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Khan A, Ammar Zahid M, Farrukh F, Salah Abdelsalam S, Mohammad A, Al-Zoubi RM, Shkoor M, Ait Hssain A, Wei DQ, Agouni A. Integrated structural proteomics and machine learning-guided mapping of a highly protective precision vaccine against mycoplasma pulmonis. Int Immunopharmacol 2024; 141:112833. [PMID: 39153303 DOI: 10.1016/j.intimp.2024.112833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/09/2024] [Accepted: 07/27/2024] [Indexed: 08/19/2024]
Abstract
Mycoplasma pulmonis (M. pulmonis) is an emerging respiratory infection commonly linked to prostate cancer, and it is classified under the group of mycoplasmas. Improved management of mycoplasma infections is essential due to the frequent ineffectiveness of current antibiotic treatments in completely eliminating these pathogens from the host. The objective of this study is to design and construct effective and protective vaccines guided by structural proteomics and machine learning algorithms to provide protection against the M. pulmonis infection. Through a thorough examination of the entire proteome of M. pulmonis, four specific targets Membrane protein P80, Lipoprotein, Uncharacterized protein and GGDEF domain-containing protein have been identified as appropriate for designing a vaccine. The proteins underwent mapping of cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) (IFN)-γ ±, and B-cell epitopes using artificial and recurrent neural networks. The design involved the creation of mRNA and peptide-based vaccine, which consisted of 8 CTL epitopes associated by GGS linkers, 7 HTL (IFN-positive) epitopes, and 8 B-cell epitopes joined by GPGPG linkers. The vaccine designed exhibit antigenic behavior, non-allergenic qualities, and exceptional physicochemical attributes. Structural modeling revealed that correct folding is crucial for optimal functioning. The coupling of the MEVC and Toll-like Receptors (TLR)1, TLR2, and TLR6 was examined through molecular docking experiments. This was followed by molecular simulation investigations, which included binding free energy estimations. The results indicated that the dynamics of the interaction were stable, and the binding was strong. In silico cloning and optimization analysis revealed an optimized sequence with a GC content of 49.776 % and a CAI of 0.982. The immunological simulation results showed strong immune responses, with elevated levels of active and plasma B-cells, regulatory T-cells, HTL, and CTL in both IgM+IgG and secondary immune responses. The antigen was completely cleared by the 50th day. This study lays the foundation for creating a potent and secure vaccine candidate to combat the newly identified M. pulmonis infection in people.
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Affiliation(s)
- Abbas Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Muhammad Ammar Zahid
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Farheen Farrukh
- Gujranwala Medical College, 5 KM Alipur Chatha Rd, Gondlanwala Rd, Gujranwala, Pakistan
| | - Shahenda Salah Abdelsalam
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Raed M Al-Zoubi
- Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha, Qatar; Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Department of Chemistry, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan.
| | - Mohanad Shkoor
- Department of Chemistry, College of Arts and Science, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad Medical Corporation, Doha, Qatar
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
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Khan K, Burki S, Alsaiari AA, Alhuthali HM, Alharthi NS, Jalal K. A therapeutic epitopes-based vaccine engineering against Salmonella enterica XDR strains for typhoid fever: a Pan-vaccinomics approach. J Biomol Struct Dyn 2024; 42:8559-8573. [PMID: 37578072 DOI: 10.1080/07391102.2023.2246587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/05/2023] [Indexed: 08/15/2023]
Abstract
A prevalent food-borne pathogen, Salmonella enterica serotypes Typhi, is responsible for gastrointestinal and systemic infections globally. Salmonella vaccines are the most effective, however, producing a broad-spectrum vaccine remains challenging due to Salmonella's many serotypes. Efforts are urgently required to develop a novel vaccine candidate that can tackle all S. Typhi strains because of their high resistance to multiple kinds of antibiotics (particularly the XDR H58 strain). In this work, we used a computational pangenome-based vaccine design technique on all available (n = 119) S. Typhi reference genomes and identified one TonB-dependent siderophore receptor (WP_001034967.1) as highly conserved and prospective vaccine candidates from the predicted core genome (n = 3,351). The applied pan-proteomics and Immunoinformatic approaches help in the identification of four epitopes that may trigger adequate host body immune responses. Furthermore, the proposed vaccine ensemble demonstrates a stable binding conformation with the examined immunological receptor (HLAs and TRL2/4) and has large interaction energy determined via molecular docking and molecular dynamics simulation techniques. Eventually, an expression vector for the Escherichia. coli K12 strain was constructed from the vaccine sequence. Additional analysis revealed that the vaccine may help to elicit strong immune responses for typhoid infections, however, experimental analysis is required to verify the vaccine's effectiveness based on these results. Moreover, the applied computer-assisted vaccine design may considerably decrease vaccine development costs and speed up the process. The study's findings are intriguing, but they must be evaluated in the experimental labs to confirm the developed vaccine's biological efficiency against XDR S. Typhi.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Samiullah Burki
- Department of Pharmacology, Institute of Pharmaceutical Sciences, Jinnah Sindh Medical University, Karachi, Pakistan
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Hayaa M Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Nahed S Alharthi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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3
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Granata I, Maddalena L, Manzo M, Guarracino MR, Giordano M. HELP: A computational framework for labelling and predicting human common and context-specific essential genes. PLoS Comput Biol 2024; 20:e1012076. [PMID: 39331694 DOI: 10.1371/journal.pcbi.1012076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/19/2024] [Indexed: 09/29/2024] Open
Abstract
Machine learning-based approaches are particularly suitable for identifying essential genes as they allow the generation of predictive models trained on features from multi-source data. Gene essentiality is neither binary nor static but determined by the context. The databases for essential gene annotation do not permit the personalisation of the context, and their update can be slower than the publication of new experimental data. We propose HELP (Human Gene Essentiality Labelling & Prediction), a computational framework for labelling and predicting essential genes. Its double scope allows for identifying genes based on dependency or not on experimental data. The effectiveness of the labelling method was demonstrated by comparing it with other approaches in overlapping the reference sets of essential gene annotations, where HELP demonstrated the best compromise between false and true positive rates. The gene attributes, including multi-omics and network embedding features, lead to high-performance prediction of essential genes while confirming the existence of essentiality nuances.
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Affiliation(s)
- Ilaria Granata
- Institute for High-Performance Computing and Networking, National Research Council, Naples, Italy
| | - Lucia Maddalena
- Institute for High-Performance Computing and Networking, National Research Council, Naples, Italy
| | - Mario Manzo
- Information Technology Services, University of Naples "L'Orientale", Naples, Italy
| | - Mario Rosario Guarracino
- Laboratory of Algorithms and Technologies for Network Analysis, National Research University Higher School of Economics, Nizhny Novgorod, Russia
- Department of Economics and Law, University of Cassino and Southern Lazio, Cassino, Frosinone, Italy
| | - Maurizio Giordano
- Institute for High-Performance Computing and Networking, National Research Council, Naples, Italy
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Borges KCM, Costa VAF, Neves B, Kipnis A, Junqueira-Kipnis AP. New antibacterial candidates against Acinetobacter baumannii discovered by in silico-driven chemogenomics repurposing. PLoS One 2024; 19:e0307913. [PMID: 39325805 PMCID: PMC11426455 DOI: 10.1371/journal.pone.0307913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/14/2024] [Indexed: 09/28/2024] Open
Abstract
Acinetobacter baumannii is a worldwide Gram-negative bacterium with a high resistance rate, responsible for a broad spectrum of hospital-acquired infections. A computational chemogenomics framework was applied to investigate the repurposing of approved drugs to target A. baumannii. This comprehensive approach involved compiling and preparing proteomic data, identifying homologous proteins in drug-target databases, evaluating the evolutionary conservation of targets, and conducting molecular docking studies and in vitro assays. Seven drugs were selected for experimental assays. Among them, tavaborole exhibited the most promising antimicrobial activity with a minimum inhibitory concentration (MIC) value of 2 μg/ml, potent activity against several clinically relevant strains, and robust efficacy against biofilms from multidrug-resistant strains at a concentration of 16 μg/ml. Molecular docking studies elucidated the binding modes of tavaborole in the editing and active domains of leucyl-tRNA synthetase, providing insights into its structural basis for antimicrobial activity. Tavaborole shows promise as an antimicrobial agent for combating A. baumannii infections and warrants further investigation in preclinical studies.
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Affiliation(s)
- Kellen Christina Malheiros Borges
- Molecular Bacteriology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
- Microbiology Laboratory, Department of Biology, Academic Areas, Federal Institute of Goiás, Anápolis, Goiás, Brazil
| | | | - Bruno Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - André Kipnis
- Molecular Bacteriology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Ana Paula Junqueira-Kipnis
- Molecular Bacteriology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
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Chand Y, Jain T, Singh S. Unveiling a Comprehensive Multi-epitope Subunit Vaccine Strategy Against Salmonella subsp. enterica: Bridging Core, Subtractive Proteomics, and Immunoinformatics. Cell Biochem Biophys 2024; 82:2901-2936. [PMID: 39018007 DOI: 10.1007/s12013-024-01407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
Salmonella subsp. enterica (SE) presents a significant global health challenge in both developed and developing countries. Current SE vaccines have limitations, targeting specific strains and demonstrating moderate efficacy in adults, while also being unsuitable for young children and often unaffordable in regions with lower income levels where the disease is prevalent. To address these challenges, this study employed a computational approach integrating core proteomics, subtractive proteomics, and immunoinformatics to develop a universal SE vaccine and identify potential drug targets. Analysis of the core proteome of 185 SE strains revealed 1964 conserved proteins. Subtractive proteomics identified 9 proteins as potential vaccine candidates and 41 as novel drug targets. Using reverse vaccinology-based immunoinformatics, four multi-epitope-based subunit vaccine constructs (MESVCs) were designed, aiming to stimulate cytotoxic T lymphocyte, helper T lymphocyte, and linear B lymphocyte responses. These constructs underwent comprehensive evaluations for antigenicity, immunogenicity, toxicity, hydropathicity, and physicochemical properties. Predictive modeling, refinement, and validation were conducted to determine the secondary and tertiary structures of the SE-MESVCs, followed by docking studies with MHC-I, MHC-II, and TLR4 receptors. Molecular docking assessments showed favorable binding with all three receptors, with SE-MESVC-4 exhibiting the most promising binding energy. Molecular dynamics simulations confirmed the binding affinity and stability of SE-MESVC-4 with the TLR4/MD2 complex. Additionally, codon optimization and in silico cloning verified the efficient translation and successful expression of SE-MESVC-4 in Escherichia coli (E. coli) str. K12. Subsequent in silico immune simulation evaluated the efficacy of SE-MESVC-4 in triggering an effective immune response. These results suggest that SE-MESVC-4 may induce both humoral and cellular immune responses, making it a potential candidate for an effective SE vaccine. However, further experimental investigations are necessary to validate the immunogenicity and efficacy of SE-MESVC-4, bringing us closer to effectively combating SE infections.
