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Arshad NF, Nordin FJ, Foong LC, In LLA, Teo MYM. Engineering receptor-binding domain and heptad repeat domains towards the development of multi-epitopes oral vaccines against SARS-CoV-2 variants. PLoS One 2024; 19:e0306111. [PMID: 39146295 PMCID: PMC11326571 DOI: 10.1371/journal.pone.0306111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/11/2024] [Indexed: 08/17/2024] Open
Abstract
The inability of existing vaccines to cope with the mutation rate has highlighted the need for effective preventative strategies for COVID-19. Through the secretion of immunoglobulin A, mucosal delivery of vaccines can effectively stimulate mucosal immunity for better protection against SARS-CoV-2 infection. In this study, various immunoinformatic tools were used to design a multi-epitope oral vaccine against SARS-CoV-2 based on its receptor-binding domain (RBD) and heptad repeat (HR) domains. T and B lymphocyte epitopes were initially predicted from the RBD and HR domains of SARS-CoV-2, and potential antigenic, immunogenic, non-allergenic, and non-toxic epitopes were identified. Epitopes that are highly conserved and have no significant similarity to human proteome were selected. The epitopes were joined with appropriate linkers, and an adjuvant was added to enhance the vaccine efficacy. The vaccine 3D structure constructs were docked with toll-like receptor 4 (TLR-4) and TLR1-TLR2, and the binding affinity was calculated. The designed multi-epitope vaccine construct (MEVC) consisted of 33 antigenic T and B lymphocyte epitopes. The results of molecular dockings and free binding energies confirmed that the MEVC effectively binds to TLR molecules, and the complexes were stable. The results suggested that the designed MEVC is a potentially safe and effective oral vaccine against SARS-CoV-2. This in silico study presents a novel approach for creating an oral multi-epitope vaccine against the rapidly evolving SARS-CoV-2 variants. These findings offer valuable insights for developing an effective strategy to combat COVID-19. Further preclinical and clinical studies are required to confirm the efficacy of the MEVC vaccine.
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Affiliation(s)
- Nur Farhanah Arshad
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Fariza Juliana Nordin
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Lian Chee Foong
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
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Khan MT, Mahmud A, Islam MM, Sumaia MSN, Rahim Z, Islam K, Iqbal A. Multi-epitope vaccine against drug-resistant strains of Mycobacterium tuberculosis: a proteome-wide subtraction and immunoinformatics approach. Genomics Inform 2023; 21:e42. [PMID: 37813638 PMCID: PMC10584640 DOI: 10.5808/gi.23021] [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: 03/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 10/11/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Toll-like receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.
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Affiliation(s)
- Md Tahsin Khan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Araf Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md. Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mst. Sayedatun Nessa Sumaia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Zeaur Rahim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kamrul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Asif Iqbal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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Kaur H, Modgil V, Chaudhary N, Mohan B, Taneja N. Computational Guided Drug Targets Identification against Extended-Spectrum Beta-Lactamase-Producing Multi-Drug Resistant Uropathogenic Escherichia coli. Biomedicines 2023; 11:2028. [PMID: 37509666 PMCID: PMC10377140 DOI: 10.3390/biomedicines11072028] [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: 06/28/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most frequent bacterial infections in the world, both in the hospital and community settings. Uropathogenic Escherichia coli (UPEC) are the predominant etiological agents causing UTIs. Extended-spectrum beta-lactamase (ESBL) production is a prominent mechanism of resistance that hinders the antimicrobial treatment of UTIs caused by UPEC and poses a substantial danger to the arsenal of antibiotics now in use. As bacteria have several methods to counteract the effects of antibiotics, identifying new potential drug targets may help in the design of new antimicrobial agents, and in the control of the rising trend of antimicrobial resistance (AMR). The public availability of the entire genome sequences of humans and many disease-causing organisms has accelerated the hunt for viable therapeutic targets. Using a unique, hierarchical, in silico technique using computational tools, we discovered and described potential therapeutic drug targets against the ESBL-producing UPEC strain NA114. Three different sets of proteins (chokepoint, virulence, and resistance genes) were explored in phase 1. In phase 2, proteins shortlisted from phase 1 were analyzed for their essentiality, non-homology to the human genome, and gut flora. In phase 3, the further shortlisted putative drug targets were qualitatively characterized, including their subcellular location, broad-spectrum potential, and druggability evaluations. We found seven distinct targets for the pathogen that showed no similarity to the human proteome. Thus, possibilities for cross-reactivity between a target-specific antibacterial and human proteins were minimized. The subcellular locations of two targets, ECNA114_0085 and ECNA114_1060, were predicted as cytoplasmic and periplasmic, respectively. These proteins play an important role in bacterial peptidoglycan biosynthesis and inositol phosphate metabolism, and can be used in the design of drugs against these bacteria. Inhibition of these proteins will be helpful to combat infections caused by MDR UPEC.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Vinay Modgil
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Naveen Chaudhary
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Balvinder Mohan
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Neelam Taneja
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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Santos AS, Borges Dos Anjos LR, Costa VAF, Freitas VAQ, Zara ALDSA, Costa CR, Neves BJ, Silva MDRR. In silico-chemogenomic repurposing of new chemical scaffolds for histoplasmosis treatment. J Mycol Med 2023; 33:101363. [PMID: 36842411 DOI: 10.1016/j.mycmed.2023.101363] [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: 09/27/2022] [Revised: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
BACKGROUND Histoplasmosis is a systemic form of endemic mycosis to the American continent and may be lethal to people living with HIV/AIDS. The drugs available for treating histoplasmosis are limited, costly, and highly toxic. New drug development is time-consuming and costly; hence, drug repositioning is an advantageous strategy for discovering new therapeutic options. OBJECTIVE This study was conducted to identify drugs that can be repositioned for treating histoplasmosis in immunocompromised patients. METHODS Homologous proteins among Histoplasma capsulatum strains were selected and used to search for homologous targets in the DrugBank and Therapeutic Target Database. Essential genes were selected using Saccharomyces cerevisiae as a model, and functional regions of the therapeutic targets were analyzed. The antifungal activity of the selected drugs was verified, and homology modeling and molecular docking were performed to verify the interactions between the drugs with low inhibitory concentration values and their corresponding targets. RESULTS We selected 149 approved drugs with potential activity against histoplasmosis, among which eight were selected for evaluating their in vitro activity. For drugs with low minimum inhibitory concentration values, such as mebendazole, everolimus, butenafine, and bifonazole, molecular docking studies were performed. A chemogenomic framework revealed lanosterol 14-α-demethylase, squalene monooxygenase, serine/threonine-protein kinase mTOR, and the β-4B tubulin chain of H. capsulatum, respectively, as the protein targets of the drugs. CONCLUSIONS Our strategy can be used to identify promising antifungal targets, and drugs with repositioning potential for treating H. capsulatum.
