Proteome level analysis of drug-resistant Prevotella melaninogenica for the identification of novel therapeutic candidates

Abstract

The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. Prevotella melaninogenica, a gram-negative bacterium, was found to be involved in various infections of the respiratory tract, aerodigestive tract, and gastrointestinal tract. The need to explore novel drug and vaccine targets against this pathogen was triggered by the emergence of antimicrobial resistance against reported antibiotics to combat P. melaninogenica infections. The study involves core genes acquired from 14 complete P. melaninogenica strain genome sequences, where promiscuous drug and vaccine candidates were explored by state-of-the-art subtractive proteomics and reverse vaccinology approaches. A stringent bioinformatics analysis enlisted 18 targets as novel, essential, and non-homologous to humans and having druggability potential. Moreover, the extracellular and outer membrane proteins were subjected to antigenicity, allergenicity, and physicochemical analysis for the identification of the candidate proteins to design multi-epitope vaccines. Two candidate proteins (ADK95685.1 and ADK97014.1) were selected as the best target for the designing of a vaccine construct. Lead B- and T-cell overlapped epitopes were joined to generate potential chimeric vaccine constructs in combination with adjuvants and linkers. Finally, a prioritized vaccine construct was found to have stable interactions with the human immune cell receptors as confirmed by molecular docking and MD simulation studies. The vaccine construct was found to have cloning and expression ability in the bacterial cloning system. Immune simulation ensured the elicitation of significant immune responses against the designed vaccine. In conclusion, our study reported novel drug and vaccine targets and designed a multi-epitope vaccine against the P. melaninogenica infection. Further experimental validation will help open new avenues in the treatment of this multi-drug-resistant pathogen.

Deciphering the Immunogenicity of Monkeypox Proteins for Designing the Potential mRNA Vaccine

“…Linkers play an essential role in joining the epitopes and help in the proper functioning of the vaccines . Following a rigorous investigation, different linkers (AAY, GPGPG, and KK) were used to connect the finalized B- and T-cell epitopes in order to create a vaccine construct. , These linkers are immunogenic and boost the immunogenicity of the designed vaccines. Furthermore, linkers help prevent the epitope-folding and keep the epitopes separated from each other .…”

“…The Swiss Homology Modeling server was applied to infer the tertiary structure, and the Galaxyrefine Web server then refined it. Additionally, the Ramachandran plot in PROCHECK and the quality factor at the ERRAT Web server were estimated to validate the structure’s 3D quality …”

“…Additionally, the Ramachandran plot in PROCHECK 48 and the quality factor at the ERRAT Web server were estimated to validate the structure's 3D quality. 49 2.9. Prediction of Conformational B-Lymphocyte Epitopes.…”

Structural informatics approach for designing an epitope-based vaccine against the brain-eating Naegleria fowleri

“…For determination of the stability between the final potential vaccine construct i.e., V1 with the human immune receptors, the MD simulation was carried for 100 ns using standard protocol of GROMACS ( 24 ). The Figure 7 shows the results obtained for V1-TLR2 where radius of gyration (Rg), RMSD and RMSF analysis of both proteins chains as function of time (ns) and residues, respectively, were analyzed.…”

“…Furthermore, their physicochemical properties were checked using the Protparam Expasy server ( 22 ) and the TMHMM server was used to check the topology values of all proteins. The most antigenic, stable, and non-allergenic proteins were selected as the vaccine candidates ( 23 , 24 ).…”