In silico quest for putative drug targets in Helicobacter pylori HPAG1: molecular modeling of candidate enzymes from lipopolysaccharide biosynthesis pathway

Abstract

Aimed at identification and structural characterization of novel putative therapeutic targets in H. pylori, the etiological agent of numerous gastrointestinal diseases including peptic ulcer and gastric cancer, the present study comprised of three phases. First, through subtractive analysis of metabolic pathways of Helicobacter pylori HPAG1 and human, as documented in the KEGG database, 11 pathogen-specific pathways were identified. Next, all proteins involved in these pathogen-specific pathways were scrutinized in search of promising targets and the study yielded 25 candidate target proteins that are likely to be essential for the pathogen viability, but have no homolog in human. The lipopolysaccharide (LPS) biosynthesis pathway was found to be the largest contributor (nine proteins) to this list of candidate proteins. Considering the importance of LPS in H. pylori virulence, 3D structural models of three predicted target enzymes of this pathway, namely 2-dehydro-3-deoxy-phosphooctonate aldolase, UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase and Phosphoheptose isomerase, were then built up using the homology modeling approaches. Binding site analysis and docking of the known biological substrate PEP to 2-dehydro-3-deoxyphosphooctonate aldolase revealed the potential binding pocket present in the single monomeric form of the enzyme and identified 11 amino acid residues that might play the key roles in this protein-ligand interaction.

Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration

“…The importance of this step is to reduce unwanted cross reactivity of the drug and thus to inhibit its binding to the active sites of the homologous proteins in host (Sarkar et al, 2012). In in silico drug target identification method, the first step is considered as the filtration of homologous proteins to human proteome (Anishetty et al, 2005; Sarkar et al, 2012). This non-similarity analysis was carried out for the gut flora non-similarity proteins datasets.…”

“…These types of proteins were considered as essential and it was clearly demonstrated that similar proteins which are crucial in one organism are likely to be essential in another. A potential drug target possesses a crucial feature for the existence of the pathogen and must be an indispensable protein (Sarkar et al, 2012). The 67 proteins (Drug Target, Data Sheet S6 and Figure 1) out of 721 non-homologous input proteins were nominated for the consecutive analysis and considered as vital for the existence of the pathogen as they have homologs with not more than the given threshold value (Supplementary Table, S1).…”

“…The sequencing of genome and revealing of proteome of disease causing organisms are advancing the search of drug targets in the field of drug research based on essential genes of specific pathogen, interacting factors of host-pathogen, proteins persistence, resistance genes/resistance-associated proteins, metabolic pathways, prediction of gene expression levels (Galperin and Koonin, 1999; Yeh et al, 2004; Briken, 2008; Raman et al, 2008; Barh et al, 2011; Vetrivel et al, 2011). To identify novel drug targets these approaches have already been utilized in several life threatening pathogens, including Mycobacterium tuberculosis (Anishetty et al, 2005; Asif et al, 2009), M. leprae (Shanmugam and Natarajan, 2010), M. ulcerans (Butt et al, 2012), Helicobacter pylori (Sarkar et al, 2012), Streptococcus pneumonia (Singh et al, 2007), Yersinia pestis (Sharma and Pan, 2012), and Pseudomonas aeruginosa (Sakharkar et al, 2004). The foremost criteria for the identification of promising therapeutic candidates are essentiality and selectivity/specificity.…”

Expression of the 2-dehydro-3-deoxyphosphooc­tonate aldolase (KdsA) gene in mulberry leaves (Morus alba L.) is down-regulated under high salt and drought stress

“…KDO8Ps is widely expressed in higher plants (Brabetz et al, 2000;Delmas et al, 2003); however, biochemical and structural investigations of the enzyme have largely been limited to bacteria (Woisetschlager and Hogenauer, 1987;Brabetz and Brade, 1997;Sarkar et al, 2012). The first evidence of a plant KDO8Ps was provided by the detection of Kdo-8-P synthase-like activities in eight different plant species, and from the partial purification of KdsA and its characterization in spinach (Doong et al, 1991).…”

Computational Identification of Putative Drug Targets in Malassezia Globosa by Subtractive Genomics and Protein Cluster Network Approach

“…The main objective of this step is to define the non-homologous proteins of the pathogen as it's likely to prevent the cross-reactivity of drug compounds with the human host proteins [17]. 'Expect' value (e-value) fixed was <0.005 and a minimum bit score was> 100 to exclude the homologous sequences.…”