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Ahammad I, Bushra Lamisa A, Sharmin S, Bhattacharjee A, Mahmud Chowdhury Z, Ahamed T, Uzzal Hossain M, Chandra Das K, Salimullah M, Ara Keya C. Subtractive genomics study for the identification of therapeutic targets against Cronobacter sakazakii: A threat to infants. Heliyon 2024; 10:e30332. [PMID: 38707387 PMCID: PMC11066692 DOI: 10.1016/j.heliyon.2024.e30332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen that has been associated with severe infection in neonates such as necrotizing enterocolitis (NEC), neonatal meningitis, and bacteremia. This pathogen can survive in a relatively dry environment, especially in powdered infant formula (PIF). Unfortunately, conventional drugs that were once effective against C. sakazakii are gradually losing their efficacy due to rising antibiotic resistance. In this study, a subtractive genomic approach was followed in order to identify potential therapeutic targets in the pathogen. The whole proteome of the pathogen was filtered through a step-by-step process, which involved removing paralogous proteins, human homologs, sequences that are less essential for survival, proteins with shared metabolic pathways, and proteins that are located in cells other than the cytoplasmic membrane. As a result, nine novel drug targets were identified. Further, the analysis also unveiled that the FDA-approved drug Terbinafine can be repurposed against the Glutathione/l-cysteine transport system ATP-binding/permease protein CydC of C. sakazakii. Moreover, molecular docking and dynamics studies of Terbinafine and CydC suggested that this drug can be used to treat C. sakazakii infection in neonates. However, for clinical purposes further in vitro and in vivo studies are necessary.
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Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Anika Bushra Lamisa
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Sadia Sharmin
- Department of Biotechnology & Genetic Engineering, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Tanvir Ahamed
- Department of Biotechnology & Genetic Engineering, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
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Begum A, Modumudi S, Subramani S, Khoont D, Vanaparti A, Master M, Khan J, Botticelli AL, Botticelli RW, Mian HS, Saad M, Abbas K. Novel putative biomarkers for infective endocarditis by serum proteomic analysis: a comprehensive review of literature. Ann Med Surg (Lond) 2023; 85:5497-5503. [PMID: 37915652 PMCID: PMC10617819 DOI: 10.1097/ms9.0000000000001249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/19/2023] [Indexed: 11/03/2023] Open
Abstract
Infective endocarditis (IE) is a challenging condition with high mortality. Prompt detection of IE has become essential for early and immediate management. The authors aimed to comprehensively review the existing literature on novel putative biomarkers for IE through serum proteomic analysis. The literature reveals high levels of N-terminal-pro-B-type natriuretic peptide (NT-proBNP) levels in IE with staphylococcal etiology, valvular lesions, and when combined with cardiac troponin I (cTnI), had a more significant value for risk stratification. A higher pro-ADM level, copeptin, NT-proBNP, and the monocyte-to-high-density lipoprotein cholesterol ratio (MHR) all impacted mortality during the hospital stay. The biomarker matrix metalloproteinase-9 was utilized to predict new-onset embolic events in patients, thus serving as a predictive marker. Procalcitonin was an important diagnostic marker in IE complicated with severe infection. Interleukin-6 (IL-6), Interleukin-8 (IL-8), Interferon-γ, cTnI, and NT-proBNP were also discovered to be useful as prognostic indicators. Early diagnosis and appropriate treatment are possible using antiphospholipid antibodies as a diagnostic test for definite IE. It is also concluded that antineutrophilic cytoplasmic antibody positive individuals with IE had a lengthier hospital stay. These noninvasive biomarkers can identify patients at risk and provide appropriate and early clinical management. NT-proBNP, Cystatin C, troponins, IL-6, IL-8, S100A11, and AQP9 are examples of possible markers that appear promising for further research. In conclusion, large-scale validation studies should study these biomarkers further to establish their use in clinical settings.
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Affiliation(s)
| | - Sravani Modumudi
- Department of Medicine, Kamineni Academy of Medical Sciences and Research Center, Hyderabad
| | - Sachin Subramani
- Department of Internal Medicine, ESIC Medical College and Hospital
| | - Dhruvi Khoont
- Department of Medicine, Narendra Modi Medical College
| | - Ankitha Vanaparti
- Department of Internal Medicine, Kakatiya Medical College, Warangal, Telangana State, India
| | - Mahima Master
- Department of Medicine, LG Hospital, Maninagar, Ahmedabad
| | - Javeria Khan
- Department of Adult Cardiology, National Institute of Cardiovascular Diseases
| | | | | | - Hafsa S. Mian
- Department of Medicine, Sheikh Zayed Hospital, Rahimyar Khan, Lahore, Pakistan
| | - Muhammad Saad
- Department of Medicine, FMH College of Medicine and Dentistry
| | - Kiran Abbas
- Department of Community Health Sciences, Aga Khan University, Karachi
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Sarker P, Mitro A, Hoque H, Hasan MN, Nurnabi Azad Jewel GM. Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Comput Biol Med 2023; 165:107436. [PMID: 37690289 DOI: 10.1016/j.compbiomed.2023.107436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.
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Affiliation(s)
- Parth Sarker
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Arnob Mitro
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Hammadul Hoque
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - Md Nazmul Hasan
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - G M Nurnabi Azad Jewel
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh.
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Šurín Hudáková N, Kačírová J, Sondorová M, Šelianová S, Mucha R, Maďar M. Inhibitory Effect of Bacillus licheniformis Strains Isolated from Canine Oral Cavity. Life (Basel) 2022; 12:life12081238. [PMID: 36013417 PMCID: PMC9409769 DOI: 10.3390/life12081238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Bacillus licheniformis is used in a broad spectrum of areas, including some probiotic preparations for human and veterinary health. Moreover, B. licheniformis strains are known producers of various bioactive substances with antimicrobial and antibiofilm effects. In searching for new potentially beneficial bacteria for oral health, the inhibitory effect of B. licheniformis strains isolated from canine dental biofilm against pathogenic oral bacteria was evaluated. The antimicrobial effect of neutralized cell-free supernatants (nCFS) was assessed in vitro on polystyrene microtiter plates. Furthermore, molecular and morphological analyses were executed to evaluate the production of bioactive substances. To determine the nature of antimicrobial substance present in nCFS of B. licheniformis A-1-5B-AP, nCFS was exposed to the activity of various enzymes. The nCFS of B. licheniformis A-1-5B-AP significantly (p < 0.0001) reduced the growth of Porphyromonas gulae 3/H, Prevotella intermedia 1/P and Streptococcus mutans ATCC 35668. On the other hand, B. licheniformis A-2-11B-AP only significantly (p < 0.0001) inhibited the growth of P. intermedia 1/P and S. mutans ATCC 35668. However, enzyme-treated nCFS of B. licheniformis A-1-5B-AP did not lose its antimicrobial effect and significantly (p < 0.0001) inhibited the growth of Micrococcus luteus DSM 1790. Further studies are needed for the identification of antimicrobial substances.
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Affiliation(s)
- Natália Šurín Hudáková
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Jana Kačírová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Miriam Sondorová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Svetlana Šelianová
- Clinic of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of Pavol Jozef Safarik in Kosice, 040 01 Kosice, Slovakia
| | - Rastislav Mucha
- Institute of Neurobiology, Biomedical Research Center of the Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
| | - Marián Maďar
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 041 81 Kosice, Slovakia
- Correspondence: ; Tel.: +421-9-4971-5632
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