In silico insights into the identification of potential novel angiogenic inhibitors against human VEGFR-2: a new SAR-based hierarchical clustering approach

Abstract

In this study, binding efficiency of new pyrrolopyrimidine structural analogs against human vascular endothelial growth factor receptor-2 (VEGFR-2) were elucidated using integrated in silico methods. Optimized high-resolution model of VEGFR-2 was generated and adopted for structure-based virtual screening approaches. Pyrrolopyrimidine inhibitor (CP15) associated compounds were screened from PubChem database and subjected to virtual screening and comparative docking methods against the receptor ligand-binding domain. Accordingly, high efficient compounds were clustered with similarity indices through PubChem structure cluster module using single-linkage algorithm. Moreover, pharmacokinetics including drug metabolism activities of high-binding leads under investigation was portrayed using ADMET and similarity ensemble analysis. Optimal energy orientations of the selected protein model have been shown to be reliable, and highly recommended for screening and docking studies. Docking and clustering strategies were shown that nineteen candidates as most effective binders for VEGFR-2 than CP15, and are grouped as three classes. Lys⁸⁶⁸, Glu⁸⁸⁵, Cys⁹¹⁹, His¹⁰²⁶, Arg¹⁰²⁷, Asp¹⁰⁴⁶, and Gly¹⁰⁴⁸ residues were predicted as novel hotspot residues, and participate in H-bonds, π-cation, π-stacking, halogen bonds, and salt-bridges formation with ligands. These additional bonds are contributing extent stability that holds the receptor structure at flexible state, this make difficult to any further conformational changes for evoking angiogenic signals. The ADMET and similarity ensemble analysis results were strongly indicated that thirteen candidates as best ligands for angiogenesis targets. Altogether, these findings indicate potential angiogenic templates and their binding levels with VEGFR-2; sorted viewpoints could be useful as a promising way to describe potential angiogenesis inhibitors with related molecular targets.     

Microsatellite marker based genetic diversity analysis among cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>) accessions differing for their response to drought stress

Genetic diversity is an essential input for any plant breeding programme. To assess the genetic divergence among the newly identified drought tolerant lines and elite cotton genotypes including popular varieties, a total of 51 distinctly polymorphic markers were identified after screening 142 genome-wide SSR markers. The identified polymorphic markers detected a total of 140 alleles with a mean of 2.75 alleles per loci and average polymorphism information content of 0.45. Jaccard coefficient based dissimilarity index between the genotypes ranged from 0.18 to 0.82 indicating existence of wide variation between and within the drought tolerant and susceptible genotypes at the DNA level. Cluster and factorial analyses have provided the structure of genetic diversity present and clearly distinguished the drought tolerant and susceptible cotton genotypes. Clustering pattern was in congruence with the source or pedigree of genotypes. The information generated in the present study on genetic divergence among genotypes having differential response to drought will help in selection of suitable lines as parents for developing drought tolerant cultivars in cotton. The polymorphic markers and diverse lines identified in the study will be of immense utility in molecular mapping and marker assisted breeding to achieve drought tolerance in cotton.     

Mitochondrial DNA analysis of field populations of <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> (Lepidoptera: Noctuidae) and of its relationship to <Emphasis Type="Italic">H. zea</Emphasis>

Background  

Helicoverpa armigera and H. zea are amongst the most significant polyphagous pest lepidopteran species in the Old and New Worlds respectively. Separation of H. armigera and H. zea is difficult and is usually only achieved through morphological differences in the genitalia. They are capable of interbreeding to produce fertile offspring. The single species status of H. armigera has been doubted, due to its wide distribution and plant host range across the Old World. This study explores the global genetic diversity of H. armigera and its evolutionary relationship to H zea.     

Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Carbamate and organophosphate resistance in cotton pests in India, 1995 to 1999

Monitoring for organophosphate and carbamate resistance was carried out on five major insect pests of cotton collected from 22 cotton-growing districts across India. Resistance was monitored in Helicoverpa armigera (Hübner) and Pectinophora gossypiella (Saunders) for the period 1995-1999 and for Spodoptera litura (Fabricius), Earias vittella (Fabricius) and Bemisia tabaci (Gennadius) in a survey conducted during the 1997-98 cropping season. Of the 53 field strains of H. armigera, only four were found to exhibit resistance to quinalphos, the highest 15-fold, whereas all 16 field strains tested were found to be resistant to monocrotophos. Similarly, out of 40 field strains tested, only eight were found to express appreciable resistance to methomyl. Resistance in P. gossypiella to quinalphos was high in the majority of the strains tested. Of the seven strains of E. vittella tested, two strains from northern India exhibited > 70-fold resistance to monocrotophos. Of the 11 S. litura strains tested, only four were found to exhibit resistance factors of 10 to 30-fold to quinalphos and monocrotophos. All of the B. tabaci field strains exhibited resistance to methomyl and monocrotophos and susceptibility to triazophos. Practical implications for pest control resulting from the observed patterns of cross-resistance between quinalphos, monocrotophos and methomyl are discussed.     

Efficient conformational sampling of multiconformational cyclic molecules: application to 1,4,7,10,13-Pentaoxacyclopentadecane

The result of an exhaustive search of low-energy conformers of 1,4,7,10,13-Pentaoxacyclopentadecane is presented. The search method combines the generation of large number of trial conformers using local nonstochastic deformations known as the Conflex method, which is coupled to AMBER force field as the minimizer. The extent of the conformational space sampled was evaluated from the view point of the number of duplicates of each conformer, generation of inclusion type structures without considering the substrate and the spread of the allowed torsion angles visited during the search. It is shown that the conformational search is exhaustive and efficient as conformers, which the metal coordinated crown ether complexes adopt, were generated. Free energies using the AMBER structures were calculated using the model of Cramer and Truhlar. The study suggests that 1,4,7,10,13-Pentaoxacyclopentadecane exists as a mixture of conformers in solution. The results show the efficiency of the method and could be the method of choice in the design of synthetic macrocyclic receptors.     

Yeast cytochrome c is a sequence-specific DNA-binding protein

A protein binding to the alcohol oxidase 2 upstream activation sequence (AOX2UAS) of the methylotropic yeast, Pichia pastoris, has been purified and identified as cytochrome c (cyt c). Cyt c purified from P. pastoris or Saccharomyces cerevisiae binds to AOX2UAS. Specific point mutations in AOX2UAS abolish cyt c binding. We conclude that yeast cyt c is a sequence-specific DNA-binding protein and may have a regulatory role in the nucleus.     

Red Mexican grapefruit: a novel source for bioactive limonoids and their antioxidant activity

Citrus limonoids have shown to inhibit the growth of cancer in colon, lung, mouth, stomach and breast in animal and cell culture studies. For the first time in the present study, an attempt has been made to isolate antioxidant fractions and five limonoids from red Mexican grapefruit seeds. Defatted seed powder was successively extracted with hexane, ethyl acetate (EtOAc), acetone, methanol (MeOH) and MeOH/water and the extracts were concentrated under vacuum. Radical scavenging activity of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and total phenolic content were also measured for comparison with the antioxidant capacity in the phosphomolybdenum method for the above extracts. Acetone and MeOH extracts, respectively, showed the highest (85.7%) and lowest (53.3%) radical scavenging activity, at 500 ppm. The total phenolic contents were found to be highest in the acetone extract (15.94%) followed by the MeOH extract (5.92%), ethyl acetate extract (5.54%) and water extract (5.26%). Antioxidant capacity of the extracts as equivalents to ascorbic acid (micromol/g of the extract) was in the order, EtOAc extract > acetone extract > water extract > methanol extract. Furthermore, the EtOAC and acetone extracts were loaded onto silica gel columns to obtain four limonoid aglycons. MeOH fraction was loaded onto a dowex-50 and sepabeads resin column to obtain a limonoid glucoside. The purity of the isolated five compounds was analyzed by HPLC using a C18 column and UV detection at 210 nm. Finally, the structures of the compounds were identified as obacunone, nomilin, limonin, deacetylnomilin (DAN) and limonin-17-beta-D-glucopyranoside (LG) using 1H and 13C NMR studies.