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Affiliation(s)
- Yamini Chand
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Tanvi Jain
- Faculty of Biotechnology, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Sachidanand Singh
- Department of Biotechnology, School of Energy and Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, Gujarat, India.
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Santos AS, Costa VAF, Freitas VAQ, Dos Anjos LRB, de Almeida Santos ES, Arantes TD, Costa CR, de Sene Amâncio Zara AL, do Rosário Rodrigues Silva M, Neves BJ. Drug to genome to drug: a computational large-scale chemogenomics screening for novel drug candidates against sporotrichosis. Braz J Microbiol 2024; 55:2655-2667. [PMID: 38888692 PMCID: PMC11405749 DOI: 10.1007/s42770-024-01406-x] [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: 03/01/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
Sporotrichosis is recognized as the predominant subcutaneous mycosis in South America, attributed to pathogenic species within the Sporothrix genus. Notably, in Brazil, Sporothrix brasiliensis emerges as the principal species, exhibiting significant sapronotic, zoonotic and enzootic epidemic potential. Consequently, the discovery of novel therapeutic agents for the treatment of sporotrichosis is imperative. The present study is dedicated to the repositioning of pharmaceuticals for sporotrichosis therapy. To achieve this goal, we designed a pipeline with the following steps: (a) compilation and preparation of Sporothrix genome data; (b) identification of orthologous proteins among the species; (c) identification of homologous proteins in publicly available drug-target databases; (d) selection of Sporothrix essential targets using validated genes from Saccharomyces cerevisiae; (e) molecular modeling studies; and (f) experimental validation of selected candidates. Based on this approach, we were able to prioritize eight drugs for in vitro experimental validation. Among the evaluated compounds, everolimus and bifonazole demonstrated minimum inhibitory concentration (MIC) values of 0.5 µg/mL and 4.0 µg/mL, respectively. Subsequently, molecular docking studies suggest that bifonazole and everolimus may target specific proteins within S. brasiliensis- namely, sterol 14-α-demethylase and serine/threonine-protein kinase TOR, respectively. These findings shed light on the potential binding affinities and binding modes of bifonazole and everolimus with their probable targets, providing a preliminary understanding of the antifungal mechanism of action of these compounds. In conclusion, our research advances the understanding of the therapeutic potential of bifonazole and everolimus, supporting their further investigation as antifungal agents for sporotrichosis in prospective hit-to-lead and preclinical investigations.
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Affiliation(s)
- Andressa Santana Santos
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | | | | | - Laura Raniere Borges Dos Anjos
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | | | - Thales Domingos Arantes
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carolina Rodrigues Costa
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Ana Laura de Sene Amâncio Zara
- Postgraduate Program in Health Technology Assistance and Assessment (PPG-AAS), Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | | | - Bruno Junior Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil.
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Zhang Y, Sun Q, Meng W, Xie L, Li N, Zhang J, Zhang T, Guan Y, Ma L. Comprehensive analysis of GINS subunit expression, prognostic value, and immune infiltration in clear cell renal cell carcinoma. Transl Androl Urol 2024; 13:1517-1536. [PMID: 39280654 PMCID: PMC11399050 DOI: 10.21037/tau-24-95] [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: 02/20/2024] [Accepted: 06/14/2024] [Indexed: 09/18/2024] Open
Abstract
Background In recent decades, there has been increasing evidence that Go-Ichi-Nii-San (GINS) subunits play an important role in the development and progression of various tumors. However, little research has been conducted on the role of GINS subunits in clear cell renal cell carcinoma (ccRCC). This study sought to explore the differential expression, prognosis, and immunological significance of GINS subunits in ccRCC. Methods We used various analysis packages of R (version 3.6.3), the University of ALabama at Birmingham CANcer (UALCAN) data analysis portal, the Cancer Cell Line Encyclopedia (CCLE), the cBio Cancer Genomics Portal (cBioPortal), and the Tumor Immune Estimation Resource (TIMER) to study the gene expression, promoter methylation level, gene mutations, prognostic and diagnostic value, immune infiltration, pathway enrichment, and other aspects of the GINS subunits. Next, the genes related to the GINS subunits were analyzed using the STRING and GeneMANIA platforms, and the correlation between GINS subunits and the functions involved were investigated. Results The expression level of GINS1/2/3/4 was significantly higher in ccRCC tumor tissues than normal tissues, and was significantly related to tumor grade and stage. The expression of GINS1/2/4 may be related to the methylation degree of the promoter region. The prognostic and diagnostic analyses showed that the increased expression of GINS1 was associated with various poor prognoses and had diagnostic value. The GINS subunit mutation also significantly affected the clinical prognosis of ccRCC patients. Finally, the correlation analysis of the immune infiltration level, co-expression, and enrichment of related genes indicated that GINS subunit expression was associated with different levels of ccRCC immune infiltration. Conclusions The analysis results showed that the differential expression of GINS subunits in ccRCC, which had prognostic and diagnostic value, was correlated with clinicopathological stage, immune infiltration, and other related aspects. GINS1 may serve as a new potential prognostic biomarker for ccRCC patients and be used to guide treatment.
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Affiliation(s)
- Yuxiang Zhang
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Qian Sun
- Department of Respiratory Medicine, The First People's Hospital of Yancheng, Yancheng, China
| | - Wei Meng
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Lingling Xie
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ningning Li
- Xinglin College, Nantong University, Nantong, China
| | - Jiayi Zhang
- Xinglin College, Nantong University, Nantong, China
| | - Tong Zhang
- Xinglin College, Nantong University, Nantong, China
| | - Yangbo Guan
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Limin Ma
- Department of Urology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
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Xu N, Zuo J, Li C, Gao C, Guo M. Reconstruction and Analysis of a Genome-Scale Metabolic Model of Acinetobacter lwoffii. Int J Mol Sci 2024; 25:9321. [PMID: 39273268 PMCID: PMC11395192 DOI: 10.3390/ijms25179321] [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: 06/30/2024] [Revised: 07/31/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii.
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Affiliation(s)
- Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jiaojiao Zuo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Chenghao Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
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Qian J, Jin P, Yang Y, Ma N, Yang Z, Zhang X. Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models. Microb Pathog 2024; 193:106727. [PMID: 38851362 DOI: 10.1016/j.micpath.2024.106727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat to public health. The protein function of this bacterium is not well known, thus a systematic investigation of K. pneumoniae proteome is in urgent need. In this study, the protein functions of this bacteria were re-annotated, and their function groups were analyzed. Moreover, three machine learning models were built to identify novel virulence factors. Results showed that the functions of 16 uncharacterized proteins were first annotated by sequence alignment. In addition, K. pneumoniae proteins share a high proportion of homology with Haemophilus influenzae and a low homology proportion with Chlamydia pneumoniae. By sequence analysis, 10 proteins were identified as potential drug targets for this bacterium. Our model achieved a high accuracy of 0.901 in the benchmark dataset. By applying our models to K. pneumoniae, we identified 39 virulence factors in this pathogen. Our findings could provide novel clues for the treatment of K. pneumoniae infection.
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Affiliation(s)
- Jinyang Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Pengfei Jin
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Yueyue Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Xiaoli Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
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Ravindranath BS, Ananya G, Hema Kumar C, Ramirez DC, Gomez Mejiba SE. Computational prediction of crucial genes involved in gonorrhea infection and neoplastic cell transformation: A multiomics approach. Microb Pathog 2024; 193:106770. [PMID: 38960215 DOI: 10.1016/j.micpath.2024.106770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/24/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Neisseria gonorrheae, the causative agent of genitourinary infections, has been associated with asymptomatic or recurrent infections and has the potential to form biofilms and induce inflammation and cell transformation. Herein, we aimed to use computational analysis to predict novel associations between chronic inflammation caused by gonorrhea infection and neoplastic transformation. Prioritization and gene enrichment strategies based on virulence and resistance genes utilizing essential genes from the DEG and PANTHER databases, respectively, were performed. Using the STRING database, protein‒protein interaction networks were constructed with 55 nodes of bacterial proteins and 72 nodes of proteins involved in the host immune response. MCODE and cytoHubba were used to identify 12 bacterial hub proteins (murA, murB, murC, murD, murE, purN, purL, thyA, uvrB, kdsB, lpxC, and ftsH) and 19 human hub proteins, of which TNF, STAT3 and AKT1 had high significance. The PPI networks are based on the connectivity degree (K), betweenness centrality (BC), and closeness centrality (CC) values. Hub genes are vital for cell survival and growth, and their significance as potential drug targets is discussed. This computational study provides a comprehensive understanding of inflammation and carcinogenesis pathways that are activated during gonorrhea infection.
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Affiliation(s)
- B S Ravindranath
- Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India.
| | - G Ananya
- Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India
| | - C Hema Kumar
- Department of Biotechnology, Dayananda Sagar College of Engineering, Shavige Malleshwara Hills, Kumaraswamy Layout, Bangalore, 560111, Karnataka, India
| | - D C Ramirez
- Laboratory of Experimental and Translational Medicine, CCT-San Luis-National University of San Luis, San Luis, 5700, San Luis, Argentina.
| | - S E Gomez Mejiba
- Laboratory of Nutrition and Experimental Therapeutics, CCT-San Luis-National University of San Luis, San Luis, 5700, San Luis, Argentina.
