A computational approach using mathematical modeling to assess the peptidoglycan biosynthesis of Clostridium botulinum ATCC 3502 for potential drug targets

Proteomic Characterization and Target Identification Against Streptococcus mutans Under Bacitracin Stress Conditions Using LC-MS and Subtractive Proteomics

The aim of the present study, is to identify potential targets against the highly pathogenic bacteria Streptococcus mutans that causes dental caries as well as the deadly infection of endocarditis. The powerful and highly sensitive technique of liquid chromatography-mass spectrometry (LC–MS/MS) identified 321 proteins of S. mutans when grown under stressful conditions induced by the antibiotic bacitracin. These 321 proteins were subjected to the insilico method of subtractive proteomics to screen out potential targets by utilizing different analyses like CD-HIT, non-homologous sequence screening, KEGG pathway, essentiality screening, gut-flora non-homology, and codon usage analysis. A database of essential proteins was employed to find sequence homology of non-paralogous proteins to determine proteins which are essential for bacterial survival. Cellular localization analysis of the selected proteins was done to localize them inside the cell along with physico-chemical characterization and druggability analysis. Using computational tools, 22 proteins out of 321, that are functionally distinguishable from their human counterparts and passed the criterion of a potential therapeutic candidate were identified. The selected proteins comprise central energy metabolic proteins, virulence factors, proteins of the sortase family, and essentiality factors. The presented analyses identified proteins of the sortase family, which appear as key therapeutic targets against caries infection. These proteins regulate a number of virulence factors, thus can be simultaneously inhibited to obstruct multiple virulence pathways.

Rapid Detection of Clostridium botulinum in Food Using Loop-Mediated Isothermal Amplification (LAMP)

Botulinum neurotoxins are considered as one of the most potent toxins and are produced by Clostridium botulinum. It is crucial to have a rapid and sensitive method to detect the bacterium Clostridium botulinum in food. In this study, a rapid detection assay of C. botulinum in food using loop-mediated isothermal amplification (LAMP) technology was developed. The optimal primers were identified among three sets of primers designed specifically based on the partial ntnh gene encoding nontoxic-nonhaemagglutinin (NTNH) for rapid detection of the target DNA in plasmids. The optimal temperature and reaction time of the LAMP assay were determined to be 64 °C and 60 min, respectively. The chemical kit could be assembled based on these optimized reaction conditions for quick, initial high-throughput screening of C. botulinum in food samples. The established LAMP assay showed high specificity and sensitivity in detecting the target DNA with a limit of 0.0001 pg/ul (i.e., ten times more sensitive than that of the PCR method) and an accuracy rate of 100%. This study demonstrated a potentially rapid, cost-effective, and easy-operating method to detect C. botulinum in food and clinical samples based on LAMP technology.

Comparative assessment of the therapeutic drug targets of C. botulinum ATCC 3502 and C. difficile str. 630 using in silico subtractive proteomics approach

Growing antimicrobial resistance of the pathogens against multiple drugs posed a serious threat to the human health worldwide. This fueled the need of identifying the novel therapeutic targets that can be used for developing new class of the drugs. Recently, there is a substantial rise in the rate of Clostridium infections as well as in the emergence of virulent and antibiotic resistant strains. Hence, there is an urgent need for the identification of potential therapeutic targets and the development of new drugs for the treatment and prevention of Clostridium infections. In the present study, a combinatorial approach involving systems biology and comparative genomics strategy was tested against Clostridium botulinum ATCC 3502 and Clostridium difficile str. 630 pathogens, to render potential therapeutic target at qualitative and quantitative level. This resulted in the identification of five common (present in both the pathogens, 34 in C. botulinum ATCC 3502 and 42 in C. difficile str. 630) drug targets followed by virtual screening-based identification of potential inhibitors employing molecular docking and molecular dynamics simulations. The identified targets will provide a solid platform for the designing of novel wide-spectrum lead compounds capable of inhibiting their catalytic activities against multidrug-resistant Clostridium in the near future.