A High Throughput In Silico Pipeline to Discover Potential Therapeutic Targets in Prokaryotic Pathogens

Abstract

Infectious diseases are emerging rapidly throughout the globe, and antibiotic resistant bacterial strains lead to the therapeutic failure; ultimately causing the high risk of cost and re-infection. Vaccination is considered as one of the most effective mechanisms for the treatment of a particular disease; and conventional vaccinology approaches have rendered certain limitations against some pathogens. Reverse vaccinology and subtractive proteomics are novel competent computational approaches to identify putative therapeutic targets against the infectious agents. In current study we have developed an in silico, multi-threaded, configurable and scalable pipeline employing subtractive-reverse vaccinology analysis technique and named it VacSol (https://sourceforge.net/projects/vacsol/). The principle objective of the VacSol development is to screen out genes/proteins from microbial genome/proteome that could be employed as potential therapeutic targets against them and furthermore be exploited for in vitro and in vivo laboratory evaluation. VacSol is multi-mode approach working as a standalone tool as well as a pipeline or a package of tools. It has two major features, first is to prioritize proteins followed by determination of the major histocompatibility complex MHCI & II for the prioritized proteins. VacSol evaluates whole proteome (composed of thousands of protein sequences) of a microbe and prioritize the proteins being essential, virulent, non-host homolog and immunogenic simultaneously and then additionally perform epitope analysis of prioritized proteins. . A study was conducted in Atta-ur-Rahman School of Applied Biosciences ASAB, NUST based on reverse vaccinology using online web based tools and evaluated the whole proteome of Helicobacter Pylori 26695. The approach took more than five months to prioritize proteins as potential therapeutic targets and their immunogenic peptides conserved among all H. pylori strains. VacSol was employed to repeat the same analysis and it evaluated Helicobacter Pylori proteome containing 1,576 proteins within one and a half hour on four core machine and provided ten protein sequences as candidates for vaccine targets which can be further subjected for laboratory evaluation by domain experts. VacSol efficiently reduces the laborious and hectic effort of months by generating results within a few hours by integrating all the required tools. VacSol results can also be accelerated in proportion to number of cores available in the machine. By default it uses maximum number of available cores, but this feature is governable. VacSol was deployed and tested at Ubuntu 12.04 64 bit machine. Its results do not depend on any universal set of rules that may vary based on the provided input and the version of tools that have integrated in this pipeline. VacSol is an efficient, cost and time effective tool that eliminates the false candidates and recognizes the potential therapeutic targets for further laboratory evaluation.