Pan-genomics allied to reverse vaccinology and drug target Identification for the Syphilis causative agent Treponema Pallidum: a multi-pronged approach towards vaccine and Drug targets

Abstract

Syphilis is caused by the Gram negative spirochete Treponema pallidum subspecies pallidum and is considered as one of the most imperious and systemic human Sexually Transmitted Infection (STIs). In general, this disease is developed by sexual contact (venereal) especially men (men having sexual relationship with men, MSM) and in some cases a new born may get it from effected mother (congenital syphilis) by transplacental transmission. There are some subspecies of Treponema pallidum that are responsible for syphilis without sexual contact (non-venereal), such as, T. pallidum subspecies endemicum responsible for bejel and T. pallidum subspecies. pertenue responsible for yaws. These pathogens are quite similar to each other and they cannot be distinguished serologically and morphologically. Every year, the global distribution of syphilis is increasing, reportedly, about six million new cases of syphilis arises around the globe in individuals aged 15 to 49 years. More than 300,000 fetal and newborn deaths are associated to syphilis, with 215,000 further infants placed at high risk of death at early stage of birth. Despite the effort made in developed countries for the elimination of syphilis, the decrease in investment towards public health and STIs control program has over shadowed previous exclusion and control efforts. Furthermore, in developed countries like USA, China and Western Europe, syphilis has been reported in key populations where men are developing sexual relationship with men. In developing or poor countries, syphilis has remained prevalent. The current worldwide prevalence of syphilis combined with the lack of effective vaccine targets and the appearing of antibiotic-resistant strains emphasizes the need for the development of new strategies. In this study, we focused on the comparative genomics studies, Pan-genome, subtractive genomics and reverse vaccinology analysis for the drug and vaccine target identification. In the pan-genomic study, we used 53 strains of Treponema pallidum to identify the pan-genome, core genome, and singletons based on subspecies level to reveal the differences in genome plasticity between venereal (Subsp. pallidum) and non-venereal (Subsp. endemicum and Subsp. pertenue) syphilis, which can disclose the close connection among all strains of Treponema pallidum. We also used reverse vaccinology, subtractive genomics and molecular docking analysis for the drug and vaccine target identification. In subtractive genomics and reverse vaccinology approaches, we compared 13 strains of Treponema pallidum for analysis. We identified 837 core genes and, considering human as host, we identified 567 conserved non-host homologous proteins. Further, using subtractive genomics and reverse vaccinology, 15 putative antigenic proteins, and 6 drug targets were identified which were essential for the bacteria. Identified drug targets were subjected to virtual screening using 28 Natural compounds library. The proposed drug molecules showing favorable interactions, lower energy and high complementarity with predicted targets have also been reported in the present study. Our proposed approach expedites the rapid and efficient selection of Treponema pallidum putative proteins for developing a broad spectrum of novel drugs and vaccines, which can be used as candidate therapeutic targets in the future against syphilis disease.