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Zheng D, Zhou S, Chen L, Pang G, Yang J. A deep learning method to predict bacterial ADP-ribosyltransferase toxins. Bioinformatics 2024; 40:btae378. [PMID: 38885365 PMCID: PMC11219481 DOI: 10.1093/bioinformatics/btae378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
MOTIVATION ADP-ribosylation is a critical modification involved in regulating diverse cellular processes, including chromatin structure regulation, RNA transcription, and cell death. Bacterial ADP-ribosyltransferase toxins (bARTTs) serve as potent virulence factors that orchestrate the manipulation of host cell functions to facilitate bacterial pathogenesis. Despite their pivotal role, the bioinformatic identification of novel bARTTs poses a formidable challenge due to limited verified data and the inherent sequence diversity among bARTT members. RESULTS We proposed a deep learning-based model, ARTNet, specifically engineered to predict bARTTs from bacterial genomes. Initially, we introduced an effective data augmentation method to address the issue of data scarcity in training ARTNet. Subsequently, we employed a data optimization strategy by utilizing ART-related domain subsequences instead of the primary full sequences, thereby significantly enhancing the performance of ARTNet. ARTNet achieved a Matthew's correlation coefficient (MCC) of 0.9351 and an F1-score (macro) of 0.9666 on repeated independent test datasets, outperforming three other deep learning models and six traditional machine learning models in terms of time efficiency and accuracy. Furthermore, we empirically demonstrated the ability of ARTNet to predict novel bARTTs across domain superfamilies without sequence similarity. We anticipate that ARTNet will greatly facilitate the screening and identification of novel bARTTs from bacterial genomes. AVAILABILITY AND IMPLEMENTATION ARTNet is publicly accessible at http://www.mgc.ac.cn/ARTNet/. The source code of ARTNet is freely available at https://github.com/zhengdd0422/ARTNet/.
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Affiliation(s)
- Dandan Zheng
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 102629, China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 102629, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 102629, China
| | - Guansong Pang
- School of Computing and Information Systems, Singapore Management University, Singapore 178902, Singapore
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 102629, China
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12
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Singh S, Singh S, Trivedi M, Dwivedi M. An insight into MDR Acinetobacter baumannii infection and its pathogenesis: Potential therapeutic targets and challenges. Microb Pathog 2024; 192:106674. [PMID: 38714263 DOI: 10.1016/j.micpath.2024.106674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Acinetobacter baumannii is observed as a common species of Gram-negative bacteria that exist in soil and water. Despite being accepted as a typical component of human skin flora, it has become an important opportunistic pathogen, especially in healthcare settings. The pathogenicity of A. baumannii is attributed to its virulence factors, which include adhesins, pili, lipopolysaccharides, outer membrane proteins, iron uptake systems, autotransporter, secretion systems, phospholipases etc. These elements provide the bacterium the ability to cling to and penetrate host cells, get past the host immune system, and destroy tissue. Its infection is a major contributor to human pathophysiological conditions including pneumonia, bloodstream infections, urinary tract infections, and surgical site infections. It is challenging to treat infections brought on by this pathogen since this bacterium has evolved to withstand numerous drugs and further emergence of drug-resistant A. baumannii results in higher rates of morbidity and mortality. The long-term survival of this bacterium on surfaces of medical supplies and hospital furniture facilitates its frequent spread in humans from one habitat to another. There is a need for urgent investigations to find effective drug targets for A. baumannii as well as designing novel drugs to reduce the survival and spread of infection. In the current review, we represent the specific features, pathogenesis, and molecular intricacies of crucial drug targets of A. baumannii. This would also assist in proposing strategies and alternative therapies for the prevention and treatment of A. baumannii infections and their spread.
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Affiliation(s)
- Sukriti Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Sushmita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Mala Trivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India; Research Cell, Amity University Uttar Pradesh, Lucknow, 226028, India.
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13
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Jebastin T, Syed Abuthakir M, Santhoshi I, Gnanaraj M, Gatasheh MK, Ahamed A, Sharmila V. Unveiling the mysteries: Functional insights into hypothetical proteins from Bacteroides fragilis 638R. Heliyon 2024; 10:e31713. [PMID: 38832264 PMCID: PMC11145332 DOI: 10.1016/j.heliyon.2024.e31713] [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: 02/21/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Humans benefit from a vast community of microorganisms in their gastrointestinal tract, known as the gut microbiota, numbering in the tens of trillions. An imbalance in the gut microbiota known as dysbiosis, can lead to changes in the metabolite profile, elevating the levels of toxins like Bacteroides fragilis toxin (BFT), colibactin, and cytolethal distending toxin. These toxins are implicated in the process of oncogenesis. However, a significant portion of the Bacteroides fragilis genome consists of functionally uncharacterized and hypothetical proteins. This study delves into the functional characterization of hypothetical proteins (HPs) encoded by the Bacteroides fragilis genome, employing a systematic in silico approach. A total of 379 HPs were subjected to a BlastP homology search against the NCBI non-redundant protein sequence database, resulting in 162 HPs devoid of identity to known proteins. CDD-Blast identified 106 HPs with functional domains, which were then annotated using Pfam, InterPro, SUPERFAMILY, SCANPROSITE, SMART, and CATH. Physicochemical properties, such as molecular weight, isoelectric point, and stability indices, were assessed for 60 HPs whose functional domains were identified by at least three of the aforementioned bioinformatic tools. Subsequently, subcellular localization analysis was examined and the gene ontology analysis revealed diverse biological processes, cellular components, and molecular functions. Remarkably, E1WPR3 was identified as a virulent and essential gene among the HPs. This study presents a comprehensive exploration of B. fragilis HPs, shedding light on their potential roles and contributing to a deeper understanding of this organism's functional landscape.
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Affiliation(s)
- Thomas Jebastin
- Computer Aided Drug Designing Lab, Department of Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, 620017, Tamil Nadu, India
| | - M.H. Syed Abuthakir
- Department of Bioinformatics, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Ilangovan Santhoshi
- Computer Aided Drug Designing Lab, Department of Bioinformatics, Bishop Heber College (Autonomous), Tiruchirappalli, 620017, Tamil Nadu, India
| | - Muniraj Gnanaraj
- Department of Biotechnology, School of Life Sciences, St Joseph's University, 36 Lalbagh Road, Bengaluru, 560027, Karnataka, India
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Anis Ahamed
- Department of Botany and Microbiology, College of Science, King Saud University, Saudi Arabia
| | - Velusamy Sharmila
- Department of Biotechnology, Nehru Arts and Science College (NASC), Thirumalayampalayam, Coimbatore, 641 105, Tamil Nadu, India
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14
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Zhang P, Zhang B, Ji Y, Jiao J, Zhang Z, Tian C. Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome. MLIFE 2024; 3:277-290. [PMID: 38948139 PMCID: PMC11211677 DOI: 10.1002/mlf2.12132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/20/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
Abstract
Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. To evaluate the robustness of fitness category assignment, Tn-seq data for three independent mutant libraries per strain were analyzed by three methods, which indicates that the Hidden Markov Model (HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size, outperforming the Bayesian and Monte Carlo simulation-based methods. Consequently, the HMM method was used to classify the fitness category. Fitness genes, categorized as essential (ES), advantage (GA), and disadvantage (GD) genes for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Accessory ES/GA genes showed a lower fitness effect than core ES/GA genes. Connectivity degrees in the cofitness network decrease in the order of ES, GD, and GA/NE. In addition to accessory genes, 1599 out of 3284 core genes display differential essentiality across test strains. Within the pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.
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Affiliation(s)
- Pan Zhang
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
- Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Biliang Zhang
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yuan‐Yuan Ji
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| | - Jian Jiao
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
| | - Ziding Zhang
- State Key Laboratory of Livestock and Poultry Biotechnology Breeding, and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chang‐Fu Tian
- State Key Laboratory of Plant Environmental Resilience, and College of Biological SciencesChina Agricultural UniversityBeijingChina
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research CenterChina Agricultural UniversityBeijingChina
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15
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Ma S, Su T, Lu X, Qi Q. Bacterial genome reduction for optimal chassis of synthetic biology: a review. Crit Rev Biotechnol 2024; 44:660-673. [PMID: 37380345 DOI: 10.1080/07388551.2023.2208285] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/13/2022] [Accepted: 02/20/2023] [Indexed: 06/30/2023]
Abstract
Bacteria with streamlined genomes, that harbor full functional genes for essential metabolic networks, are able to synthesize the desired products more effectively and thus have advantages as production platforms in industrial applications. To obtain streamlined chassis genomes, a large amount of effort has been made to reduce existing bacterial genomes. This work falls into two categories: rational and random reduction. The identification of essential gene sets and the emergence of various genome-deletion techniques have greatly promoted genome reduction in many bacteria over the past few decades. Some of the constructed genomes possessed desirable properties for industrial applications, such as: increased genome stability, transformation capacity, cell growth, and biomaterial productivity. The decreased growth and perturbations in physiological phenotype of some genome-reduced strains may limit their applications as optimized cell factories. This review presents an assessment of the advancements made to date in bacterial genome reduction to construct optimal chassis for synthetic biology, including: the identification of essential gene sets, the genome-deletion techniques, the properties and industrial applications of artificially streamlined genomes, the obstacles encountered in constructing reduced genomes, and the future perspectives.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
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16
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Zhu F, Zhou Z, Ma S, Xu Y, Tan C, Yang H, Zhang P, Qin R, Luo Y, Pan P, Chen J. Design of a cryptococcus neoformans vaccine by subtractive proteomics combined with immunoinformatics. Int Immunopharmacol 2024; 135:112242. [PMID: 38772296 DOI: 10.1016/j.intimp.2024.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The emergence of Cryptococcus neoformans has posed an undeniable burden to many regions worldwide, with its strains mainly entering the lungs through the respiratory tract and spreading throughout the body. Limitations of drug regimens, such as high costs and limited options, have directed our attention toward the promising field of vaccine development. In this study, the subtractive proteomics approach was employed to select target proteins from databases that can accurately cover serotypes A and D of the Cryptococcus neoformans. Further, two multi-epitope vaccines consisting of T and B cell epitopes were demonstrated that they have good structural stability and could bind with immune receptor to induce desired immune responses in silico. After further evaluation, these vaccines show the potential for large-scale production and applicability to the majority of the population of the world. In summary, these two vaccines have been theoretically proven to combat Cryptococcus neoformans infections, awaiting further experimental validation of their actual protective effects.
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Affiliation(s)
- Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China.
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China; FuRong Laboratory, Changsha 410078, Hunan, China.
