Structural investigation of APRs to improve the solubility of outer membrane protease (PgtE) from Salmonella enterica serotype typhi- A multi-constraint approach.

Outer membrane proteins were playing a crucial role on the several functions controlled by cell membranes even though they are not naturally expressed at higher levels. In order to obtain biologically active protein, the denaturation of these inclusion bodies must be optimized using chaotropic agents. Hence, this study focuses on improving the yield of Outer Membrane Protease (PgtE) from Salmonella enterica serotype Typhi (S. Typhi) using chaotropes and additives. Denaturation methods were tried with various pH, detergents, and reducing agents were used to optimize the solubility of PgtE with biologically active form. Due to the aggregation, we failed to achieve the maximum yield of PgtE. Consequently, we predicted 9 Aggregation Prone Regions (APRs) in PgtE, which are mutated by known structural Gatekeepers. We calculated the Aggregation Index (AI) of PgtE with 10 mM of aspartic acid as an additive in optimized buffer. In addition, the mutations at specific positions within the protein structure can act as APRs suppressors without affecting protein stability with CABS flex dynamics. The multiple sequence analysis demonstrate that aspartic acid is appropriate denaturing additive for other Gram-negative pathogens of Omptin family.

In silico epitope identification of unique multidrug resistance proteins from Salmonella Typhi for vaccine development.

Typhoid fever is a multisystemic illness caused by Salmonella enterica serovars Typhi and is resistant to most antibiotics and drugs. The resistance is conferred through multidrug resistance (MDR) proteins, which efflux most antibiotics and other drugs. We predicted potential candidate B-cell and T-cell epitopes using bio- and immune-informatics tools in the 11 MDR proteins - EmrA, EmrB, EmrD, MdtA, MdtB, MdtC, MdtG, MdtH, MdtK, MdtL and TolC. The antigenic potential of the MDR proteins was calculated using VaxiJen server. The B-cell and T-cell epitopes of the MDR proteins were predicted using BCPred and ProPredI and ProPred respectively. The binding affinities of the predicted T-cell epitopes were estimated using T-epitope designer and MHCPred tools. 10, 7, 5, 12, 14, 21, 26, 3, 3 and 3 B-cell epitopes were identified in EmrA, EmrB, EmrD, TolC, MdtA, MdtB, MdtC, MdtG, MdtH and MdtL respectively. We predicted 9 T-cell epitopes - YVSRRAVQP (EmrA), FGVANAISI (EmrB), MVNSQVKQA and YQGGMVNSQ (TolC), WDRTNSHKL (MdtA), FLRNIPTAI (MdtB), YVEQLGVTG (MdtG), VKWMYAIEA (MdtH) and LAHTNTVTL (MdtL) capable of eliciting both humoral and adaptive immune responses. These T-cell epitopes specifically bind to HLA alleles - DRB1*0101 and DRB1*0401. This is the first report of epitope prediction in the MDR proteins of S. Typhi. Taken together, these results indicate the MDR proteins - EmrA, MdtA and TolC are the most suitable vaccine candidates for S. Typhi. The findings of our study on the MDR proteins prove to be useful in the development of peptide-based vaccine for the prevention and/or treatment of typhoid fever.

In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine Design of Salmonella typhi PgtE: A Molecular Dynamics Simulation Approach.

Typhoid fever is an acute illness in humans, caused by Salmonella typhi, a gram-negative bacterium. Outer membrane proteins of S. typhi have strong potential for its use in the development of subunit vaccine against typhoid. In the current study, peptide-based subunit vaccine was constructed from outer membrane protease E (PgtE) against S. typhi. B cell and T cell epitopes were identified at fold level with a validated three-dimensional modeled structure. T cell epitopes from PgtE (IHPDTSANY) have 99.5% binding to a maximum number of major histocompatibility complex class I and class II alleles. They also bind to the typhoid-resistant human leukocyte antigen (HLA) alleles DRB1*0401. PgtE epitopes were docked with HLA-DR4 (PDB ID: 1D5M) and a contact map was constructed. A simulation search for the binding site for full flexibility of the peptide from CABS- (Cα, Cß, side-chain)-dock shows stable interactions. Molecular dynamics simulation studies revealed that the PgtE-epitope complex structure was more stable throughout the simulation (20 ns) and interaction did not change the radius of gyration. In conclusion, computational analysis, molecular docking, and molecular dynamics (MD) simulation of PgtE-epitope complex were used to elucidate the binding mode, and the dynamical changes of epitopes were more suitable for vaccine development against typhoid.

B-cell and T-cell epitope identification with stability analysis of AI-2 import ATP-binding cassette LsrA from S. typhiIn silico approach.

Typhoid fever is a severe illness in humans, caused by Salmonella typhi, a Gram-negative bacterium. Membrane proteins of S. typhi have strong potential for its use in development of subunit vaccine against typhoid. In current study, peptide-based subunit vaccine constructed from AI-2 import ATP-binding cassette transporter protein (LsrA) against S. typhi. B-cell and T-cell epitopes were identified at fold level with validated 3-D theoretical modelled structure. T-cell epitope from LsrA (LELPGSRPQ) has binds to maximum number (82.93%) of MHC class I and class II alleles. LsrA epitope was docked with HLA-DR4 and contact map were constructed to analyze molecular interaction (docking) studies. Simulation search for the binding site for full flexibility of the peptide from CABS-dock shows the stable interactions. MD simulation analysis reveals that LsrA epitope was binding and interacting firmly with the HLA-DR4. Hence, we are proposing that LsrA epitope would be a prominent epitope vaccine for human specific pathogen of S. typhi, which requires further steps to be elevated as a vaccine drug in near future.

Mutation and docking studies on NS2b-NS3 complex from yellow fever virus towards drug discovery.

UNLABELLED: Yellow fever virus is the causative agent of Yellow fever. The genome of the virus contains three structural and seven non-structural proteins. Of these seven nonstructural proteins, NS2B-NS3 protein complex has protease activity required for viral replication. Predicting the 3D structure of this complex and studying the interaction of residues at the recognized catalytic triad of the complex is an integral part to understand the virus replication mechanism. In the present study, the structure was determined for NS2B-NS3 complex by Homology modeling and modeled structure was validated for its stability. Mutation studies at the residues His94, Asp118 and Ser176 revealed that Asp118-His94 bond played an important role in the structural stability of NS2B-NS3 complex. This indicates site-directed mutagenesis, controlling YFV replication, as one mechanism to design vaccine strains. Docking studies of the bioactive compounds at the active site of NS2B-NS3 complex also indicated 4-hydroxypanduratin A as potential lead compound for drug development. The theoretical models will further pave way to experimentally verify our mutation and docking studies, thus taking a lead in pharmacogenomics and drug development. ABBREVIATIONS: YFV - Yellow Fever Virus, WNV - West Nile Virus, H-bonds - hydrogen bonds, SNP - Single nucleotide polymorphism.