SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/while ASSAM can be accessed at http://mfrlab.org/grafss/assam/

IN SILICO METABOLIC PATHWAY ANALYSIS AND DOCKING ANALYSIS OF TREPONEMA PALLIDUM SUBS. PALLIDUM NICHOLS FOR POTENTIAL DRUG TARGETS

Objective: Syphilis is a sexually transmitted infection caused by the spirochaete, Treponema pallidum subspecies pallidum nichols. In this study, a comparative metabolic pathway analysis and molecular docking was performed to identify putative drug targets.Methods: The biochemical pathways of Treponema pallidum subs. pallidum nichols and Homo sapiens were compared using KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway. The amino acid sequence of the selected enzymes were retrieved and Blastp was performed. Out of 9 enzymes, enolase was modeled using ModWeb and the structure was validated using RAMPAGE. The active sites were identified using Metapocket 2.0 and further docked using AutoDock 4.2.Results: The enzymes which were not similar to that of Homo sapiens were filtered out as potential drug targets. A total of 9 enzymes were retrieved which were present only in the Treponema pallidum subs. pallidum nichols. The structure obtained from Homology modeling was validated and further active sites were predicted. The docking analysis results showed the interaction between enolase and doxycycline and the structures were obtained using PyMol.Conclusion: Through this study, doxycycline which has antibacterial effect and a derivative of tetracycline could be one of the potential ligands.  Â

SYNTHESIS OF NOVEL CYCLOHEXANONE DERIVATIVES AS BCR-ABL T1351 INHIBITORS

Objective: Several 3(rd) generation inhibitors are being developed for the treatment of patients with Chronic myelogenous leukemia (CML). The present work mainly aims to discover novel small molecular inhibitors against important molecular target T3151 ABL mutant involved in leukemia.Methods: Docking study was carried out and the binding affinity of the proteins with the phenothiazine compounds 3a-h and 7a-c was measured. The docking scores of the N-acylated compounds 7a-c are higher than 3a-h. The drug likeliness of these compounds was tested by the Lipinski's rule of five. The phenothiazine compounds with good docking scores and 7a-c were synthesized and screened by in-vitro methods for inducing antiproliferative effect by trypan blue and MTT assay and induction of apoptosis in K562 cells.Results: All the N-acylated compounds and, in particular, 7c with a chloro substituent in the para position of the phenyl ring appeared to be most potent molecule with an IC50 value of 32.44 and 24.01(µg/ml) by trypan blue and MTT assay respectively. Further, a dose-dependent increase in LDH release was observed, confirming the antiproliferative potential of the compounds.Conclusion: The compounds 7a-c was tested for antiproliferative effect against K562 cell lines by MTT assay LDH assay and Trypan blue assay. All the compounds 7a-h behaves as 3(rd) generation inhibitors for the treatment of patients with Chronic myelogenous leukemia (CML). These can act as a template for the further development and optimization studies.Â

In silico pharmacodynamics, toxicity profile and biological activities of the Saharan medicinal plant Limoniastrum feei

ABSTRACT In-silico study was performed to find the pharmacodynamics, toxicity profiles and biological activities of three phytochemicals isolated from Limoniastrum feei (Plumbagenaceae). Online pharmacokinetic tools were used to estimate the potential of Quercetin, kaempferol-3-O-β-D-glucopyranoside (astragalin) and quercitin-7-O-β-D-glucopyranoside as specific drugs. Then the prediction of potential targets of these compounds were investigated using PharmMapper. Auto-Dock 4.0 software was used to investigate the different interactions of these compounds with the targets predicted earlier. The permeability of quercetin was found within the range stated by Lipinski ׳s rule of five. Hematopoietic prostaglandin (PG) D synthase (HPGDS), farnesyl diphosphate synthetase (FPPS) and the deoxycytidine kinase (DCK) were potential targets for quercetin, astragalin and quercetin 7, respectively. Quercetin showed antiallergic and anti-inflammatory activity, while astragalin and quercetin 7 were predicted to have anticancer activities. The activity of Astragalin appeared to be mediated by FPPS inhibition. The inhibition of DCK was predicted as the anticancer mechanisms of quercetin 7. The compounds showed interesting interactions and satisfactory binding energies when docked into their targets. These compounds are proposed to have activities against a variety of human aliments such as allergy, tumors, muscular dystrophy, and diabetic cataracts

In silico pharmacodynamics, toxicity profile and biological activities of the Saharan medicinal plant Limoniastrum feei

In-silico study was performed to find the pharmacodynamics, toxicity profiles and biological activities of three phytochemicals isolated from Limoniastrum feei (Plumbagenaceae). Online pharmacokinetic tools were used to estimate the potential of Quercetin, kaempferol-3-O-β-D-glucopyranoside (astragalin) and quercitin-7-O-β-D-glucopyranoside as specific drugs. Then the prediction of potential targets of these compounds were investigated using PharmMapper. Auto-Dock 4.0 software was used to investigate the different interactions of these compounds with the targets predicted earlier. The permeability of quercetin was found within the range stated by Lipinski ׳s rule of five. Hematopoietic prostaglandin (PG) D synthase (HPGDS), farnesyl diphosphate synthetase (FPPS) and the deoxycytidine kinase (DCK) were potential targets for quercetin, astragalin and quercetin 7, respectively. Quercetin showed antiallergic and anti-inflammatory activity, while astragalin and quercetin 7 were predicted to have anticancer activities. The activity of Astragalin appeared to be mediated by FPPS inhibition. The inhibition of DCK was predicted as the anticancer mechanisms of quercetin 7. The compounds showed interesting interactions and satisfactory binding energies when docked into their targets. These compounds are proposed to have activities against a variety of human aliments such as allergy, tumors, muscular dystrophy, and diabetic cataracts