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17
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Rahman S, Chiou CC, Ahmad S, Islam ZU, Tanaka T, Alouffi A, Chen CC, Almutairi MM, Ali A. Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development against Bartonella henselae Strain Houston-1. Bioengineering (Basel) 2024; 11:505. [PMID: 38790371 PMCID: PMC11118080 DOI: 10.3390/bioengineering11050505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes and endothelial cells emphasize its clinical significance. Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to the B. henselae strain Houston-1. Exploring these aspects is crucial for targeted therapeutic strategies against this versatile pathogen. Using reverse-vaccinology-based subtractive proteomics, this research aimed to identify the most antigenic proteins for formulating a multi-epitope vaccine against the B. henselae strain Houston-1. One crucial virulent and antigenic protein, the PAS domain-containing sensor histidine kinase protein, was identified. Subsequently, the identification of B-cell and T-cell epitopes for the specified protein was carried out and the evaluated epitopes were checked for their antigenicity, allergenicity, solubility, MHC binding capability, and toxicity. The filtered epitopes were merged using linkers and an adjuvant to create a multi-epitope vaccine construct. The structure was then refined, with 92.3% of amino acids falling within the allowed regions. Docking of the human receptor (TLR4) with the vaccine construct was performed and demonstrated a binding energy of -1047.2 Kcal/mol with more interactions. Molecular dynamic simulations confirmed the stability of this docked complex, emphasizing the conformation and interactions between the molecules. Further experimental validation is necessary to evaluate its effectiveness against B. henselae.
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Affiliation(s)
- Sudais Rahman
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Chien-Chun Chiou
- Department of Dermatology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan;
| | - Shabir Ahmad
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Brazil;
| | - Zia Ul Islam
- Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
- Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Abid Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
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18
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Khan MF, Ali A, Rehman HM, Noor Khan S, Hammad HM, Waseem M, Wu Y, Clark TG, Jabbar A. Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis. Sci Rep 2024; 14:10904. [PMID: 38740859 DOI: 10.1038/s41598-024-61752-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, ranks among the top causes of global human mortality, as reported by the World Health Organization's 2022 TB report. The prevalence of M. tuberculosis strains that are multiple and extensive-drug resistant represents a significant barrier to TB eradication. Fortunately, having many completely sequenced M. tuberculosis genomes available has made it possible to investigate the species pangenome, conduct a pan-phylogenetic investigation, and find potential new drug targets. The 442 complete genome dataset was used to estimate the pangenome of M. tuberculosis. This study involved phylogenomic classification and in-depth analyses. Sequential filters were applied to the conserved core genome containing 2754 proteins. These filters assessed non-human homology, virulence, essentiality, physiochemical properties, and pathway analysis. Through these intensive filtering approaches, promising broad-spectrum therapeutic targets were identified. These targets were docked with FDA-approved compounds readily available on the ZINC database. Selected highly ranked ligands with inhibitory potential include dihydroergotamine and abiraterone acetate. The effectiveness of the ligands has been supported by molecular dynamics simulation of the ligand-protein complexes, instilling optimism that the identified lead compounds may serve as a robust basis for the development of safe and efficient drugs for TB treatment, subject to further lead optimization and subsequent experimental validation.
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Affiliation(s)
- Muhammad Fayaz Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Hafiz Muhammad Hammad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Maaz Waseem
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yurong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
| | - Abdul Jabbar
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan.
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19
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Tominaga K, Ozaki S, Sato S, Katayama T, Nishimura Y, Omae K, Iwasaki W. Frequent nonhomologous replacement of replicative helicase loaders by viruses in Vibrionaceae. Proc Natl Acad Sci U S A 2024; 121:e2317954121. [PMID: 38683976 PMCID: PMC11087808 DOI: 10.1073/pnas.2317954121] [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: 10/18/2023] [Accepted: 03/14/2024] [Indexed: 05/02/2024] Open
Abstract
Several microbial genomes lack textbook-defined essential genes. If an essential gene is absent from a genome, then an evolutionarily independent gene of unknown function complements its function. Here, we identified frequent nonhomologous replacement of an essential component of DNA replication initiation, a replicative helicase loader gene, in Vibrionaceae. Our analysis of Vibrionaceae genomes revealed two genes with unknown function, named vdhL1 and vdhL2, that were substantially enriched in genomes without the known helicase-loader genes. These genes showed no sequence similarities to genes with known function but encoded proteins structurally similar with a viral helicase loader. Analyses of genomic syntenies and coevolution with helicase genes suggested that vdhL1/2 encodes a helicase loader. The in vitro assay showed that Vibrio harveyi VdhL1 and Vibrio ezurae VdhL2 promote the helicase activity of DnaB. Furthermore, molecular phylogenetics suggested that vdhL1/2 were derived from phages and replaced an intrinsic helicase loader gene of Vibrionaceae over 20 times. This high replacement frequency implies the host's advantage in acquiring a viral helicase loader gene.
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Affiliation(s)
- Kento Tominaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
| | - Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka812-8582, Japan
| | - Shohei Sato
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka812-8582, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka812-8582, Japan
| | - Yuki Nishimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
| | - Kimiho Omae
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba277-0882, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba277-8564, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo113-0032, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
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20
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Zoltek M, Vázquez Maldonado AL, Zhang X, Dadina N, Lesiak L, Schepartz A. HOPS-Dependent Endosomal Escape Demands Protein Unfolding. ACS CENTRAL SCIENCE 2024; 10:860-870. [PMID: 38680556 PMCID: PMC11046473 DOI: 10.1021/acscentsci.4c00016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 05/01/2024]
Abstract
The inefficient translocation of proteins across biological membranes limits their application as potential therapeutics and research tools. In many cases, the translocation of a protein involves two discrete steps: uptake into the endocytic pathway and endosomal escape. Certain charged or amphiphilic molecules can achieve high protein uptake, but few are capable of efficient endosomal escape. One exception to this rule is ZF5.3, a mini-protein that exploits elements of the natural endosomal maturation machinery to translocate across endosomal membranes. Although some ZF5.3-protein conjugates are delivered efficiently to the cytosol or nucleus, overall delivery efficiency varies widely for different cargoes with no obvious design rules. Here we show that delivery efficiency depends on the ability of the cargo to unfold. Using fluorescence correlation spectroscopy, a single-molecule technique that precisely measures intracytosolic protein concentration, we show that regardless of size and pI, low-Tm cargoes of ZF5.3 (including intrinsically disordered domains) bias endosomal escape toward a high-efficiency pathway that requires the homotypic fusion and protein sorting (HOPS) complex. Small protein domains are delivered with moderate efficiency through the same HOPS portal, even if the Tm is high. These findings imply a novel pathway out of endosomes that is exploited by ZF5.3 and provide clear guidance for the selection or design of optimally deliverable therapeutic cargo.
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Affiliation(s)
- Madeline Zoltek
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | | | - Xizi Zhang
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Neville Dadina
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Lauren Lesiak
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alanna Schepartz
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
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21
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Gorityala N, Baidya AS, Sagurthi SR. Genome mining of Mycobacterium tuberculosis: targeting SufD as a novel drug candidate through in silico characterization and inhibitor screening. Front Microbiol 2024; 15:1369645. [PMID: 38686111 PMCID: PMC11057465 DOI: 10.3389/fmicb.2024.1369645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Tuberculosis (TB) stands as the second most fatal infectious disease globally, causing 1.3 million deaths in 2022. The resurgence of TB and the alarming rise of antibiotic resistance demand urgent call to develop novel antituberculosis drugs. Despite concerted efforts to control TB, the disease persists and spreads rapidly on a global scale. Targeting stress response pathways in Mycobacterium tuberculosis (Mtb) has become imperative to achieve complete eradication. This study employs subtractive genomics to identify and prioritize potential drug targets among the hypothetical proteins of Mtb, focusing on indispensable pathways. Amongst 177 essential hypothetical proteins, 152 were nonhomologous to human. These proteins participated in 34 pathways, and a 20-fold enrichment of SUF pathway genes led to its selection as a target pathway. Fe-S clusters are fundamental, widely distributed protein cofactors involved in vital cellular processes. The survival of Mtb in a hypoxic environment relies on the iron-sulfur (Fe-S) cluster biogenesis pathway for the repair of damaged Fe-S clusters. It also protects pathogen against drugs, ensuring controlled iron utilization and contributing to drug resistance. In Mtb, six proteins of Fe-S cluster assembly pathway are encoded by the suf operon. The present study was focused on SufD because of its role in iron acquisition and prevention of Fenton reaction. The research further delves into the in silico characterization of SufD, utilizing bioinformatics tools for sequence and structure based analysis. The protein's structural features, including the identification of conserved regions, motifs, and 3D structure prediction enhanced functional annotation. Target based virtual screening of compounds from the ChEMBL database resulted in 12 inhibitors with best binding affinities. Drug likeness and ADMET profiling of potential inhibitors identified promising compounds with favorable drug-like properties. The study also involved cloning in SUMO-pRSF-Duet1 expression vector, overexpression, and purification of recombinant SufD from E. coli BL21 (DE3) cells. Optimization of expression conditions resulted in soluble production, and subsequent purification highlighting the efficacy of the SUMO fusion system for challenging Mtb proteins in E. coli. These findings provide valuable insights into pharmacological targets for future experimental studies, holding promise for the development of targeted therapy against Mtb.
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Affiliation(s)
- Neelima Gorityala
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Anthony Samit Baidya
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
| | - Someswar R Sagurthi
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, Telangana, India
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22
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Galano-Frutos JJ, Maity R, Iguarbe V, Aínsa JA, Velázquez-Campoy A, Schaible UE, Mamat U, Sancho J. L-Thyroxine and L-thyroxine-based antimicrobials against Streptococcus pneumoniae and other Gram-positive bacteria. Heliyon 2024; 10:e27982. [PMID: 38689973 PMCID: PMC11059415 DOI: 10.1016/j.heliyon.2024.e27982] [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: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Objectives The rise of antibiotic-resistant Streptococcus pneumoniae (Sp) poses a significant global health threat, urging the quest for novel antimicrobial solutions. We have discovered that the human hormone l-thyroxine has antibacterial properties. In order to explore its drugability we perform here the characterization of a series of l-thyroxine analogues and describe the structural determinants influencing their antibacterial efficacy. Method We performed a high-throughput screening of a library of compounds approved for use in humans, complemented with ITC assays on purified Sp-flavodoxin, to pinpoint molecules binding to this protein. Antimicrobial in vitro susceptibility assays of the hit compound (l-thyroxine) as well as of 13 l-thyroxine analogues were done against a panel of Gram-positive and Gram-negative bacteria. Toxicity of compounds on HepG2 cells was also assessed. A combined structure-activity and computational docking analysis was carried out to uncover functional groups crucial for the antimicrobial potency of these compounds. Results Human l-thyroxine binds to Sp-flavodoxin, forming a 1:1 complex of low micromolar Kd. While l-thyroxine specifically inhibited Sp growth, some derivatives displayed activity against other Gram-positive bacteria like Staphylococcus aureus and Enterococcus faecalis, while remaining inactive against Gram-negative pathogens. Neither l-thyroxine nor some selected derivatives exhibited toxicity to HepG2 cells. Conclusions l-thyroxine derivatives targeting bacterial flavodoxins represent a new and promising class of antimicrobials.