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Affiliation(s)
- Andressa Santana Santos
- Institute of Tropical Pathology and Public Health (IPTSP), Federal University of Goiás, Goiânia, Brazil
| | | | | | | | | | - Carolina Rodrigues Costa
- Institute of Tropical Pathology and Public Health (IPTSP), Federal University of Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics (LabChem), Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
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Rouse WB, Gart J, Peysakhova L, Moss WN. Analysis of key genes in Mycobacterium ulcerans reveals conserved RNA structural motifs and regions with apparent pressure to remain unstructured. FRONTIERS IN TROPICAL DISEASES 2022; 3. [PMID: 37006713 PMCID: PMC10062443 DOI: 10.3389/fitd.2022.1009362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Buruli Ulcer is a neglected tropical disease that results in disfiguring and dangerous lesions in affected persons across a wide geographic area, including much of West Africa. The causative agent of Buruli Ulcer is Mycobacterium ulcerans, a relative of the bacterium that causes tuberculosis and leprosy. Few therapeutic options exist for the treatment of this disease beyond antibiotics in the early stages, which are frequently ineffective, and surgical removal in the later stage. In this study we analyze six genes in Mycobacterium ulcerans that have high potential of therapeutic targeting. We focus our analysis on a combined in silico and comparative sequence study of potential RNA secondary structure across these genes. The result of this work was the comprehensive local RNA structural landscape across each of these significant genes. This revealed multiple sites of ordered and evolved RNA structure interspersed between sequences that either have no bias for structure or, indeed, appear to be ordered to be unstructured and (potentially) accessible. In addition to providing data that could be of interest to basic biology, our results provide guides for efforts aimed at targeting this pathogen at the RNA level. We explore this latter possibility through the in silico analysis of antisense oligonucleotides that could potentially be used to target pathogen RNA.
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Affiliation(s)
- Warren B. Rouse
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Jessica Gart
- Science and Engineering Research Program (SERP), Staten Island Technical High School, Staten Island, NY, United States
| | - Lauren Peysakhova
- Science and Engineering Research Program (SERP), Staten Island Technical High School, Staten Island, NY, United States
| | - Walter N. Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- CORRESPONDENCE: Walter N. Moss,
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Hafsa U, Chuwdhury GS, Hasan MK, Ahsan T, Moni MA. An in silico approach towards identification of novel drug targets in Klebsiella oxytoca. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pyogenes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111355. [PMID: 34769873 PMCID: PMC8582943 DOI: 10.3390/ijerph182111355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/18/2022]
Abstract
Streptococcus pyogenes is a significant pathogen that causes skin and upper respiratory tract infections and non-suppurative complications, such as acute rheumatic fever and post-strep glomerulonephritis. Multidrug resistance has emerged in S. pyogenes strains, making them more dangerous and pathogenic. Hence, it is necessary to identify and develop therapeutic methods that would present novel approaches to S. pyogenes infections. In the current study, a subtractive proteomics approach was employed to core proteomes of four strains of S. pyogenes using several bioinformatic software tools and servers. The core proteome consists of 1324 proteins, and 302 essential proteins were predicted from them. These essential proteins were analyzed using BLASTp against human proteome, and the number of potential targets was reduced to 145. Based on subcellular localization prediction, 46 proteins with cytoplasmic localization were chosen for metabolic pathway analysis. Only two cytoplasmic proteins, i.e., chromosomal replication initiator protein DnaA and two-component response regulator (TCR), were discovered to have the potential to be novel drug target candidates. Three-dimensional (3D) structure prediction of target proteins was carried out via the Swiss Model server. Molecular docking approach was employed to screen the library of 1000 phytochemicals against the interacting residues of the target proteins through the MOE software. Further, the docking studies were validated by running molecular dynamics simulation and highly popular binding free energy approaches of MM-GBSA and MM-PBSA. The findings revealed a promising candidate as a novel target against S. pyogenes infections.
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Kaur H, Kalia M, Singh V, Modgil V, Mohan B, Taneja N. In silico identification and characterization of promising drug targets in highly virulent uropathogenic Escherichia coli strain CFT073 by protein-protein interaction network analysis. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Rajamanickam K, Yang J, Chidambaram SB, Sakharkar MK. Enhancing Drug Efficacy against Mastitis Pathogens-An In Vitro Pilot Study in Staphylococcus aureus and Staphylococcus epidermidis. Animals (Basel) 2020; 10:E2117. [PMID: 33203170 PMCID: PMC7696410 DOI: 10.3390/ani10112117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Bovine mastitis is one of the major infectious diseases in dairy cattle, resulting in large economic loss due to decreased milk production and increased production cost to the dairy industry. Antibiotics are commonly used to prevent/treat bovine mastitis infections. However, increased antibiotic resistance and consumers' concern regarding antibiotic overuse make it prudent and urgent to develop novel therapeutic protocols for this disease. MATERIALS AND METHODS Potential druggable targets were found in 20 mastitis-causing pathogens and conserved and unique targets were identified. Bacterial strains Staphylococcus aureus (ATCC 29213, and two clinical isolates CI 1 and CI 2) and Staphylococcus epidermidis (ATCC 12228, and two clinical isolates CI 1 and CI 2) were used in the present study for validation of an effective drug combination. RESULTS In the current study, we identified the common and the unique druggable targets for twenty mastitis-causing pathogens using an integrative approach. Furthermore, we showed that phosphorylcholine, a drug for a unique target gamma-hemolysin component B in Staphylococcus aureus, and ceftiofur, the mostly used veterinary antibiotic that is FDA approved for treating mastitis infections, exhibit a synergistic effect against S. aureus and a strong additive effect against Staphylococcus epidermidis in vitro. CONCLUSION Based on the data generated in this study, we propose that combination therapy with drugs that work synergistically against conserved and unique targets can help increase efficacy and lower the usage of antibiotics for treating bacterial infections. However, these data need further validations in animal models of infection.
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Affiliation(s)
- Karthic Rajamanickam
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.R.); (J.Y.)
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.R.); (J.Y.)
| | - Saravana Babu Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research (JSS AHER), Mysuru-570015, Karnataka, India;
| | - Meena Kishore Sakharkar
- College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; (K.R.); (J.Y.)
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Kaur H, Kalia M, Taneja N. Identification of novel non-homologous drug targets against Acinetobacter baumannii using subtractive genomics and comparative metabolic pathway analysis. Microb Pathog 2020; 152:104608. [PMID: 33166618 DOI: 10.1016/j.micpath.2020.104608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 11/02/2020] [Indexed: 11/19/2022]
Abstract
Lack of effective antibiotics and the development of multidrug resistance in clinical isolates of nosocomial pathogen Acinetobacter baumanni has necessitated the identification of novel drug targets. The study is divided into three phases, in phase I, four different sets of proteins were subjected to a chokepoint, plasmid, resistance genes, and virulence factors analysis. After phase 1 analysis we obtained two hundred twenty-two proteins which were analyzed further in the phase II for essentiality and homology. Fifty-eight proteins identified as target candidates were studied for qualitative characteristics. Among them, 32 were identified as cytoplasmic membrane, 17 as cytoplasmic, one as periplasmic, one as outer membrane, two as extracellular, and location of 5 was not known. Druggability analysis revealed that 18 proteins were druggable, and 40 were novel. Drug targets obtained in the present study can be utilized for the identification of novel antimicrobials for the treatment of infections caused by multidrug-resistant A. baumannii. Predicted drug targets can be evaluated for their binding affinity by molecular docking studies and thus accelerating the process of drug discovery.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manmohit Kalia
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Swain A, Gnanasekar P, Prava J, Rajeev AC, Kesarwani P, Lahiri C, Pan A. A Comparative Genomics Approach for Shortlisting Broad-Spectrum Drug Targets in Nontuberculous Mycobacteria. Microb Drug Resist 2020; 27:212-226. [PMID: 32936741 DOI: 10.1089/mdr.2020.0161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Many members of nontuberculous mycobacteria (NTM) are opportunistic pathogens causing several infections in animals. The incidence of NTM infections and emergence of drug-resistant NTM strains are rising worldwide, emphasizing the need to develop novel anti-NTM drugs. The present study is aimed to identify broad-spectrum drug targets in NTM using a comparative genomics approach. The study identified 537 core proteins in NTM of which 45 were pathogen specific and essential for the survival of pathogens. Furthermore, druggability analysis indicated that 15 were druggable among those 45 proteins. These 15 proteins, which were core proteins, pathogen-specific, essential, and druggable, were considered as potential broad-spectrum candidates. Based on their locations in cytoplasm and membrane, targets were classified as drug and vaccine targets. The identified 15 targets were different enzymes, carrier proteins, transcriptional regulator, two-component system protein, ribosomal, and binding proteins. The identified targets could further be utilized by researchers to design inhibitors for the discovery of antimicrobial agents.
