHA-P, low expression of IL-2 was observed in the high compared to the low line. In conclusion, the study revealed that divergent selection for response to PHA-P resulted in a divergent effect on T(H)1 cell activity, resulting in altered macrophage function in chickens. Selection, based on response to PHA-P, could lead to more resistant birds or birds with an enhanced immune response.