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Affiliation(s)
- Juan José Galano-Frutos
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR, Largo Francesco Vito 1, 00168, Rome, Italy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
| | - Ritwik Maity
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
| | - Verónica Iguarbe
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
| | - José Antonio Aínsa
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Microbiología, Pediatría, Radiología y Salud Pública, Facultad de Medicina, University of Zaragoza, Zaragoza 50009, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
- CIBER de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Ulrich E. Schaible
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, & Leibniz Research Alliance INFECTIONS, Borstel, Germany
- Biochemical Microbiology & Immunochemistry, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel Germany
| | - Uwe Mamat
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, & Leibniz Research Alliance INFECTIONS, Borstel, Germany
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
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23
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Boob AG, Zhu Z, Intasian P, Jain M, Petrov V, Lane ST, Tan SI, Xun G, Zhao H. CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration. Nucleic Acids Res 2024; 52:e30. [PMID: 38346683 PMCID: PMC11014336 DOI: 10.1093/nar/gkae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 04/14/2024] Open
Abstract
The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhixin Zhu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pattarawan Intasian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan Valley, Rayong 21210, Thailand
| | - Manan Jain
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vassily Andrew Petrov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Guanhua Xun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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24
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Saravanan KS, Satish KS, Saraswathy GR, Kuri U, Vastrad SJ, Giri R, Dsouza PL, Kumar AP, Nair G. Innovative target mining stratagems to navigate drug repurposing endeavours. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:303-355. [PMID: 38789185 DOI: 10.1016/bs.pmbts.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
The conventional theory linking a single gene with a particular disease and a specific drug contributes to the dwindling success rates of traditional drug discovery. This requires a substantial shift focussing on contemporary drug design or drug repurposing, which entails linking multiple genes to diverse physiological or pathological pathways and drugs. Lately, drug repurposing, the art of discovering new/unlabelled indications for existing drugs or candidates in clinical trials, is gaining attention owing to its success rates. The rate-limiting phase of this strategy lies in target identification, which is generally driven through disease-centric and/or drug-centric approaches. The disease-centric approach is based on exploration of crucial biomolecules such as genes or proteins underlying pathological cascades of the disease of interest. Investigating these pathological interplays aids in the identification of potential drug targets that can be leveraged for novel therapeutic interventions. The drug-centric approach involves various strategies such as exploring the mechanism of adverse drug reactions that can unearth potential targets, as these untoward reactions might be considered desirable therapeutic actions in other disease conditions. Currently, artificial intelligence is an emerging robust tool that can be used to translate the aforementioned intricate biological networks to render interpretable data for extracting precise molecular targets. Integration of multiple approaches, big data analytics, and clinical corroboration are essential for successful target mining. This chapter highlights the contemporary strategies steering target identification and diverse frameworks for drug repurposing. These strategies are illustrated through case studies curated from recent drug repurposing research inclined towards neurodegenerative diseases, cancer, infections, immunological, and cardiovascular disorders.
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Affiliation(s)
- Kamatchi Sundara Saravanan
- Department of Pharmacognosy, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Kshreeraja S Satish
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Ganesan Rajalekshmi Saraswathy
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.
| | - Ushnaa Kuri
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Soujanya J Vastrad
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Ritesh Giri
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Prizvan Lawrence Dsouza
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Adusumilli Pramod Kumar
- Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Gouri Nair
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
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25
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Basharat Z, Meshal A. Pan-genome mediated therapeutic target mining in Kingella kingae and inhibition assessment using traditional Chinese medicinal compounds: an informatics approach. J Biomol Struct Dyn 2024; 42:2872-2885. [PMID: 37144759 DOI: 10.1080/07391102.2023.2208221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023]
Abstract
Kingella kingae causes bacteremia, endocarditis, osteomyelitis, septic arthritis, meningitis, spondylodiscitis, and lower respiratory tract infections in pediatric patients. Usually it demonstrates disease after inflammation of mouth, lips or infections of the upper respiratory tract. To date, therapeutic targets in this bacterium remain unexplored. We have utilized a battery of bioinformatics tools to mine these targets in this study. Core genes were initially inferred from 55 genomes of K. kingae and 39 therapeutic targets were mined using an in-house pipeline. We selected aroG product (KDPG aldolase) involved in chorismate pathway, for inhibition analysis of this bacterium using lead-like metabolites from traditional Chinese medicinal plants. Pharmacophore generation was done using control ZINC36444158 (1,16-bis[(dihydroxyphosphinyl)oxy]hexadecane), followed by molecular docking of top hits from a library of 36,000 compounds. Top prioritized compounds were ZINC95914016, ZINC33833283 and ZINC95914219. ADME profiling and simulation of compound dosing (100 mg tablet) was done to infer compartmental pharmacokinetics in a population of 300 individuals in fasting state. PkCSM based toxicity analysis revealed the compounds ZINC95914016 and ZINC95914219 as safe and with almost similar bioavailability. However, ZINC95914016 takes less time to reach maximum concentration in the plasma and shows several optimal parameters compared to other leads. In light of obtained data, we recommend this compound for further testing and induction in experimental drug design pipeline.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Alotaibi Meshal
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Albatin, Saudi Arabia
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26
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Ye A, Shen JN, Li Y, Lian X, Ma BG, Guo FB. Reconstruction of the genome-scale metabolic network model of Sinorhizobium fredii CCBAU45436 for free-living and symbiotic states. Front Bioeng Biotechnol 2024; 12:1377334. [PMID: 38590605 PMCID: PMC10999553 DOI: 10.3389/fbioe.2024.1377334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Sinorhizobium fredii CCBAU45436 is an excellent rhizobium that plays an important role in agricultural production. However, there still needs more comprehensive understanding of the metabolic system of S. fredii CCBAU45436, which hinders its application in agriculture. Therefore, based on the first-generation metabolic model iCC541 we developed a new genome-scale metabolic model iAQY970, which contains 970 genes, 1,052 reactions, 942 metabolites and is scored 89% in the MEMOTE test. Cell growth phenotype predicted by iAQY970 is 81.7% consistent with the experimental data. The results of mapping the proteome data under free-living and symbiosis conditions to the model showed that the biomass production rate in the logarithmic phase was faster than that in the stable phase, and the nitrogen fixation efficiency of rhizobia parasitized in cultivated soybean was higher than that in wild-type soybean, which was consistent with the actual situation. In the symbiotic condition, there are 184 genes that would affect growth, of which 94 are essential; In the free-living condition, there are 143 genes that influence growth, of which 78 are essential. Among them, 86 of the 94 essential genes in the symbiotic condition were consistent with the prediction of iCC541, and 44 essential genes were confirmed by literature information; meanwhile, 30 genes were identified by DEG and 33 genes were identified by Geptop. In addition, we extracted four key nitrogen fixation modules from the model and predicted that sulfite reductase (EC 1.8.7.1) and nitrogenase (EC 1.18.6.1) as the target enzymes to enhance nitrogen fixation by MOMA, which provided a potential focus for strain optimization. Through the comprehensive metabolic model, we can better understand the metabolic capabilities of S. fredii CCBAU45436 and make full use of it in the future.
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Affiliation(s)
- Anqiang Ye
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan, China
| | - Jian-Ning Shen
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yong Li
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiang Lian
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan, China
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27
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Ward RD, Tran JS, Banta AB, Bacon EE, Rose WE, Peters JM. Essential gene knockdowns reveal genetic vulnerabilities and antibiotic sensitivities in Acinetobacter baumannii. mBio 2024; 15:e0205123. [PMID: 38126769 PMCID: PMC10865783 DOI: 10.1128/mbio.02051-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities that can be therapeutically exploited. The Gram-negative pathogen, Acinetobacter baumannii, is considered an urgent threat due to its propensity to evade antibiotic treatments. Essential cellular processes are the target of existing antibiotics and a likely source of new vulnerabilities. Although A. baumannii essential genes have been identified by transposon sequencing, they have not been prioritized by sensitivity to knockdown or antibiotics. Here, we take a systems biology approach to comprehensively characterize A. baumannii essential genes using CRISPR interference (CRISPRi). We show that certain essential genes and pathways are acutely sensitive to knockdown, providing a set of vulnerable targets for future therapeutic investigation. Screening our CRISPRi library against last-resort antibiotics uncovered genes and pathways that modulate beta-lactam sensitivity, an unexpected link between NADH dehydrogenase activity and growth inhibition by polymyxins, and anticorrelated phenotypes that may explain synergy between polymyxins and rifamycins. Our study demonstrates the power of systematic genetic approaches to identify vulnerabilities in Gram-negative pathogens and uncovers antibiotic-essential gene interactions that better inform combination therapies.IMPORTANCEAcinetobacter baumannii is a hospital-acquired pathogen that is resistant to many common antibiotic treatments. To combat resistant A. baumannii infections, we need to identify promising therapeutic targets and effective antibiotic combinations. In this study, we comprehensively characterize the genes and pathways that are critical for A. baumannii viability. We show that genes involved in aerobic metabolism are central to A. baumannii physiology and may represent appealing drug targets. We also find antibiotic-gene interactions that may impact the efficacy of carbapenems, rifamycins, and polymyxins, providing a new window into how these antibiotics function in mono- and combination therapies. Our studies offer a useful approach for characterizing interactions between drugs and essential genes in pathogens to inform future therapies.