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Affiliation(s)
- Aishwarya Swain
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Jyoti Prava
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Athira C Rajeev
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Pragya Kesarwani
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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Chand Y, Alam MA, Singh S. Pan-genomic analysis of the species Salmonella enterica: Identification of core essential and putative essential genes. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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13
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Shahid F, Ashfaq UA, Saeed S, Munir S, Almatroudi A, Khurshid M. In Silico Subtractive Proteomics Approach for Identification of Potential Drug Targets in Staphylococcus saprophyticus. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103644. [PMID: 32455889 PMCID: PMC7277342 DOI: 10.3390/ijerph17103644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 11/16/2022]
Abstract
Staphylococcus saprophyticus is a uropathogenic bacteria responsible for acute urinary tract infections (UTIs) mainly in young female patients. Patients suffering from urinary catheterization, pregnant patients, the elderly as well as those with nosocomial UTIs are at greater risk of the colonizing S. saprophyticus infection. The causative factors include benign prostatic hyperplasia, indwelling catheter, neurogenic bladder, pregnancy, and history of frequent UTIs. Recent findings have exhibited that S. saprophyticus is resistant to several antimicrobial agents. Moreover, there is a global concern regarding the increasing level of antimicrobial resistance, which leads to treatment failure and reduced effectiveness of broad-spectrum antimicrobials. Therefore, a novel approach is being utilized to combat resistant microbes since the past few years. Subtractive proteome analysis has been performed with the entire proteome of S. saprophyticus strain American Type Culture Collection (ATCC) 15305 using several bioinformatics servers and software. The proteins that were non-homologous to humans and bacteria were identified for metabolic pathway analysis. Only four cytoplasmic proteins were found possessing the potential of novel drug target candidates. The development of innovative therapeutic agents by targeting the inhibition of any essential proteins may disrupt the metabolic pathways specific to the pathogen, thus causing destruction as well as eradication of the pathogen from a particular host. The identified targets can facilitate in designing novel and potent drugs against S. saprophyticus strain ATCC 15305.
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Affiliation(s)
- Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
- Correspondence:
| | - Sania Saeed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
| | - Samman Munir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Punjab 38000, Pakistan; (F.S.); (S.S.); (S.M.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Punjab 38000, Pakistan;
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Boby N, Abbas MA, Lee EB, Park SC. Pharmacodynamics of Ceftiofur Selected by Genomic and Proteomic Approaches of Streptococcus parauberis Isolated from the Flounder, Paralichthys olivaceus. Int J Genomics 2020; 2020:4850290. [PMID: 32318593 PMCID: PMC7150728 DOI: 10.1155/2020/4850290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/14/2020] [Accepted: 03/13/2020] [Indexed: 11/17/2022] Open
Abstract
We employed an integrative strategy to present subtractive and comparative metabolic and genomic-based findings of therapeutic targets against Streptococcus parauberis. For the first time, we not only identified potential targets based on genomic and proteomic database analyses but also recommend a new antimicrobial drug for the treatment of olive flounder (Paralichthys olivaceus) infected with S. parauberis. To do that, 102 total annotated metabolic pathways of this bacterial strain were extracted from computational comparative metabolic and genomic databases. Six druggable proteins were identified from these metabolic pathways from the DrugBank database with their respective genes as mtnN, penA, pbp2, murB, murA, coaA, and fni out of 112 essential nonhomologous proteins. Among these hits, 26 transmembrane proteins and 77 cytoplasmic proteins were extracted as potential vaccines and drug targets, respectively. From the FDA DrugBank, ceftiofur was selected to prevent antibiotic resistance as it inhibited our selected identified target. Florfenicol is used for treatment of S. parauberis infection in flounder and was chosen as a comparator drug. All tested strains of fish isolates with S. parauberis were susceptible to ceftiofur and florfenicol with minimum inhibitory concentrations (MIC) of 0.0039-1 μg/mL and 0.5-8 μg/mL, IC50 of 0.001-0.5 μg/mL and 0.7-2.7 μg/mL, and minimum biofilm eradication concentrations (MBEC) of 2-256 μg/mL and 4-64 μg/mL, respectively. Similar susceptibility profiles for ceftiofur and florfenicol were found, with ceftiofur observed as an effective and potent antimicrobial drug against both planktonic and biofilm-forming strains of the fish pathogen Streptococcus parauberis, and it can be applied in the aquaculture industry. Thus, our predictive approach not only showed novel therapeutic agents but also indicated that marketed drugs should also be tested for efficacy against newly identified targets of this important fish pathogen.
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Affiliation(s)
- Naila Boby
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41569, Republic of Korea
| | - Muhammad Aleem Abbas
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41569, Republic of Korea
| | - Eon-Bee Lee
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41569, Republic of Korea
| | - Seung-Chun Park
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41569, Republic of Korea
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15
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Abstract
With advancements in sequencing technologies, vast amount of experimental data has accumulated. Due to rapid progress in the development of bioinformatics tools and the accumulation of data, immunoinformatics or computational immunology emerged as a special branch of bioinformatics which utilizes bioinformatics approaches for understanding and interpreting immunological data. One extensively studied aspect of applied immunology involves using available databases and tools for prediction of B- and T-cell epitopes. B and T cells comprise two arms of adaptive immunity.This chapter first reviews the methodology we used for computational identification of B- and T-cell epitopes against enterotoxigenic Escherichia coli (ETEC). Then we discuss other databases of epitopes and analysis tools for T-cell and B-cell epitope prediction and vaccine design. The predicted peptides were analyzed for conservation and population coverage. HLA distribution analysis for predicted epitopes identified efficient MHC binders. Epitopes were further tested using computational docking studies to bind in MHC-I molecule cleft. The predicted epitopes were conserved and covered more than 80% of the world population.
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MESH Headings
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Computational Biology
- Databases, Protein
- Enterotoxigenic Escherichia coli/genetics
- Enterotoxigenic Escherichia coli/immunology
- Epitope Mapping/methods
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Escherichia coli Vaccines/genetics
- Escherichia coli Vaccines/immunology
- Humans
- Models, Molecular
- Molecular Docking Simulation
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Affiliation(s)
- Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, HP, India.
| | - Kusum Mehla
- National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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16
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Identifying miltefosine-resistant key genes in protein-protein interactions network and experimental verification in Iranian Leishmania major. Mol Biol Rep 2019; 46:5371-5388. [PMID: 31385238 DOI: 10.1007/s11033-019-04992-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/19/2019] [Indexed: 12/23/2022]
Abstract
Drug resistance is a complex phenomenon during leishmaniasis chemotherapy. In this study, the genes and pathways involved in miltefosine (MIL)-resistant Leishmania were identified using microarray data and in silico approaches. GSE30685 and GSE45496 were obtained from GEO database and analyzed with GEO2R tool to identify genes involved in MIL-resistant Leishmania. 177 differentially expressed genes (DEGs) were selected from these GSEs, which about half of them were uncharacterized/hypothetical proteins. The interactions between DEGs were investigated using STRING database and protein-protein interaction (PPI) networks. Five hub nodes were found in the PPI network. The gene ontology (GO) analysis of the resulting network revealed that DNA replication (GO:0006260) and ATP hydrolysis coupled proton transport (GO:0015991) were the most enriched GO term. Iranian MIL-resistant Leishmania major (L. major) parasites were generated by exposure of wild-type isolates to the increasing concentrations of MIL over a period of 5 months. Proof of mRNA expression levels of the obtained hub genes was assessed in Iranian wild-type and acquired resistant L. major parasites by real-time PCR. A significant higher expression level of LDBPK_150170 (encoding protein phosphatase 2C, PP2C), was only observed in Iranian L. major parasites resistance to MIL. Moreover, the RT-PCR results showed that the expression of metacyclic marker (small hydrophilic endoplasmic reticulum-associated protein, SHERP) and MIL-resistant marker (Leishmania MIL-transporter, LMT) was significantly increased and decreased, respectively, in Iranian MIL-resistant L. major parasites. Taken together, these data suggested that PP2C as well as SHERP and LMT genes may be prospective targets for the treatment of MIL-resistant Leishmania.
