Computational and Simulation Studies to unveil Promising Drug and Vaccine Targets against the Multidrug Resistant Pathogens

Abstract

The emergence of multi-drug resistance (MDR) in pathogens and cancers is a worldwide public health problem. Bacteria are evolving continuously due to endogenous and exogenous resistance mechanisms, similarly, cancers are adopting drug resistance with more use of drugs. Drug abuse and environmental misfortunes facilitate the pathogens to gain resistance. Therefore, tackling these pathogens and treating cancers is a demanding job in public health research issues. The primarily focus of this dissertation is to target the multi-drug resistant (MDR) potential vaccine and drug targets to design new therapeutics for MDR pathogens along with addressing drug resistance appearing in cancers. Globally, MDR pathogens are serious concerns as they are posing alarming threats to public health. Bioinformatics, immunoinformatics, and in silico approaches are applied to complete the designed sections of this dissertation. Furthermore, a molecular dynamics simulation strategy is employed to evaluate the binding and inhibition mechanism of potential vaccine and drug targets. This dissertation consists of six chapters. Chapter 1 provides a general introduction to multi-drug resistance, MDR impacts on public health, and its future threats to mankind. It also highlights the significance of different therapeutic strategies as a matter of designing new medicines for MDR pathogens along with resistance to drugs in use for cancer patients. Chapter 2 introduces the background of methods devised to identify the potential vaccine and drug targets. Additionally, it also illustrates the implications of each method for reverse vaccinology and computer-aided drug designing (CADD) pipelines. Immunoinformatics, subtractive proteomics, molecular docking, and molecular dynamics simulation are depicted in detail here. In chapter 3, we have proposed an in-silico multi-epitope peptide (MEP) vaccination against Vibrio vulnificus infections. V. vulnificus is an opportunistic MDR pathogen that causes lethal necrotizing fasciitis, sepsis, septicemia, and gastroenteritis in people. Reverse vaccinology pipeline along with subtractive proteomics identified two potential vaccine candidates: vibC and flgL. The 9-mer β-cell derived T-cell antigenic epitopes are anticipating a strong affinity for the HLA allele (DRB1*0101) that are surface exposed and non-allergenic. Furthermore, the designed MEP is docked with a Toll-like receptor (TLR4) and simulated to decipher the binding mechanism. Vaccinologists might make use of this constructed MEP vaccine to evaluate its protective effectiveness in in-vivo animals. DRSML QAU Summary xiv Chapter 4 discusses the involvement of five flagellar proteins (flaA-E) in motility, biofilm formation, adhesion, and invasion of host cells. Flagellar flaA-E proteins belong to MDR vibrio species V. cholera, V. parahaemolyticus, V. fischeri, and V. vulnificus that represent the chemotaxis and motility region of bacteria. This work is planned to develop the MEP vaccine constructs by following the comparative construct mapping and multi-epitope designing approach to counter MDR vibrio species infections and diseases. Sixteen β-cell derived T-cell 9- mers epitopes are selected to design three MEP vaccine constructs VC-1, VC-2, and VC-3, and then underwent the simulation procedure. This comparative construct mapping approach evaluated MEP VC-3 construct bears the potential to induce a substantial immune response and it can be a possible immunogenic agent for MDR vibrio species. In chapter 5, we designed and proposed a lead compound to combat Clostridium difficile infections using subtractive proteomics and the CADD pipeline. C. difficile is involved in intestinal and urinary tract infections that affect millions of people every year. These infections are significant causes of morbidity and mortality around the world. The druggable and essential protein histidyl-tRNA synthetase (Hars) is selected as a potential therapeutic drug target. Indispensable approaches to molecular docking and molecular dynamic simulation highlight the binding mechanism of top-docked compounds with Hars. Findings suggest (S)- (methyleneamino)(4-(thiazole-4-carbonyl)morpholin-2-yl)methanideaminium) as a lead compound against C. difficile Hars protein. The study could decipher the identification of potential inhibitors against C. difficile infections. Final chapter 6 deciphered the inhibition mechanisms of Hsp90 inhibitors. Hsp90 is a universal cancer-causing agent of humans, and it is evolutionary conserved. Hsp90 contributes to the development of lung and breast cancer. It has become a potential therapeutic candidate, and inhibition of it may have an impact on several signaling pathways linked to cancer metastasis. Concurrent computational techniques and cutting-edge drug designing tools are utilized in this work to describe insights into Hsp90 inhibitors to present it as a new cancer therapeutic drug. Hsp90 inhibitors and their analogues are discovered to have a considerable interaction and to be bound to active site residues as well as to be located in the same cavity region. Hydrogen bonding observed during the simulation affirmed the strength of the bound cavity. Similarly, axial frequency distribution produced noteworthy knowledge of hydrogen-bonding patterns. Findings obtained from the results imply that MPC-3100 may be a suitable Hsp90 inhibitor and DRSML QAU Summary xv starting point for the actual development of an anti-cancer medication for final clinical verification. This work is an articulated example of achieving dynamics of drug repurposing for the subject addressed.