Structural Mapping of Inhibitors Binding Sites on P-glycoprotein: Mechanism of Inhibition of P-Glycoprotein by Herbal Isoflavones.

Understanding the pattern of inhibitors binding to p-glycoprotein (Pgp). Study Design: Pgp is an ATP dependent transporter protein, responsible for multi-drug resistance in metastatic tumors. It removes toxins by exporting a variety of structurally unrelated compounds outside the cells, which make Pgp a promising target for designing anti cancer supplementary therapeutic molecules. Isoflavones are present in soyabean and other herbal extracts. The idea was to explore inhibitor binding sites on Pgp to find hotspots which eventually may prove useful in designing compounds with higher specificity and affinity. Place and Duration of Study: School of Biotechnology, Gautam Buddha University, Greater Noida, between February 2012 and December 2012. Methodology: The biochemical nature of binding of isoflavones to Pgp has been extensively studied, but the atomic details of their interactions were not understood. Therefore, we have used in silico methods to study binding of eleven isoflavones to Pgp. The docking studies were performed using grid-based ligand docking with energetic (GLIDE). Results: Isoflavones binds at two slightly distinct sites perpendicular to each other, present in the large hydrophobic cavity of Pgp. Three isoflavones bind to site 1, whereas eight isoflavones bind to site 2 by forming van der Waals and H-bonded interactions. Both the sites are highly hydrophobic in nature and are contributed mainly by side chain of non polar residues present on twelve transmembrane -helices. Site 1 has minimum dimension of 7.5Å and maximum as 22Å whereas, site 2 is wider and deeper than site1. One sidewall of the site 2 is formed by polar amino acid residues of helix H12, which makes several hydrogen bonds with ligands. Conclusion: Structure analysis revealed that addition of polar group to hydrophobic ligand may enhance its binding affinity for Pgp, which may be used for designing potent inhibitors to find lead compounds for drug design.

SSR and AFLP based genetic diversity of soybean germplasm differing in photoperiod sensitivity

Forty-four soybean genotypes with different photoperiod response were selected after screening of 1000 soybean accessions under artificial condition and were profiled using 40 SSR and 5 AFLP primer pairs. The average polymorphism information content (PIC) for SSR and AFLP marker systems was 0.507 and 0.120, respectively. Clustering of genotypes was done using UPGMA method for SSR and AFLP and correlation was 0.337 and 0.504, respectively. Mantel's correlation coefficients between Jaccard's similarity coefficient and the cophenetic values were fairly high in both the marker systems (SSR = 0.924; AFLP = 0.958) indicating very good fit for the clustering pattern. UPGMA based cluster analysis classified soybean genotypes into four major groups with fairly moderate bootstrap support. These major clusters corresponded with the photoperiod response and place of origin. The results indicate that the photoperiod insensitive genotypes, 11/2/1939 (EC 325097) and MACS 330 would be better choice for broadening the genetic base of soybean for this trait.

Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice.

Rice is the fi rst cereal genome with a fi nished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specifi c RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had signifi cant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplifi cation showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specifi c RGAs in rice.