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17
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Sohrabi SM, Mohammadi M, Tabatabaiepour SN, Tabatabaiepour SZ, Hosseini-Nave H, Soltani MF, Alizadeh H, Hadizadeh M. A SystematicIn SilicoAnalysis of theLegionellaceaeFamily for Identification of Novel Drug Target Candidates. Microb Drug Resist 2019; 25:157-166. [DOI: 10.1089/mdr.2017.0328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Mohsen Mohammadi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
| | | | | | - Hossein Hosseini-Nave
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Fazel Soltani
- Molecular Genetics and Genetic Engineering, Department of Crop Production and Plant Breeding, School of Agriculture, Razi University, Kermanshah, Iran
| | - Hosniyeh Alizadeh
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
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18
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Nazir Z, Afridi SG, Shah M, Shams S, Khan A. Reverse vaccinology and subtractive genomics-based putative vaccine targets identification for Burkholderia pseudomallei Bp1651. Microb Pathog 2018; 125:219-229. [PMID: 30243554 DOI: 10.1016/j.micpath.2018.09.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/16/2018] [Accepted: 09/18/2018] [Indexed: 12/16/2022]
Abstract
The Burkholderia pseudomallei is a unique bio-threat and causative agent of melioidosis. The B. pseudomallei Bp1651 strain has been isolated from a chronic cystic fibrosis patient. The genome-level DNA sequences information of this strain has recently been published. Unfortunately, there is no commercial vaccine available till date to combat B. pseudomallei infection. The genome-wide prioritization approaches are widely used for the identification of potential therapeutic candidates against pathogens. In the present study, we utilized the recently available annotated genomic information of B. pseudomallei Bp1651 through subtractive genomics and reverse-vaccinology strategies to identify its potential vaccine targets. The analyses identified more than 60 pathogen-specific, human host non-homologous proteins that may prioritize in future studies to investigate therapeutic targets for B. pseudomallei Bp1651. The potential B and T-cells antigenic determinant peptides from these pathogen-specific proteins were cataloged using antigenicity and epitope prediction tools. The analyses unveiled a promising antigenic peptide "FQWEFSLSV" from protein-export membrane protein (SecF) of Bp1651 strain, which was predicted to interact with multiple class I and class II MHC alleles with IC50 value < 100 nM. The molecular docking analysis verified favorable molecular interaction of this lead antigenic peptide with the ligand-binding pocket residues of HLA A*02:06 human host immune cell surface receptor. This peptide is predicted to be a suitable epitope capable to elicit the cell-mediated immune response against the B. pseudomallei pathogen. The putative epitopes and proteins identified in this study may be promising vaccine targets against Bp1651 as well as other pathogenic strains of B. pseudomallei.
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Affiliation(s)
- Zarghoona Nazir
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University Multan, Punjab, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Khyber Pakhtunkhwa, Pakistan.
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19
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Novel Insight from Computational Virtual Screening Depict the Binding Potential of Selected Phytotherapeutics Against Probable Drug Targets of Clostridium difficile. Interdiscip Sci 2018; 10:583-604. [PMID: 28217823 DOI: 10.1007/s12539-017-0215-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 12/28/2016] [Accepted: 01/03/2017] [Indexed: 10/20/2022]
Abstract
This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase. The three-dimensional structures of these targets were predicted by molecular modelling. The herbal bioactive compounds were screened by computer-aided virtual screening and binding potentials against the drug targets were predicted by molecular docking. Quercetin present in Psidium guajava (binding energy of -9.1 kcal/mol), Ellagic acid found in Punica granatum and Psidium guajava (binding energy -9.0 kcal/mol) and Curcumin, present in Curcuma longa (binding energy -7.8 kcal/mol) demonstrated minimum binding energy and more number of interacting residues with the drug targets. Further, comparative study revealed that phytoligands demonstrated better binding affinities to the drug targets in comparison with usual ligands. Thus, this investigation explores the therapeutic probabilities of selected phytoligands against the putative drug targets of C. difficile.
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20
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Birhanu BT, Lee SJ, Park NH, Song JB, Park SC. In silico analysis of putative drug and vaccine targets of the metabolic pathways of Actinobacillus pleuropneumoniae using a subtractive/comparative genomics approach. J Vet Sci 2018; 19:188-199. [PMID: 29032659 PMCID: PMC5879067 DOI: 10.4142/jvs.2018.19.2.188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/04/2017] [Accepted: 10/07/2017] [Indexed: 11/20/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a Gram-negative bacterium that resides in the respiratory tract of pigs and causes porcine respiratory disease complex, which leads to significant losses in the pig industry worldwide. The incidence of drug resistance in this bacterium is increasing; thus, identifying new protein/gene targets for drug and vaccine development is critical. In this study, we used an in silico approach, utilizing several databases including the Kyoto Encyclopedia of Genes and Genomes (KEGG), the Database of Essential Genes (DEG), DrugBank, and Swiss-Prot to identify non-homologous essential genes and prioritize these proteins for their druggability. The results showed 20 metabolic pathways that were unique and contained 273 non-homologous proteins, of which 122 were essential. Of the 122 essential proteins, there were 95 cytoplasmic proteins and 11 transmembrane proteins, which are potentially suitable for drug and vaccine targets, respectively. Among these, 25 had at least one hit in DrugBank, and three had similarity to metabolic proteins from Mycoplasma hyopneumoniae, another pathogen causing porcine respiratory disease complex; thus, they could serve as common therapeutic targets. In conclusion, we identified glyoxylate and dicarboxylate pathways as potential targets for antimicrobial therapy and tetra-acyldisaccharide 4'-kinase and 3-deoxy-D-manno-octulosonic-acid transferase as vaccine candidates against A. pleuropneumoniae.
