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Chakraborty S, Askari M, Barai RS, Idicula‐Thomas S. PBIT V3 : A robust and comprehensive tool for screening pathogenic proteomes for drug targets and prioritizing vaccine candidates. Protein Sci 2024; 33:e4892. [PMID: 38168465 PMCID: PMC10804677 DOI: 10.1002/pro.4892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Abstract
Rise of life-threatening superbugs, pandemics and epidemics warrants the need for cost-effective and novel pharmacological interventions. Availability of publicly available proteomes of pathogens supports development of high-throughput discovery platforms to prioritize potential drug-targets and develop testable hypothesis for pharmacological screening. The pipeline builder for identification of target (PBIT) was developed in 2016 and updated in 2021, with the purpose of accelerating the search for drug-targets by integration of methods like comparative and subtractive genomics, essentiality/virulence and druggability analysis. Since then, it has been used for identification of drugs and vaccine targets, safety profiling of multiepitope vaccines and mRNA vaccine construction against a broad-spectrum of pathogens. This tool has now been updated with functionalities related to systems biology and immuno-informatics and validated by analyzing 48 putative antigens of Mycobacterium tuberculosis documented in literature. PBITv3 available as both online and offline tools will enhance drug discovery against emerging drug-resistant infectious agents. PBITv3 can be freely accessed at http://pbit.bicnirrh.res.in/.
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Affiliation(s)
- Shuvechha Chakraborty
- Biomedical Informatics Centre, ICMR‐National Institute for Research in Reproductive and Child HealthMumbaiMaharashtraIndia
| | - Mehdi Askari
- Department of BioinformaticsGuru Nanak Khalsa College, Nathalal Parekh MargMumbaiMaharashtraIndia
| | - Ram Shankar Barai
- Biological Sciences DivisionICMR‐National Institute of Occupational HealthAhmedabadGujratIndia
| | - Susan Idicula‐Thomas
- Biomedical Informatics Centre, ICMR‐National Institute for Research in Reproductive and Child HealthMumbaiMaharashtraIndia
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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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