Identification of protein-ligand binding site using multi-clustering and support vector machine

© 2016 IEEE. Multi-clustering has been widely used. It acts as a pre-training process for identifying protein-ligand binding in structure-based drug design. Then, the Support Vector Machine (SVM) is employed to classify the sites most likely for binding ligands. Three types of attributes are used, namely geometry-based, energy-based, and sequence conservation. Comparison is made on 198 drug-target protein complexes with LIGSITECSC, SURFNET, Fpocket, Q-SiteFinder, ConCavity, and MetaPocket. The results show an improved success rate of up to 86%

STRUCTURE-BASED DRUG DESIGNING STUDIES TOWARDS EXPLORING THE POTENTIAL ANTICANCER ACTIVITY OF SELECTED PHYTOCOMPOUNDS AGAINST HISTONE DEACETYLASE 10 PROTEIN

Objective: Histone deacetylases (HDACs) are proteins which play a crucial role in cell growth, maintenance, and regulation. Abnormal HDAC proteins produced by genetic mutations are common in human cancers. HDAC10 is a class II HDAC member, and its expression in many cancers has been documented. The aim of this study was to determine the best docking of phytocompounds selected from a list of such compounds in the database of chemicals for HDAC10.Methods: The crystal structure of HDAC10 was retrieved from Protein Data Bank and prepared for docking studies by post-translational modification (PTM) analysis. Then, we have screened 450 phytocompounds for molecular docking studies and determined their binding affinities against HDAC10 by using PatchDock server.Results: The PTM analysis showed that myristoylation sites were more abundant in HDAC10 which might be important functional sites for the gene regulation. The results revealed the receptor/inhibitor interactions within an active domain consisting of 30 important amino acid residues. Affinity-based studies have indicated the docking energy levels by calculating hydrogen bonding, steric, and hydrophobic interactions. Among the inhibitors, we could shortlist four compounds which showed excellent binding affinity. Hence, we evaluated drug binding affinities of these four compounds and determined their atomic contact energy values. Analysis of the docking results showed holacurtine>periplogenin>3,3'-diindolylmethane>epigallocat echin as the order of binding affinities, with holacurtine having the best docking score.Conclusion: It is proposed from these studies that the docking and scoring methods could be useful for selecting and shortlisting the promising antitumor molecules. These molecules could be further tested using in vitro and in vivo methods to confirm their role in HDAC10-associated cancers. Furthermore, myristoylation sites in HDAC10 could form an important binding site for selecting hit inhibitor compounds. The PTM studies together with the binding mode analysis facilitate the protein-protein interaction studies of HDAC10, and thioredoxin-interacting protein is considered as one of the transcriptional regulators of HDAC10

Inspecting the potential physiological and biomedical value of 44 conserved uncharacterised proteins of Streptococcus pneumoniae

BACKGROUND: The major Gram-positive coccoid pathogens cause similar invasive diseases and show high rates of antimicrobial resistance. Uncharacterised proteins shared by these organisms may be involved in virulence or be targets for antimicrobial therapy. RESULTS: Forty four uncharacterised proteins from Streptococcus pneumoniae with homologues in Enterococcus faecalis and/or Staphylococcus aureus were selected for analysis. These proteins showed differences in terms of sequence conservation and number of interacting partners. Twenty eight of these proteins were monodomain proteins and 16 were modular, involving domain combinations and, in many cases, predicted unstructured regions. The genes coding for four of these 44 proteins were essential. Genomic and structural studies showed one of the four essential genes to code for a promising antibacterial target. The strongest impact of gene removal was on monodomain proteins showing high sequence conservation and/or interactions with many other proteins. Eleven out of 40 knockouts (one for each gene) showed growth delay and 10 knockouts presented a chaining phenotype. Five of these chaining mutants showed a lack of putative DNA-binding proteins. This suggest this phenotype results from a loss of overall transcription regulation. Five knockouts showed defective autolysis in response to penicillin and vancomycin, and attenuated virulence in an animal model of sepsis. CONCLUSIONS: Uncharacterised proteins make up a reservoir of polypeptides of different physiological importance and biomedical potential. A promising antibacterial target was identified. Five of the 44 examined proteins seemed to be virulence factors.This work was supported by a Miguel Servet Research contract funded by the Fondo de Investigación Sanitaria (Ministerio de Economía y Competitividad de España) to Antonio J. Martin-Galiano, a Plan Nacional de I + D + I of Ministerio de Ciencia e Innovación grant (BIO2011-25343) to Adela G. de la Campa, and funds from the CIBER Enfermedades Respiratorias group (an initiative of the Instituto de Salud Carlos III).S