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Affiliation(s)
- Biruk T Birhanu
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Seung-Jin Lee
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Na-Hye Park
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Ju-Beom Song
- Department of Chemistry Education, Teachers College, Kyungpook National University, Daegu 41566, Korea
| | - Seung-Chun Park
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
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21
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Gawade P, Ghosh P. Genomics driven approach for identification of novel therapeutic targets in Salmonella enterica. Gene 2018; 668:211-220. [DOI: 10.1016/j.gene.2018.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023]
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22
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Kwofie SK, Dankwa B, Odame EA, Agamah FE, Doe LPA, Teye J, Agyapong O, Miller WA, Mosi L, Wilson MD. In Silico Screening of Isocitrate Lyase for Novel Anti-Buruli Ulcer Natural Products Originating from Africa. Molecules 2018; 23:E1550. [PMID: 29954088 PMCID: PMC6100440 DOI: 10.3390/molecules23071550] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022] Open
Abstract
Buruli ulcer (BU) is caused by Mycobacterium ulcerans and is predominant in both tropical and subtropical regions. The neglected debilitating disease is characterized by chronic necrotizing skin lesions attributed to a mycolactone, which is a macrolide toxin secreted by M. ulcerans. The preferred treatment is surgical excision of the lesions followed by a prolonged combination antibiotic therapy using existing drugs such as rifampicin and streptomycin or clarithromycin. These antibiotics appear not to be adequately potent and efficacious against persistent and late stage ulcers. In addition, emerging drug resistance to treatment poses great challenges. There is a need to identify novel natural product-derived lead compounds, which are potent and efficacious for the treatment of Buruli ulcer. Natural products present a rich diversity of chemical compounds with proven activity against various infectious diseases, and therefore, are considered in this study. This study sought to computationally predict natural product-derived lead compounds with the potential to be developed further into potent drugs with better therapeutic efficacy than the existing anti-buruli ulcer compounds. The three-dimensional (3D) structure of Isocitrate lyase (ICL) of Mycobacterium ulcerans was generated using homology modeling and was further scrutinized with molecular dynamics simulations. A library consisting of 885 compounds retrieved from the AfroDb database was virtually screened against the validated ICL model using AutoDock Vina. AfroDb is a compendium of “drug-like” and structurally diverse 3D structures of natural products originating from different geographical regions in Africa. The molecular docking with the ICL model was validated by computing a Receiver Operating Characteristic (ROC) curve with a reasonably good Area Under the Curve (AUC) value of 0.89375. Twenty hit compounds, which docked firmly within the active site pocket of the ICL receptor, were assessed via in silico bioactivity and pharmacological profiling. The three compounds, which emerged as potential novel leads, comprise ZINC38143792 (Euscaphic acid), ZINC95485880, and ZINC95486305 with reasonable binding energies (high affinity) of −8.6, −8.6, and −8.8 kcal/mol, respectively. Euscaphic acid has been reported to show minimal inhibition against a drug-sensitive strain of M. tuberculosis. The other two leads were both predicted to possess dermatological activity while one was antibacterial. The leads have shown promising results pertaining to efficacy, toxicity, pharmacokinetic, and safety. These leads can be experimentally characterized to assess their anti-mycobacterial activity and their scaffolds may serve as rich skeletons for developing anti-buruli ulcer drugs.
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Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
- Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology and Infectious Pathogens, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Bismark Dankwa
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Emmanuel A Odame
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Francis E Agamah
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Lady P A Doe
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Joshua Teye
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Odame Agyapong
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Whelton A Miller
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Chemistry & Physics, College of Science and Technology, Lincoln University, Philadelphia, PA 19104, USA.
| | - Lydia Mosi
- Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology and Infectious Pathogens, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
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23
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Ahmad S, Navid A, Akhtar AS, Azam SS, Wadood A, Pérez-Sánchez H. Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae. Interdiscip Sci 2018; 11:508-526. [PMID: 29721784 DOI: 10.1007/s12539-018-0299-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/24/2018] [Indexed: 12/17/2022]
Abstract
The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K. pneumoniae LpxC (KpLpxC) topology distinct from its orthologous counterparts in other bacterial species. Molecular docking study of the protein recognized receptor antagonist compound 106, a uridine-based LpxC inhibitory compound, as a ligand best able to fit the binding pocket with a Gold Score of 67.53. Molecular dynamics simulation of docked KpLpxC revealed an alternate binding pattern of ligand in the active site. The ligand tail exhibited preferred binding to the domain I residues as opposed to the substrate binding hydrophobic channel of subdomain II, usually targeted by inhibitory compounds. Comparison with the undocked KpLpxC system demonstrated ligand induced high conformational changes in the hydrophobic channel of subdomain II in KpLpxC. Hence, ligand exerted its inhibitory potential by rendering the channel unstable for substrate binding.
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Affiliation(s)
- Sajjad Ahmad
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Afifa Navid
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amina Saleem Akhtar
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University-Mardan, Shankar Campus, Mardan, Khyber Pukhtoonkhwa, Pakistan
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
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24
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Cesur MF, Abdik E, Güven-Gülhan Ü, Durmuş S, Çakır T. Computational Systems Biology of Metabolism in Infection. EXPERIENTIA SUPPLEMENTUM (2012) 2018; 109:235-282. [PMID: 30535602 DOI: 10.1007/978-3-319-74932-7_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A systems approach to elucidate the effect of infection on cell metabolism provides several opportunities from a better understanding of molecular mechanisms to the identification of potential biomarkers and drug targets. This is obvious from the fact that we have witnessed the accelerated use of computational systems biology in the last five years to study metabolic changes in pathogen and/or host cells in response to infection. In this chapter, we aim to present a comprehensive review of the recent research by focusing on genome-scale metabolic network models of pathogen-host systems and genome-wide metabolomics and fluxomics analysis of infected cells.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ecehan Abdik
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ünzile Güven-Gülhan
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.
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25
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Hadizadeh M, Tabatabaiepour SN, Tabatabaiepour SZ, Hosseini Nave H, Mohammadi M, Sohrabi SM. Genome-Wide Identification of Potential Drug Target in Enterobacteriaceae Family: A Homology-Based Method. Microb Drug Resist 2018; 24:8-17. [DOI: 10.1089/mdr.2016.0259] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Morteza Hadizadeh
- Department of Agriculture, Payame Noor University (PNU), Tehran, Iran
| | | | | | - Hossein Hosseini Nave
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Mohammadi
- Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, Lorestan University of Medical Sciences, Khorramabad, Iran
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26
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Jamal SB, Hassan SS, Tiwari S, Viana MV, Benevides LDJ, Ullah A, Turjanski AG, Barh D, Ghosh P, Costa DA, Silva A, Röttger R, Baumbach J, Azevedo VAC. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One 2017; 12:e0186401. [PMID: 29049350 PMCID: PMC5648181 DOI: 10.1371/journal.pone.0186401] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 09/29/2017] [Indexed: 01/03/2023] Open
Abstract
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics based core-genome and core-modelome analyses. Further, using subtractive proteomics and modelomics approaches for target identification, a set of 23 proteins was selected as essential for the bacteria. Considering human as a host, eight of these proteins (glpX, nusB, rpsH, hisE, smpB, bioB, DIP1084, and DIP0983) were considered as essential and non-host homologs, and have been subjected to virtual screening using four different compound libraries (extracted from the ZINC database, plant-derived natural compounds and Di-terpenoid Iso-steviol derivatives). The proposed ligand molecules showed favorable interactions, lowered energy values and high complementarity with the predicted targets. Our proposed approach expedites the selection of C. diphtheriae putative proteins for broad-spectrum development of novel drugs and vaccines, owing to the fact that some of these targets have already been identified and validated in other organisms.
