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A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough
Bordetella pertussis is a Gram-negative bacterium known to cause pertussis or whooping cough. The disease affects the respiratory system and is contagious. Pertussis causes high mortality among infants aged less than one-year-old, although it can affect anyone of any age. Globally, 16 million cases...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9692278/ https://www.ncbi.nlm.nih.gov/pubmed/36423010 http://dx.doi.org/10.3390/vaccines10111915 |
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author | Jamal, Alam Jahan, Sadaf Choudhry, Hani Rather, Irfan A. Khan, Mohammad Imran |
author_facet | Jamal, Alam Jahan, Sadaf Choudhry, Hani Rather, Irfan A. Khan, Mohammad Imran |
author_sort | Jamal, Alam |
collection | PubMed |
description | Bordetella pertussis is a Gram-negative bacterium known to cause pertussis or whooping cough. The disease affects the respiratory system and is contagious. Pertussis causes high mortality among infants aged less than one-year-old, although it can affect anyone of any age. Globally, 16 million cases of pertussis were reported in 2008, 95% of which were in developing nations, and approximately 195,000 children died from the disease. Under a computational subtractive genomics approach, the total proteome of a pathogen is gently trimmed down to a few potential drug targets. First, from NCBI, we obtained the pathogen proteins followed by CD hit for removal of duplicate proteins. The BLAST step was applied to find non-similar proteins, and then, we applied BLAST to these non-similar bacterial proteins with DEG to find essential bacterial proteins. After this, to find the location, these vital proteins were screened via PSORTb; the majority of proteins were in cytoplasm. The KASS server was used to determine the involvement of these proteins in the metabolic pathways of bacteria, and KEGG was applied to find the unique metabolic pathways of the pathogen. Finally, we applied BLAST to these vital, unique, and non-similar proteins with FDA-approved drug targets, and four proteins of the B. pertussis strain B1917 were identified that might be powerful drug targets. A variety of therapeutic molecules could be designed to target these proteins in order to treat infections caused by bacteria. |
format | Online Article Text |
id | pubmed-9692278 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96922782022-11-26 A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough Jamal, Alam Jahan, Sadaf Choudhry, Hani Rather, Irfan A. Khan, Mohammad Imran Vaccines (Basel) Article Bordetella pertussis is a Gram-negative bacterium known to cause pertussis or whooping cough. The disease affects the respiratory system and is contagious. Pertussis causes high mortality among infants aged less than one-year-old, although it can affect anyone of any age. Globally, 16 million cases of pertussis were reported in 2008, 95% of which were in developing nations, and approximately 195,000 children died from the disease. Under a computational subtractive genomics approach, the total proteome of a pathogen is gently trimmed down to a few potential drug targets. First, from NCBI, we obtained the pathogen proteins followed by CD hit for removal of duplicate proteins. The BLAST step was applied to find non-similar proteins, and then, we applied BLAST to these non-similar bacterial proteins with DEG to find essential bacterial proteins. After this, to find the location, these vital proteins were screened via PSORTb; the majority of proteins were in cytoplasm. The KASS server was used to determine the involvement of these proteins in the metabolic pathways of bacteria, and KEGG was applied to find the unique metabolic pathways of the pathogen. Finally, we applied BLAST to these vital, unique, and non-similar proteins with FDA-approved drug targets, and four proteins of the B. pertussis strain B1917 were identified that might be powerful drug targets. A variety of therapeutic molecules could be designed to target these proteins in order to treat infections caused by bacteria. MDPI 2022-11-12 /pmc/articles/PMC9692278/ /pubmed/36423010 http://dx.doi.org/10.3390/vaccines10111915 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Jamal, Alam Jahan, Sadaf Choudhry, Hani Rather, Irfan A. Khan, Mohammad Imran A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough |
title | A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough |
title_full | A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough |
title_fullStr | A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough |
title_full_unstemmed | A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough |
title_short | A Subtraction Genomics-Based Approach to Identify and Characterize New Drug Targets in Bordetella pertussis: Whooping Cough |
title_sort | subtraction genomics-based approach to identify and characterize new drug targets in bordetella pertussis: whooping cough |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9692278/ https://www.ncbi.nlm.nih.gov/pubmed/36423010 http://dx.doi.org/10.3390/vaccines10111915 |
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