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Affiliation(s)
- Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jennifer S. Tran
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy B. Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emily E. Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Warren E. Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Khan A, Khanzada MH, Khan K, Jalal K, Uddin R. Integrating core subtractive proteomics and reverse vaccinology for multi-epitope vaccine design against Rickettsia prowazekii endemic typhus. Immunol Res 2024; 72:82-95. [PMID: 37608125 DOI: 10.1007/s12026-023-09415-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
Rickettsia prowazekii is an intracellular, obligate, gram-negative coccobacillus responsible for epidemic typhus. Usually, the infected body louse or its excrement when rubbed into the skin abrasions transmits the disease. The infection with R. prowazekii causes the highest death rate (> 20% without antibiotic treatment and now 1-7%), followed by epidemic typhus, which often manifests in unsanitary conditions (up to 15-30%). Conventionally, vaccine design has required pathogen growth and both assays (in vivo and in vitro), which are costly and time-consuming. However, advancements in bioinformatics and computational biology have accelerated the development of effective vaccine designs, reducing the need for traditional, time-consuming laboratory experiments. Subtractive genomics and reverse vaccinology have become prominent computational methods for vaccine model construction. Therefore, the RefSeq sequence of Rickettsia prowazekii (strain Madrid E) (Proteome ID: UP000002480) was subjected to subtractive genomic analysis, including factors such as non-similarity to host proteome, essentiality, subcellular localization, antigenicity, non-allergenicity, and stability. Based on these parameters, the vaccine design process selected specific proteins such as outer membrane protein R (O05971_RICPR PETR; OmpR). Eventually, the OmpR was subjected to a reverse vaccinology approach that included molecular docking, immunological simulation, and the discovery of B-cell epitopes and MHC-I and MHC-II epitopes. Consequently, a chimeric or multi-epitope-based vaccine was proposed by selecting the V11 vaccine and its 3D structure modeling along with molecular docking against TLR and HLA protein, in silico simulation, and vector designing. The obtained results from this investigation resulted in a new perception of inhibitory ways against Rickettsia prowazekii by instigating novel immunogenic targets. To further assess the efficacy and protective ability of the newly designed V11 vaccine against Rickettsia prowazekii infections, additional evaluation such as in vitro or in vivo immunoassays is recommended.
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Affiliation(s)
- Ariba Khan
- Department of Biotechnology, University of Karachi, Karachi, Pakistan
- Lab 103, PCMD ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Hassan Khanzada
- Department of Biotechnology, University of Karachi, Karachi, Pakistan
- Lab 103, PCMD ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Kanwal Khan
- Lab 103, PCMD ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Lab 103, PCMD ext. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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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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30
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Liang Y, Luo H, Lin Y, Gao F. Recent advances in the characterization of essential genes and development of a database of essential genes. IMETA 2024; 3:e157. [PMID: 38868518 PMCID: PMC10989110 DOI: 10.1002/imt2.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 06/14/2024]
Abstract
Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.
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Affiliation(s)
| | - Hao Luo
- Department of PhysicsTianjin UniversityTianjinChina
| | - Yan Lin
- Department of PhysicsTianjin UniversityTianjinChina
| | - Feng Gao
- Department of PhysicsTianjin UniversityTianjinChina
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjinChina
- SynBio Research PlatformCollaborative Innovation Center of Chemical Science and Engineering (Tianjin)TianjinChina
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31
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Ye C, Wu Q, Chen S, Zhang X, Xu W, Wu Y, Zhang Y, Yue Y. ECDEP: identifying essential proteins based on evolutionary community discovery and subcellular localization. BMC Genomics 2024; 25:117. [PMID: 38279081 PMCID: PMC10821549 DOI: 10.1186/s12864-024-10019-5] [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: 12/07/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND In cellular activities, essential proteins play a vital role and are instrumental in comprehending fundamental biological necessities and identifying pathogenic genes. Current deep learning approaches for predicting essential proteins underutilize the potential of gene expression data and are inadequate for the exploration of dynamic networks with limited evaluation across diverse species. RESULTS We introduce ECDEP, an essential protein identification model based on evolutionary community discovery. ECDEP integrates temporal gene expression data with a protein-protein interaction (PPI) network and employs the 3-Sigma rule to eliminate outliers at each time point, constructing a dynamic network. Next, we utilize edge birth and death information to establish an interaction streaming source to feed into the evolutionary community discovery algorithm and then identify overlapping communities during the evolution of the dynamic network. SVM recursive feature elimination (RFE) is applied to extract the most informative communities, which are combined with subcellular localization data for classification predictions. We assess the performance of ECDEP by comparing it against ten centrality methods, four shallow machine learning methods with RFE, and two deep learning methods that incorporate multiple biological data sources on Saccharomyces. Cerevisiae (S. cerevisiae), Homo sapiens (H. sapiens), Mus musculus, and Caenorhabditis elegans. ECDEP achieves an AP value of 0.86 on the H. sapiens dataset and the contribution ratio of community features in classification reaches 0.54 on the S. cerevisiae (Krogan) dataset. CONCLUSIONS Our proposed method adeptly integrates network dynamics and yields outstanding results across various datasets. Furthermore, the incorporation of evolutionary community discovery algorithms amplifies the capacity of gene expression data in classification.
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Affiliation(s)
- Chen Ye
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Qi Wu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Shuxia Chen
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Xuemei Zhang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Wenwen Xu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Yunzhi Wu
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Youhua Zhang
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China
| | - Yi Yue
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, 230036, China.
- Anhui Beidou Precision Agriculture Information Engineering Research Center, Anhui Agricultural University, Hefei, 230036, China.
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Collins C, Baker S, Brown J, Zheng H, Chan A, Stenius U, Narita M, Korhonen A. Text mining for contexts and relationships in cancer genomics literature. Bioinformatics 2024; 40:btae021. [PMID: 38258418 PMCID: PMC10822582 DOI: 10.1093/bioinformatics/btae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/27/2023] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
MOTIVATION Scientific advances build on the findings of existing research. The 2001 publication of the human genome has led to the production of huge volumes of literature exploring the context-specific functions and interactions of genes. Technology is needed to perform large-scale text mining of research papers to extract the reported actions of genes in specific experimental contexts and cell states, such as cancer, thereby facilitating the design of new therapeutic strategies. RESULTS We present a new corpus and Text Mining methodology that can accurately identify and extract the most important details of cancer genomics experiments from biomedical texts. We build a Named Entity Recognition model that accurately extracts relevant experiment details from PubMed abstract text, and a second model that identifies the relationships between them. This system outperforms earlier models and enables the analysis of gene function in diverse and dynamically evolving experimental contexts. AVAILABILITY AND IMPLEMENTATION Code and data are available here: https://github.com/cambridgeltl/functional-genomics-ie.
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Affiliation(s)
- Charlotte Collins
- Language Technology Laboratory, Theoretical and Applied Linguistics, Faculty of Modern and Medieval Languages and Linguistics, University of Cambridge, Cambridge CB3 9DA, United Kingdom
| | - Simon Baker
- Language Technology Laboratory, Theoretical and Applied Linguistics, Faculty of Modern and Medieval Languages and Linguistics, University of Cambridge, Cambridge CB3 9DA, United Kingdom
| | - Jason Brown
- Language Technology Laboratory, Theoretical and Applied Linguistics, Faculty of Modern and Medieval Languages and Linguistics, University of Cambridge, Cambridge CB3 9DA, United Kingdom
| | - Huiyuan Zheng
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Adelyne Chan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Ulla Stenius
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Anna Korhonen
- Language Technology Laboratory, Theoretical and Applied Linguistics, Faculty of Modern and Medieval Languages and Linguistics, University of Cambridge, Cambridge CB3 9DA, United Kingdom
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Jouan R, Lextrait G, Lachat J, Yokota A, Cossard R, Naquin D, Timchenko T, Kikuchi Y, Ohbayashi T, Mergaert P. Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola. ISME COMMUNICATIONS 2024; 4:ycad001. [PMID: 38282642 PMCID: PMC10809759 DOI: 10.1093/ismeco/ycad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/30/2024]
Abstract
Caballeronia insecticola is a bacterium belonging to the Burkholderia genus sensu lato, which is able to colonize multiple environments like soils and the gut of the bean bug Riptortus pedestris. We constructed a saturated Himar1 mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of Caballeronia insecticola for growth in free-living conditions. By comparing essential gene sets of Caballeronia insecticola and seven related Burkholderia s.l. strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of Riptortus pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in Riptortus pedestris gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.
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Grants
- JSPS Research Fellowship for Young Scientists, Japan
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan
- Ministry of Higher Education, Research, and Innovation, France
- CNRS International Research Project, France
- JSPS-CNRS Bilateral Open Partnership Joint Research Project, France-Japan
- Agence Nationale de la Recherche, France
- Saclay Plant Sciences-SPS
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Affiliation(s)
- Romain Jouan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Gaëlle Lextrait
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Aya Yokota
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Raynald Cossard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, Sapporo 062-8517, Japan
| | - Tsubasa Ohbayashi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8604, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
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Chamberlain AR, Huynh L, Huang W, Taylor DJ, Harris ME. The specificity landscape of bacterial ribonuclease P. J Biol Chem 2024; 300:105498. [PMID: 38013087 PMCID: PMC10731613 DOI: 10.1016/j.jbc.2023.105498] [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: 07/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Developing quantitative models of substrate specificity for RNA processing enzymes is a key step toward understanding their biology and guiding applications in biotechnology and biomedicine. Optimally, models to predict relative rate constants for alternative substrates should integrate an understanding of structures of the enzyme bound to "fast" and "slow" substrates, large datasets of rate constants for alternative substrates, and transcriptomic data identifying in vivo processing sites. Such data are either available or emerging for bacterial ribonucleoprotein RNase P a widespread and essential tRNA 5' processing endonuclease, thus making it a valuable model system for investigating principles of biological specificity. Indeed, the well-established structure and kinetics of bacterial RNase P enabled the development of high throughput measurements of rate constants for tRNA variants and provided the necessary framework for quantitative specificity modeling. Several studies document the importance of conformational changes in the precursor tRNA substrate as well as the RNA and protein subunits of bacterial RNase P during binding, although the functional roles and dynamics are still being resolved. Recently, results from cryo-EM studies of E. coli RNase P with alternative precursor tRNAs are revealing prospective mechanistic relationships between conformational changes and substrate specificity. Yet, extensive uncharted territory remains, including leveraging these advances for drug discovery, achieving a complete accounting of RNase P substrates, and understanding how the cellular context contributes to RNA processing specificity in vivo.
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Affiliation(s)
| | - Loc Huynh
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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Giordano M, Falbo E, Maddalena L, Piccirillo M, Granata I. Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience. Biomolecules 2023; 14:18. [PMID: 38254618 PMCID: PMC10813179 DOI: 10.3390/biom14010018] [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: 10/18/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Gene essentiality is a genetic concept crucial for a comprehensive understanding of life and evolution. In the last decade, many essential genes (EGs) have been determined using different experimental and computational approaches, and this information has been used to reduce the genomes of model organisms. A growing amount of evidence highlights that essentiality is a property that depends on the context. Because of their importance in vital biological processes, recognising context-specific EGs (csEGs) could help for identifying new potential pharmacological targets and to improve precision therapeutics. Since most of the computational procedures proposed to identify and predict EGs neglect their context-specificity, we focused on this aspect, providing a theoretical and experimental overview of the literature, data and computational methods dedicated to recognising csEGs. To this end, we adapted existing computational methods to exploit a specific context (the kidney tissue) and experimented with four different prediction methods using the labels provided by four different identification approaches. The considerations derived from the analysis of the obtained results, confirmed and validated also by further experiments for a different tissue context, provide the reader with guidance on exploiting existing tools for achieving csEGs identification and prediction.