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Affiliation(s)
- Syed Babar Jamal
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Syed Shah Hassan
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Sandeep Tiwari
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcus V. Viana
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leandro de Jesus Benevides
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Asad Ullah
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, Argentina
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Daniela Arruda Costa
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Artur Silva
- Institute of Biologic Sciences, Federal University of Para, Belém, PA, Brazil
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Vasco A. C. Azevedo
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of General Biology (LGCM), Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- * E-mail:
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27
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Shen X, Wang Z, Huang X, Hu H, Wang W, Zhang X. Developing genome-reduced Pseudomonas chlororaphis strains for the production of secondary metabolites. BMC Genomics 2017; 18:715. [PMID: 28893188 PMCID: PMC5594592 DOI: 10.1186/s12864-017-4127-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The current chassis organisms or various types of cell factories have considerable advantages and disadvantages. Therefore, it is necessary to develop various chassis for an efficient production of different bioproducts from renewable resources. In this context, synthetic biology offers unique potentialities to produce value-added products of interests. Microbial genome reduction and modification are important strategies for constructing cellular chassis and cell factories. Many genome-reduced strains from Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum and Streptomyces, have been widely used for the production of amino acids, organic acids, and some enzymes. Some Pseudomonas strains could serve as good candidates for ideal chassis cells since they grow fast and can produce many valuable metabolites with low nutritional requirements and strong environmental adaptability. Pseudomonas chlororaphis GP72 is a non-pathogenic plant growth-promoting rhizobacterium that possesses capacities of tolerating various environmental stresses and synthesizing many kinds of bioactive compounds with high yield. These include phenazine-1-carboxylic acid (PCA) and 2-hydroxyphenazine (2-OH-PHZ), which exhibit strong bacteriostatic and antifungal activity toward some microbial pathogens. RESULTS We depleted 685 kb (10.3% of the genomic sequence) from the chromosome of P. chlororaphis GP72(rpeA-) by a markerless deletion method, which included five secondary metabolic gene clusters and 17 strain-specific regions (525 non-essential genes). Then we characterized the 22 multiple-deletion series (MDS) strains. Growth characteristics, production of phenazines and morphologies were changed greatly in mutants with large-fragment deletions. Some of the genome-reduced P. chlororaphis mutants exhibited more productivity than the parental strain GP72(rpeA-). For example, strain MDS22 had 4.4 times higher production of 2-OH-PHZ (99.1 mg/L) than strain GP72(rpeA-), and the specific 2-OH-PHZ production rate (mmol/g/h) increased 11.5-fold. Also and MDS10 had the highest phenazine production (852.0 mg/L) among all the studied strains with a relatively high specific total phenazine production rate (0.0056 g/g/h). CONCLUSIONS In conclusion, P. chlororaphis strains with reduced genome performed better in production of secondary metabolites than the parent strain. The newly developed mutants can be used for the further genetic manipulation to construct chassis cells with the less complex metabolic network, better regulation and more efficient productivity for diverse biotechnological applications.
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Affiliation(s)
- Xuemei Shen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.,Beijing Key Laboratory of Nutrition, Health and Food Safety, Nutrition and Health Research Institute, COFCO Corporation, No.4 Road, Future Science and Technology Park South, Beijing, 102209, People's Republic of China
| | - Zheng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
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Lohani M, Dhasmana A, Haque S, Wahid M, Jawed A, Dar SA, Mandal RK, Areeshi MY, Khan S. Proteome mining for the identification and in-silico characterization of putative drug targets of multi-drug resistant Clostridium difficile strain 630. J Microbiol Methods 2017; 136:6-10. [PMID: 28235560 DOI: 10.1016/j.mimet.2017.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/19/2017] [Accepted: 02/19/2017] [Indexed: 10/20/2022]
Abstract
Clostridium difficile is an enteric pathogen that causes approximately 20% to 30% of antibiotic-associated diarrhea. In recent years, there has been a substantial rise in the rate of C. difficile infections as well as the emergence of virulent and antibiotic resistant C. difficile strains. So, there is an urgent need for the identification of therapeutic potential targets and development of new drugs for the treatment and prevention of C. difficile infections. In the current study, we used a hybrid approach by combining sequence similarity-based approach and protein-protein interaction network topology-based approach to identify and characterize the potential drug targets of C. difficile. A total of 155 putative drug targets of C. difficile were identified and the metabolic pathway analysis of these putative drug targets using DAVID revealed that 46 of them are involved in 9 metabolic pathways. In-silico characterization of these proteins identified seven proteins involved in pathogen-specific peptidoglycan biosynthesis pathway. Three promising targets viz. homoserine dehydrogenase, aspartate-semialdehyde dehydrogenase and aspartokinase etc. were found to be involved in multiple enzymatic pathways of the pathogen. These 3 drug targets are of particular interest as they can be used for developing effective drugs against multi-drug resistant C. difficile strain 630 in the near future.
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Affiliation(s)
- Mohtashim Lohani
- Department of Biosciences, Integral University, Lucknow, India; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia.
| | - Anupam Dhasmana
- Department of Biotechnology, Amity University, Lucknow, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sajad A Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Raju K Mandal
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saif Khan
- College of Applied Medical Sciences, Hail University, Hail, Saudi Arabia
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Malekzadeh S, Sardari S, Azerang P, Khorasanizadeh D, Agha Amiri S, Azizi M, Mohajerani N, Khalaj V. Identification and Evaluation of Novel Drug Targets against the Human Fungal Pathogen Aspergillus fumigatus with Elaboration on the Possible Role of RNA-Binding Protein. IRANIAN BIOMEDICAL JOURNAL 2016; 21:84-93. [PMID: 28000798 PMCID: PMC5274715 DOI: 10.18869/acadpub.ibj.21.2.84] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Aspergillus fumigatus is an airborne opportunistic fungal pathogen that can cause fatal infections in immunocompromised patients. Although the current anti-fungal therapies are relatively efficient, some issues such as drug toxicity, drug interactions, and the emergence of drug-resistant fungi have promoted the intense research toward finding the novel drug targets. METHODS In search of new antifungal drug targets, we have used a bioinformatics approach to identify novel drug targets. We compared the whole proteome of this organism with yeast Saccharomyces cerevisiae to come up with 153 specific proteins. Further screening of these proteins revealed 50 potential molecular targets in A. fumigatus. Amongst them, RNA-binding protein (RBP) was selected for further examination. The aspergillus fumigatus RBP (AfuRBP), as a peptidylprolyl isomerase, was evaluated by homology modeling and bioinformatics tools. RBP-deficient mutant strains of A. fumigatus were generated and characterized. Furthermore, the susceptibility of these strains to known peptidylprolyl isomerase inhibitors was assessed. RESULTS AfuRBP-deficient mutants demonstrated a normal growth phenotype. MIC assay results using inhibitors of peptidylprolyl isomerase confirmed a higher sensitivity of these mutants compared to the wild type. CONCLUSION Our bioinformatics approach revealed a number of fungal-specific proteins that may be considered as new targets for drug discovery purposes. Peptidylprolyl isomerase, as a possible drug target, was evaluated against two potential inhibitors and the promising results were investigated mechanistically. Future studies would confirm the impact of such target on the antifungal discovery investigations.
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Affiliation(s)
- Saeid Malekzadeh
- Fungal Biotechnology Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran.,Bioinformatics and Drug Design Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Soroush Sardari
- Bioinformatics and Drug Design Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Parisa Azerang
- Bioinformatics and Drug Design Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Dorsa Khorasanizadeh
- Fungal Biotechnology Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Solmaz Agha Amiri
- Fungal Biotechnology Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Mohammad Azizi
- Fungal Biotechnology Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Nazanin Mohajerani
- Fungal Biotechnology Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Vahid Khalaj
- Fungal Biotechnology Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
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30
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Mehla K, Ramana J. Identification of epitope-based peptide vaccine candidates against enterotoxigenic Escherichia coli: a comparative genomics and immunoinformatics approach. MOLECULAR BIOSYSTEMS 2016; 12:890-901. [PMID: 26766131 DOI: 10.1039/c5mb00745c] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Enterotoxigenic Escherichia coli (ETEC) associated diarrhea remains a global killer with an estimated annual incidence rate of 840 million infections and 3 800 000 deaths worldwide. There are no vaccines available for ETEC and the traditional vaccine development approach is arduous and time consuming. Thus, alternative in silico approaches for epitope prediction have engrossed the interest of researchers to reduce resources and time of vaccine development. Computational approaches are playing a crucial role in fighting against rapidly growing infectious organisms. In this study we employed an integrated comparative genomics and immunoinformatics approach for proteome scale identification of peptide vaccine candidates. The proteins shared between both ETEC E24377A and H10407 strains, but lacking in commensal E. coli SE11, were subjected to immunoinformatics analysis. For a protein pool shared between different pathogenic ETEC strains, we investigated varied physicochemical and immunogenic properties to prioritize potential vaccine candidates. Epitopes were further tested using docking studies to bind in the MHC-I binding cleft. Predicted epitopes provided more than a 95% population coverage in diarrhea endemic regions presented by major MHC-I supertypes, and bind efficiently to a MHC molecule. We conclude by accentuating that the epitopes predicted in this study are believed to accelerate the development of successful vaccines to control or prevent ETEC infections, albeit the results require experimental validation using model organisms. This study underscores that in silico approaches, together with omics data, hold great potential to be utilized for rapid and reliable genome-wide screening for identification of vaccine candidates against devastating infectious diseases.
