Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the trickiest pathogens. We have only a few protective shields, like the BCG vaccine against the pathogen, which itself has poor efficacy in preventing adult tuberculosis. Even though different vaccine trials for an alternative vaccine have been conducted, those studies have not shown much promising results. In the current study, advanced computational technology was used to study the potential of a novel hypothetical mycobacterial protein, identified by subtractive hybridization, to be a vaccine candidate. NHP2 (Novel Hypothetical Protein 2), housed in the RD7 region of the clinical strains of M. tuberculosis, was studied for its physical, chemical, immunological and structural properties using different computational tools. PFAM studies and Gene ontology studies depicted NHP2 protein to be functionally active with a possible antibiotic binding domain too. Different computational tools used to assess the toxicity, allergenicity and antigenicity of the protein indicated its antigenic nature. Immune Epitope Database (IEDB) tools were used to study the T and B cell determinants of the protein. The 3D structure of the protein was designed, refined and authenticated using bioinformatics tools. The validated tertiary structure of the protein was docked against the TLR3 immune receptor to study the binding affinity and docking scores. Molecular dynamic simulation of the protein-protein complex formed were studied. NHP2 was found to activate host immune response against tubercle bacillus and could be explored as a potential vaccine in the fight against tuberculosis.
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Data availability
All data supporting the findings of this study are available within the paper and its Supplementary Information. Nucleotide sequence is available in NCBI; GenBank Accession Number—GU994138.2.
Abbreviations
- BCG:
-
Bacillus Calmette Guerin
- NHP2:
-
Novel Hypothetical Protein 2
- IEDB:
-
Immune Epitope Database
- TLR3:
-
Toll Like receptor
- TB:
-
Tuberculosis
- MDR TB:
-
Multi Drug Resistant Tuberculosis
- RD:
-
Region of Differences
- ESAT:
-
Early Secreted Antigenic Target
- RvDs:
-
Rv Deletions
- NHP1:
-
Novel Hypothetical Protein 1
- NCBI:
-
National Center for Biotechnology Information
- ORF:
-
Open Reading Frames
- EMBL:
-
European Molecular Biology Laboratory
- SMS:
-
Sequence Manipulation Suite
- CDD:
-
Conserved Domain Search
- BLAST:
-
Basic Local Alignment Search Tool
- SMART:
-
Simple Modular Architecture Research Tool
- PFAM:
-
Protein Family Database
- CELLO:
-
SubCELlular LOcalization prediction
- TMHMM:
-
Trans Membrane Hidden Markov Model
- PFP FunDSeq:
-
Predicting Protein Fold Pattern with Functional Domain and Sequential Evolution Information
- CTL:
-
Cytotoxic T Lymphocyte
- HLA:
-
Human Leukocytes Antigen
- MHC:
-
Major Histocompatibility Complex
- pMHC:
-
Peptide MHC
- PSIPRED:
-
PSI-blast based secondary structure PREDiction
- SOPMA:
-
Self-Optimized Prediction Method with Alignment
- NMR:
-
Nuclear magnetic Resonance
- PDB:
-
Protein Data Bank
- MD:
-
Molecular Dynamic Simulation
- NMA:
-
Normal Mode Analysis
- Tet-R:
-
Tetracyclin Repressor
- NK cells:
-
Natural Killer cells
- RMSD:
-
Root Mean Square Deviation
- 3-D:
-
3 Dimensional
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The research work was supported by the Karnataka Science and Technology Academy (KSTA), Govt of Karnataka through the ShortTerm Research Grant.
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SS conceived the idea and KPK performed the experimental parts. Both authors were involved in data analysis, interpretation and writing the article. Both authors have read the final draft of the article.
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Kootery, K.P., Sarojini, S. In silico analysis of NHP2 membrane protein, a novel vaccine candidate present in the RD7 region of Mycobacterium tuberculosis. Biologia 79, 355–372 (2024). https://doi.org/10.1007/s11756-023-01559-4
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DOI: https://doi.org/10.1007/s11756-023-01559-4