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Affiliation(s)
- Maurizio Giordano
- Institute for High-Performance Computing and Networking (ICAR), National Research Council (CNR), V. Pietro Castellino 111, 80131 Naples, Italy; (E.F.); (L.M.); (M.P.); (I.G.)
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Marques PH, Rodrigues TCV, Santos EH, Bleicher L, Aburjaile FF, Martins FS, Oliveira CJF, Azevedo V, Tiwari S, Soares S. Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches. J Biomol Struct Dyn 2023:1-16. [PMID: 38112302 DOI: 10.1080/07391102.2023.2293256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pedro Henrique Marques
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thais Cristina Vilela Rodrigues
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Horta Santos
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flaviano S Martins
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo Jose Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Siomar Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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Mendoza B, Zheng X, Clements JC, Cotter C, Trinh CT. Potency of CRISPR-Cas Antifungals Is Enhanced by Cotargeting DNA Repair and Growth Regulatory Machinery at the Genetic Level. ACS Infect Dis 2023; 9:2494-2503. [PMID: 37955405 PMCID: PMC10714396 DOI: 10.1021/acsinfecdis.3c00342] [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: 07/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023]
Abstract
The emergence of virulent, resistant, and rapidly evolving fungal pathogens poses a significant threat to public health, agriculture, and the environment. Targeting cellular processes with standard small-molecule intervention may be effective but requires long development times and is prone to antibiotic resistance. To overcome the current limitations of antibiotic development and treatment, this study harnesses CRISPR-Cas systems as antifungals by capitalizing on their adaptability, specificity, and efficiency in target design. The conventional design of CRISPR-Cas antimicrobials, based on induction of DNA double-strand breaks (DSBs), is potentially less effective in fungi due to robust eukaryotic DNA repair machinery. Here, we report a novel design principle to formulate more effective CRISPR-Cas antifungals by cotargeting essential genes with DNA repair defensive genes that remove the fungi's ability to repair the DSB sites of essential genes. By evaluating this design on the model fungus Saccharomyces cerevisiae, we demonstrated that essential and defensive gene cotargeting is more effective than either essential or defensive gene targeting alone. The top-performing CRISPR-Cas antifungals performed as effectively as the antibiotic Geneticin. A gene cotargeting interaction analysis revealed that cotargeting essential genes with RAD52 involved in homologous recombination (HR) was the most synergistic combination. Fast growth kinetics of S. cerevisiae induced resistance to CRISPR-Cas antifungals, where genetic mutations mostly occurred in defensive genes and guide RNA sequences.
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Affiliation(s)
- Brian
J. Mendoza
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Xianliang Zheng
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jared C. Clements
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Christopher Cotter
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Cong T. Trinh
- Department
of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
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Li YW, Qian JY, Huang JC, Guo DS, Nie ZK, Ye C, Shi TQ. Improving Gibberellin GA 3 Production with the Construction of a Genome-Scale Metabolic Model of Fusarium fujikuroi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18890-18897. [PMID: 37931026 DOI: 10.1021/acs.jafc.3c05309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Liquid fermentation is the primary method for GA3 production usingFusarium fujikuroi. However, production capacity is limited due to unknown metabolic pathways. To address this, we constructed a genome-scale metabolic model (iCY1235) with 1753 reactions, 1979 metabolites, and 1235 genes to understand the GA3 regulation mechanisms. The model was validated by analyzing growth rates under different glucose uptake rates and identifying essential genes. We used the model to optimize fermentation conditions, including carbon sources and dissolved oxygen. Through the OptForce algorithm, we identified 20 reactions as targets. Overexpressing FFUJ_02053 and FFUJ_14337 resulted in a 37.5 and 75% increase in GA3 titers, respectively. These targets enhance carbon flux toward GA3 production. Our model holds promise for guiding the metabolic engineering of F. fujikuroi to achieve targeted overproduction. In summary, our study utilizes the iCY1235 model to understand GA3 regulation, optimize fermentation conditions, and identify specific targets for enhancing GA3 production through metabolic engineering.
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Affiliation(s)
- Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Jin-Yi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Jia-Cong Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Dong-Sheng Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Zhi-Kui Nie
- Jiangxi New Reyphon Biochemical Co., Ltd., Salt and Chemical Industry, Ji'an 331300, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
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Khan K, Jalal K, Uddin R. Pangenome diversification and resistance gene characterization in Salmonella Typhi prioritized RfaJ as a significant therapeutic marker. J Genet Eng Biotechnol 2023; 21:125. [PMID: 37975995 PMCID: PMC10656401 DOI: 10.1186/s43141-023-00591-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Salmonella Typhi stands as the etiological agent responsible for the onset of human typhoid fever. The pressing demand for innovative therapeutic targets against S. Typhi is underscored by the escalating prevalence of this pathogen and the severe nature of its infections. Consequently, this study employs pangenome analysis to scrutinize 119 S. Typhi-resistant strains, aiming to identify the most promising therapeutic targets originating from its core genome. RESULTS Subtractive genomics was employed to systematically eliminate non-homologous (n=1147), essential (n=551), drug-like (n=80), and pathogenicity-related (n=18) proteins from the initial pool of 3351 core genome proteins. Consequently, lipopolysaccharide 1,2-glucosyltransferase RfaJ was designated as the optimal pharmacological target due to its potential versatility. Furthermore, a compendium of 9000 FDA-approved compounds was repurposed for evaluation against the RfaJ drug target, with the specific intent of prioritizing novel, high-potency therapeutic candidates for combating S. Typhi. Ultimately, four compounds, namely DB00549 (Zafirlukast), DB15637 (Fluzoparib), DB15688 (Zavegepant), and DB12411 (Bemcentinib), were singled out as potential inhibitors based on the ligand-protein binding affinity (indicated by the lowest anticipated binding energy) and the overall stability of these compounds. Notably, molecular dynamics simulations, conducted over a 50 nanosecond interval, convincingly demonstrated the stability of these compounds in the context of the RfaJ protein. CONCLUSION In summary, the present findings hold significant promise as an initial stride in the broader drug discovery endeavor against S. Typhi infections. However, the experimental validation of the identified drug target and drug candidate is further required to increase the effectiveness of the applied methodology.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Zoltek M, Vázquez A, Zhang X, Dadina N, Lesiak L, Schepartz A. Design rules for efficient endosomal escape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565388. [PMID: 37961597 PMCID: PMC10635116 DOI: 10.1101/2023.11.03.565388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The inefficient translocation of proteins across biological membranes limits their application as therapeutic compounds and research tools. In most cases, translocation involves two steps: uptake into the endocytic pathway and endosomal escape. Certain charged or amphiphilic molecules promote protein uptake but few enable efficient endosomal escape. One exception is ZF5.3, a mini-protein that exploits natural endosomal maturation machinery to translocate across endosomal membranes. Although certain ZF5.3-protein conjugates are delivered efficiently into the cytosol or nucleus, overall delivery efficiency varies widely with no obvious design rules. Here we evaluate the role of protein size and thermal stability in the ability to efficiently escape endosomes when attached to ZF5.3. Using fluorescence correlation spectroscopy, a single-molecule technique that provides a precise measure of intra-cytosolic protein concentration, we demonstrate that delivery efficiency depends on both size and the ease with which a protein unfolds. Regardless of size and pI, low-Tm cargos of ZF5.3 (including intrinsically disordered domains) bias its endosomal escape route toward a high-efficiency pathway that requires the homotypic fusion and protein sorting (HOPS) complex. Small protein domains are delivered with moderate efficiency through the same HOPS portal even if the Tm is high. These findings imply a novel protein- and/or lipid-dependent pathway out of endosomes that is exploited by ZF5.3 and provide clear guidance for the selection or design of optimally deliverable therapeutic cargo.
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Affiliation(s)
- Madeline Zoltek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Angel Vázquez
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Xizi Zhang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Neville Dadina
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Lauren Lesiak
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Alanna Schepartz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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41
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Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem 2023; 106:107919. [PMID: 37463554 DOI: 10.1016/j.compbiolchem.2023.107919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Mimicry of host proteins is a strategy employed by pathogens to hijack host functions. Domain and motif mimicry was explored in the experimental and predicted SARS-CoV-2-human interactome. The host first interactor proteins were also added to capture the continuum of the interactions. The domains and motifs of the proteins were annotated using NCBI CD Search and ScanProsite, respectively. Host and pathogen proteins with a common host interactor and similar domain/motif constitute a mimicry pair indicating global structural similarity (domain mimicry pair; DMP) or local sequence similarity (motif mimicry pair; MMP). 593 DMPs and 7,02,472 MMPs were determined. AAA, DEXDc and Macro domains were frequent among DMPs whereas glycosylation, myristoylation and RGD motifs were abundant among MMP. The proteins involved in mimicry were visualised as a SARS-CoV-2 mimicry interaction network. The host proteins were enriched in multiple CVD pathways indicating the role of mimicry in COVID-19 associated CVDs. Bridging nodes were identified as potential drug targets. Approved antihypertensive and anti-inflammatory drugs are proposed for repurposing against COVID-19 associated CVDs. The SARS-CoV-2 mimicry data has been updated in ImitateDB (http://imitatedb.sblab-nsit.net/SARSCoV2Mimicry). Determination of key mechanisms, proteins, pathways, drug targets and repurposing candidates is critical for developing therapeutics for SARS CoV-2 associated CVDs.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India.