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Affiliation(s)
- Kusum Mehla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN-173234, Himachal Pradesh, India.
| | - Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN-173234, Himachal Pradesh, India.
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31
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Mehla K, Ramana J. Tapping into Salmonella typhimurium LT2 genome in a quest to explore its therapeutic arsenal: A metabolic network modeling approach. Biomed Pharmacother 2016; 86:57-66. [PMID: 27939520 DOI: 10.1016/j.biopha.2016.11.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/24/2016] [Accepted: 11/27/2016] [Indexed: 01/17/2023] Open
Abstract
S. typhimurium, the classical broad-host-range serovar is a widely distributed cause of food-borne illness. Escalating antibiotic resistance and potential of conjugal transmission to other pathogens attributable to its broad spectrum host specificities have aided S. typhimurium to emerge as a global health threat. To keep pace with ever evolving bacterial defenses, there is dire need to restock the antibiotic pipeline. Genome scale metabolic reconstructions present immense possibilities to decipher physiological properties of an organism using constraint-based methods The systems-level approaches of genome scale metabolic networks interrogation open up new avenues of drug target identification against deadly infectious diseases. We performed flux balance analysis and minimization of metabolic adjustment studies of genome scale reconstruction model of S. typhimurium targeted at identifying large number of metabolites with a potential to be utilized as therapeutic drug targets. These constraint based approaches initially predict a set of genes indispensable to bacterial survival by performing gene knockout studies which are then prioritized through a multistep process. Metabolites involved in l-rhamnose biosynthesis, peptidoglycan biosynthesis, fatty acid biosynthesis, and folate biosynthesis pathways were prioritized as candidate drug targets. This study provides a general therapeutic approach which can be effectively applied to other pathogens as well.
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Affiliation(s)
- Kusum Mehla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN 173234 Himachal Pradesh, India
| | - Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, PIN 173234 Himachal Pradesh, India.
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32
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Hossain MU, Khan MA, Hashem A, Islam MM, Morshed MN, Keya CA, Salimullah M. Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration. Front Microbiol 2016; 7:1817. [PMID: 27920755 PMCID: PMC5118456 DOI: 10.3389/fmicb.2016.01817] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/28/2016] [Indexed: 11/13/2022] Open
Abstract
Background:Shigella flexneri is a gram negative bacteria that causes the infectious disease “shigellosis.” S. flexneri is responsible for developing diarrhea, fever, and stomach cramps in human. Antibiotics are mostly given to patients infected with shigella. Resistance to antibiotics can hinder its treatment significantly. Upon identification of essential therapeutic targets, vaccine and drug could be effective therapy for the treatment of shigellosis. Methods: The study was designed for the identification and qualitative characterization for potential drug targets from S. flexneri by using the subtractive proteome analysis. A set of computational tools were used to identify essential proteins those are required for the survival of S. flexneri. Total proteome (13,503 proteins) of S. flexneri was retrieved from NCBI and further analyzed by subtractive channel analysis. After identification of the metabolic proteins we have also performed its qualitative characterization to pave the way for the identification of promising drug targets. Results: Subtractive analysis revealed that a list of 53 targets of S. flexneri were human non-homologous essential metabolic proteins that might be used for potential drug targets. We have also found that 11 drug targets are involved in unique pathway. Most of these proteins are cytoplasmic, can be used as broad spectrum drug targets, can interact with other proteins and show the druggable properties. The functionality and drug binding site analysis suggest a promising effective way to design the new drugs against S. flexneri. Conclusion: Among the 53 therapeutic targets identified through this study, 13 were found highly potential as drug targets based on their physicochemical properties whilst only one was found as vaccine target against S. flexneri. The outcome might also be used as module as well as circuit design in systems biology.
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Affiliation(s)
- Mohammad Uzzal Hossain
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University Tangail, Bangladesh
| | - Md Arif Khan
- Department of Science and Humanities, Military Institute of Science and Technology, Mirpur Cantonment Dhaka, Bangladesh
| | - Abu Hashem
- Microbial Biotechnology Division, National Institute of Biotechnology Savar, Bangladesh
| | - Md Monirul Islam
- Department of Biotechnology and Genetic Engineering, Life Science Faculty, Mawlana Bhashani Science and Technology University Tangail, Bangladesh
| | - Mohammad Neaz Morshed
- Department of Science and Humanities, Military Institute of Science and Technology, Mirpur Cantonment Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University Bashundhara, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology Savar, Bangladesh
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Surface proteome mining for identification of potential vaccine candidates against Campylobacter jejuni: an in silico approach. Funct Integr Genomics 2016; 17:27-37. [PMID: 27778110 DOI: 10.1007/s10142-016-0530-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 01/23/2023]
Abstract
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task. Omics techniques coupled with sequencing data have engaged researcher's attention to reduce the time and resources applied in the process of vaccine development. Recently, there has been remarkable increase in development of in silico analysis tools for efficiently mining biological information obscured in the genome. In silico approaches have been crucial for combating infectious diseases by accelerating the pace of vaccine development. This study employed a range of bioinformatics approaches for proteome scale identification of peptide vaccine candidates. Whole proteome of C. jejuni was investigated for varied properties like antigenicity, allergenicity, major histocompatibility class (MHC)-peptide interaction, immune cell processivity, HLA distribution, conservancy, and population coverage. Predicted epitopes were further tested for binding in MHC groove using computational docking studies. The predicted epitopes were conserved; covered more than 80 % of the world population and were presented by MHC-I supertypes. We conclude by underscoring that the epitopes predicted are believed to expedite the development of successful vaccines to control or prevent C. jejuni infections albeit the results need to be experimentally validated.
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Hassan A, Naz A, Obaid A, Paracha RZ, Naz K, Awan FM, Muhmmad SA, Janjua HA, Ahmad J, Ali A. Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics 2016; 17:732. [PMID: 27634541 PMCID: PMC5025611 DOI: 10.1186/s12864-016-2951-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/19/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. RESULTS The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. CONCLUSION The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
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Affiliation(s)
- Afreenish Hassan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Anam Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Ayesha Obaid
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Kanwal Naz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Faryal Mehwish Awan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Syed Aun Muhmmad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
- Department of Computer Science and Information Technology, Stratford University, Falls Church, VA 22043 USA
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan
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Drug Target Identification and Prioritization for Treatment of Ovine Foot Rot: An In Silico Approach. Int J Genomics 2016; 2016:7361361. [PMID: 27379247 PMCID: PMC4917682 DOI: 10.1155/2016/7361361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/16/2016] [Indexed: 02/06/2023] Open
Abstract
Ovine foot rot is an infection of the feet of sheep, mainly caused by Dichelobacter nodosus. In its virulent form, it is highly contagious and debilitating, causing significant losses in the form of decline in wool growth and quality and poor fertility. Current methods of treatment are ineffective in complete eradication. Effective antibiotic treatment of foot rot is hence necessary to ensure better outcomes during control phases by reduction in culling count and the possibility of carriers of the infection. Using computational approaches, we have identified a set of 297 proteins that are essential to the D. nodosus and nonhomologous with sheep proteins. These proteins may be considered as potential vaccine candidates or drug targets for designing antibiotics against the bacterium. This core set of drug targets have been analyzed for pathway annotation to identify 67 proteins involved in unique bacterial pathways. Choke-point analysis on the drug targets identified 138 choke-point proteins, 29 involved in unique bacterial pathways. Subcellular localization was also predicted for each target to identify the ones that are membrane associated or secreted extracellularly. In addition, a total of 13 targets were identified that are common in at least 10 pathogenic bacterial species.