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Shah M, Anwar A, Qasim A, Jaan S, Sarfraz A, Ullah R, Ali EA, Nishan U, Shehroz M, Zaman A, Ojha SC. Proteome level analysis of drug-resistant Prevotella melaninogenica for the identification of novel therapeutic candidates. Front Microbiol 2023; 14:1271798. [PMID: 37808310 PMCID: PMC10556700 DOI: 10.3389/fmicb.2023.1271798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
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.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Amna Anwar
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Aqsa Qasim
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Center, College of Pharmacy King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree, Pakistan
| | - Aqal Zaman
- Department of Microbiology and Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Zhou J, Ma H, Zhang L. Mechanisms of Virulence Reprogramming in Bacterial Pathogens. Annu Rev Microbiol 2023; 77:561-581. [PMID: 37406345 DOI: 10.1146/annurev-micro-032521-025954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Bacteria are single-celled organisms that carry a comparatively small set of genetic information, typically consisting of a few thousand genes that can be selectively activated or repressed in an energy-efficient manner and transcribed to encode various biological functions in accordance with environmental changes. Research over the last few decades has uncovered various ingenious molecular mechanisms that allow bacterial pathogens to sense and respond to different environmental cues or signals to activate or suppress the expression of specific genes in order to suppress host defenses and establish infections. In the setting of infection, pathogenic bacteria have evolved various intelligent mechanisms to reprogram their virulence to adapt to environmental changes and maintain a dominant advantage over host and microbial competitors in new niches. This review summarizes the bacterial virulence programming mechanisms that enable pathogens to switch from acute to chronic infection, from local to systemic infection, and from infection to colonization. It also discusses the implications of these findings for the development of new strategies to combat bacterial infections.
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Affiliation(s)
- Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Hongmei Ma
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
| | - Lianhui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China;
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44
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Cacheiro P, Smedley D. Essential genes: a cross-species perspective. Mamm Genome 2023; 34:357-363. [PMID: 36897351 PMCID: PMC10382395 DOI: 10.1007/s00335-023-09984-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023]
Abstract
Protein coding genes exhibit different degrees of intolerance to loss-of-function variation. The most intolerant genes, whose function is essential for cell or/and organism survival, inform on fundamental biological processes related to cell proliferation and organism development and provide a window on the molecular mechanisms of human disease. Here we present a brief overview of the resources and knowledge gathered around gene essentiality, from cancer cell lines to model organisms to human development. We outline the implications of using different sources of evidence and definitions to determine which genes are essential and highlight how information on the essentiality status of a gene can inform novel disease gene discovery and therapeutic target identification.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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45
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Ward RD, Tran JS, Banta AB, Bacon EE, Rose WE, Peters JM. Essential Gene Knockdowns Reveal Genetic Vulnerabilities and Antibiotic Sensitivities in Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551708. [PMID: 37577569 PMCID: PMC10418195 DOI: 10.1101/2023.08.02.551708] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities that can be therapeutically exploited. The Gram-negative pathogen, Acinetobacter baumannii, is considered an urgent threat due to its propensity to evade antibiotic treatments. Essential cellular processes are the target of existing antibiotics and a likely source of new vulnerabilities. Although A. baumannii essential genes have been identified by transposon sequencing (Tn-seq), they have not been prioritized by sensitivity to knockdown or antibiotics. Here, we take a systems biology approach to comprehensively characterize A. baumannii essential genes using CRISPR interference (CRISPRi). We show that certain essential genes and pathways are acutely sensitive to knockdown, providing a set of vulnerable targets for future therapeutic investigation. Screening our CRISPRi library against last-resort antibiotics uncovered genes and pathways that modulate beta-lactam sensitivity, an unexpected link between NADH dehydrogenase activity and growth inhibition by polymyxins, and anticorrelated phenotypes that underpin synergy between polymyxins and rifamycins. Our study demonstrates the power of systematic genetic approaches to identify vulnerabilities in Gram-negative pathogens and uncovers antibiotic-essential gene interactions that better inform combination therapies.
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Affiliation(s)
- Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Jennifer S Tran
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Amy B Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Emily E Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Warren E Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706
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46
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Liu L, Yu W, Cai K, Ma S, Wang Y, Ma Y, Zhao H. Identification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach. Heliyon 2023; 9:e18623. [PMID: 37576287 PMCID: PMC10413060 DOI: 10.1016/j.heliyon.2023.e18623] [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: 04/27/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein. All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.
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Affiliation(s)
- Lu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Wanli Yu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Kuojun Cai
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Siyuan Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yanfeng Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yuhui Ma
- Zhaosu Xiyu Horse Industry Co., Ltd. Zhaosu County 835699, Yili Prefecture, Xinjiang, China
| | - Hongqiong Zhao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
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Ittiprasert W, Moescheid MF, Chaparro C, Mann VH, Quack T, Rodpai R, Miller A, Wisitpongpun P, Buakaew W, Mentink-Kane M, Schmid S, Popratiloff A, Grevelding CG, Grunau C, Brindley PJ. Targeted insertion and reporter transgene activity at a gene safe harbor of the human blood fluke, Schistosoma mansoni. CELL REPORTS METHODS 2023; 3:100535. [PMID: 37533651 PMCID: PMC10391569 DOI: 10.1016/j.crmeth.2023.100535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/22/2023] [Accepted: 06/25/2023] [Indexed: 08/04/2023]
Abstract
The identification and characterization of genomic safe harbor sites (GSHs) can facilitate consistent transgene activity with minimal disruption to the host cell genome. We combined computational genome annotation and chromatin structure analysis to predict the location of four GSHs in the human blood fluke, Schistosoma mansoni, a major infectious pathogen of the tropics. A transgene was introduced via CRISPR-Cas-assisted homology-directed repair into one of the GSHs in the egg of the parasite. Gene editing efficiencies of 24% and transgene-encoded fluorescence of 75% of gene-edited schistosome eggs were observed. The approach advances functional genomics for schistosomes by providing a tractable path for generating transgenics using homology-directed, repair-catalyzed transgene insertion. We also suggest that this work will serve as a roadmap for the development of similar approaches in helminths more broadly.
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Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Max F. Moescheid
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Cristian Chaparro
- IHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University Montpellier, Perpignan, France
| | - Victoria H. Mann
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Thomas Quack
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Rutchanee Rodpai
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Department of Parasitology and Excellence in Medical Innovation, and Technology Research Group, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - André Miller
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA
| | - Prapakorn Wisitpongpun
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Faculty of Medical Technology, Rangsit University, Pathum Thani 12000, Thailand
| | - Watunyoo Buakaew
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Margaret Mentink-Kane
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA
| | - Sarah Schmid
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA
| | - Anastas Popratiloff
- Nanofabrication and Imaging Center, Science & Engineering Hall, George Washington University, Washington, DC 20052, USA
| | - Christoph G. Grevelding
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Grunau
- IHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University Montpellier, Perpignan, France
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
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48
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Falgarone T, Villain E, Richard F, Osmanli Z, Kajava AV. Census of exposed aggregation-prone regions in proteomes. Brief Bioinform 2023; 24:bbad183. [PMID: 37200152 DOI: 10.1093/bib/bbad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 05/20/2023] Open
Abstract
Loss of solubility usually leads to the detrimental elimination of protein function. In some cases, the protein aggregation is also required for beneficial functions. Given the duality of this phenomenon, it remains a fundamental question how natural selection controls the aggregation. The exponential growth of genomic sequence data and recent progress with in silico predictors of the aggregation allows approaching this problem by a large-scale bioinformatics analysis. Most of the aggregation-prone regions are hidden within the 3D structure, rendering them inaccessible for the intermolecular interactions responsible for aggregation. Thus, the most realistic census of the aggregation-prone regions requires crossing aggregation prediction with information about the location of the natively unfolded regions. This allows us to detect so-called 'exposed aggregation-prone regions' (EARs). Here, we analyzed the occurrence and distribution of the EARs in 76 reference proteomes from the three kingdoms of life. For this purpose, we used a bioinformatics pipeline, which provides a consensual result based on several predictors of aggregation. Our analysis revealed a number of new statistically significant correlations about the presence of EARs in different organisms, their dependence on protein length, cellular localizations, co-occurrence with short linear motifs and the level of protein expression. We also obtained a list of proteins with the conserved aggregation-prone sequences for further experimental tests. Insights gained from this work led to a deeper understanding of the relationship between protein evolution and aggregation.
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Affiliation(s)
- Théo Falgarone
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Francois Richard
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
| | - Zarifa Osmanli
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
- Biophysics Institute, Ministry of Science and Education of Azerbaijan Republic, Az1141, Baku, Azerbaijan
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier, 34293, France
- Institut de Biologie Computationnelle, Université Montpellier, 34095 Montpellier, France
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Singh AK, Amar I, Ramadasan H, Kappagantula KS, Chavali S. Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialome. Cell Rep 2023; 42:112811. [PMID: 37453061 DOI: 10.1016/j.celrep.2023.112811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/30/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Protein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this functional versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about crosstalk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat-containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies, including cancers and neurological disorders.
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Affiliation(s)
- Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ishita Amar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Harikrishnan Ramadasan
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Keertana S Kappagantula
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India.
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Liu W, Ou P, Tian F, Liao J, Ma Y, Wang J, Jin X. Anti- Vibrio parahaemolyticus compounds from Streptomyces parvus based on Pan-genome and subtractive proteomics. Front Microbiol 2023; 14:1218176. [PMID: 37485508 PMCID: PMC10361664 DOI: 10.3389/fmicb.2023.1218176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Vibrio parahaemolyticus is a foodborne pathogen commonly found in seafood, and drug resistance poses significant challenges to its control. This study aimed to identify novel drug targets for antibacterial drug discovery. Methods To identify drug targets, we performed a pan-genome analysis on 58 strains of V. parahaemolyticus genomes to obtain core genes. Subsequently, subtractive proteomics and physiochemical checks were conducted on the core proteins to identify potential therapeutic targets. Molecular docking was then employed to screen for anti-V. parahaemolyticus compounds using a in-house compound library of Streptomyces parvus, chosen based on binding energy. The anti-V. parahaemolyticus efficacy of the identified compounds was further validated through a series of experimental tests. Results and Discussion Pangenome analysis of 58 V. parahaemolyticus genomes revealed that there were 1,392 core genes. After Subtractive proteomics and physiochemical checks, Flagellar motor switch protein FliN was selected as a therapeutic target against V. parahaemolyticus. FliN was modeled and docked with Streptomyces parvus source compounds, and Actinomycin D was identified as a potential anti-V. parahaemolyticus agent with a strong binding energy. Experimental verification confirmed its effectiveness in killing V. parahaemolyticus and significantly inhibiting biofilm formation and motility. This study is the first to use pan-genome and subtractive proteomics to identify new antimicrobial targets for V. parahaemolyticus and to identify the anti-V. parahaemolyticus effect of Actinomycin D. These findings suggest potential avenues for the development of new antibacterial drugs to control V. parahaemolyticus infections.
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Affiliation(s)
- Wenbin Liu
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Peiyu Ou
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fangyuan Tian
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jingyang Liao
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yan Ma
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jie Wang
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaobao Jin
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, China
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