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Batool N, Waqar M, Batool S. Comparative genomics study for identification of putative drug targets in Salmonella typhi Ty2. Gene 2016; 576:544-59. [PMID: 26555890 DOI: 10.1016/j.gene.2015.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 11/16/2022]
Abstract
Typhoid presents a major health concern in developing countries with an estimated annual infection rate of 21 million. The disease is caused by Salmonella typhi, a pathogenic bacterium acquiring multiple drug resistance. We aim to identify proteins that could prove to be putative drug targets in the genome of S. typhi str. Ty2. We employed comparative and subtractive genomics to identify targets that are absent in humans and are essential to S. typhi Ty2. We concluded that 46 proteins essential to pathogen are absent in the host genome. Filtration on the basis of drug target prioritization singled out 20 potentially therapeutic targets. Their absence in the host and specificity to S. typhi Ty2 makes them ideal targets for treating typhoid in Homo sapiens. 3D structures of two of the final target enzymes, MurA and MurB have been predicted via homology modeling which are then used for a docking study.
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Affiliation(s)
- Nisha Batool
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45520, Pakistan.
| | - Maleeha Waqar
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45520, Pakistan.
| | - Sidra Batool
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45520, Pakistan.
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Mondal SI, Ferdous S, Jewel NA, Akter A, Mahmud Z, Islam MM, Afrin T, Karim N. Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach. Adv Appl Bioinform Chem 2015; 8:49-63. [PMID: 26677339 PMCID: PMC4677596 DOI: 10.2147/aabc.s88522] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen’s survival but absent in its human host. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified 350 putative target proteins in E. coli O157:H7 which showed no similarity to human proteins. Further bio-informatic approaches including prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characteristics greatly aided in filtering the potential drug targets from 350 to 120. Ultimately, 44 non-homologous essential proteins of E. coli O157:H7 were prioritized and proved to have the eligibility to become novel broad-spectrum antibiotic targets and DNA polymerase III alpha (dnaE) was the top-ranked among these targets. Moreover, druggability of each of the identified drug targets was evaluated by the DrugBank database. In addition, 3D structure of the dnaE was modeled and explored further for in silico docking with ligands having potential druggability. Finally, we confirmed that the compounds N-coeleneterazine and N-(1,4-dihydro-5H-tetrazol-5-ylidene)-9-oxo-9H-xanthene-2-sulfon-amide were the most suitable ligands of dnaE and hence proposed as the potential inhibitors of this target protein. The results of this study could facilitate the discovery and release of new and effective drugs against E. coli O157:H7 and other deadly human bacterial pathogens.
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Affiliation(s)
- Shakhinur Islam Mondal
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh ; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Sabiha Ferdous
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nurnabi Azad Jewel
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Arzuba Akter
- Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh ; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Zabed Mahmud
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Muzahidul Islam
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Tanzila Afrin
- Department of Pharmacy, East West University, Aftabnagar, Bangladesh
| | - Nurul Karim
- Biochemistry and Molecular Biology Department, Jahangirnagar University, Savar, Bangladesh ; Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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Vishnu US, Sankarasubramanian J, Gunasekaran P, Rajendhran J. Novel Vaccine Candidates against Brucella melitensis Identified through Reverse Vaccinology Approach. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:722-9. [PMID: 26479901 DOI: 10.1089/omi.2015.0105] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Global health therapeutics is a rapidly emerging facet of postgenomics medicine. In this connection, Brucella melitensis is an intracellular bacterium that causes the zoonotic infectious disease, brucellosis. Presently, no licensed vaccines are available for human brucellosis. Here, we report the identification of potential vaccine candidates against B. melitensis using a reverse vaccinology approach. Based on a systematic screening of exoproteome and secretome of B. melitensis 16 M, we identified eight proteins as potential vaccine candidates, including LPS-assembly protein LptD, a polysaccharide export protein, a cell surface protein, heme transporter BhuA, flagellin FliC, 7-alpha-hydroxysteroid dehydrogenase, immunoglobulin-binding protein EIBE, and hemagglutinin. Among these, the roles of BhuA and hemagglutinin in the virulence of Brucella are essential to establish infection. Roles of other proteins in the virulence are yet to be studied. Prediction of protein-protein interactions revealed that these proteins can interact with other proteins involved in virulence, secretion system, metabolism, and transport. From these eight potential vaccine candidates, we predicted three surface exposed novel antigenic epitopes that can induce both B-cell and T-cell immune responses. These peptides can be used for the development of either exclusive peptide vaccines or multi-component vaccines against human brucellosis. Reverse vaccinology is an important strategy for discovery of novel global health therapeutics.
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Affiliation(s)
- Udayakumar S Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University , Madurai, India
| | | | - Paramasamy Gunasekaran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University , Madurai, India
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University , Madurai, India
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Mehla K, Ramana J. Novel Drug Targets for Food-Borne Pathogen Campylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:393-406. [PMID: 26061459 DOI: 10.1089/omi.2015.0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Campylobacters are a major global health burden and a cause of food-borne diarrheal illness and economic loss worldwide. In developing countries, Campylobacter infections are frequent in children under age two and may be associated with mortality. In developed countries, they are a common cause of bacterial diarrhea in early adulthood. In the United States, antibiotic resistance against Campylobacter is notably increased from 13% in 1997 to nearly 25% in 2011. Novel drug targets are urgently needed but remain a daunting task to accomplish. We suggest that omics-guided drug discovery is timely and worth considering in this context. The present study employed an integrated subtractive genomics and comparative metabolic pathway analysis approach. We identified 16 unique pathways from Campylobacter when compared against H. sapiens with 326 non-redundant proteins; 115 of these were found to be essential in the Database of Essential Genes. Sixty-six proteins among these were non-homologous to the human proteome. Six membrane proteins, of which four are transporters, have been proposed as potential vaccine candidates. Screening of 66 essential non-homologous proteins against DrugBank resulted in identification of 34 proteins with drug-ability potential, many of which play critical roles in bacterial growth and survival. Out of these, eight proteins had approved drug targets available in DrugBank, the majority serving crucial roles in cell wall synthesis and energy metabolism and therefore having the potential to be utilized as drug targets. We conclude by underscoring that screening against these proteins with inhibitors may aid in future discovery of novel therapeutics against campylobacteriosis in ways that will be pathogen specific, and thus have minimal toxic effect on host. Omics-guided drug discovery and bioinformatics analyses offer the broad potential for veritable advances in global health relevant novel therapeutics.
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Affiliation(s)
- Kusum Mehla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology , Solan, Himachal Pradesh, India
| | - Jayashree Ramana
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology , Solan, Himachal Pradesh, India
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Rahman MA, Sobia P, Dwivedi VP, Bhawsar A, Singh DK, Sharma P, Moodley P, Van Kaer L, Bishai WR, Das G. Mycobacterium tuberculosis TlyA Protein Negatively Regulates T Helper (Th) 1 and Th17 Differentiation and Promotes Tuberculosis Pathogenesis. J Biol Chem 2015; 290:14407-17. [PMID: 25847237 PMCID: PMC4505508 DOI: 10.1074/jbc.m115.653600] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, is an ancient pathogen and a major cause of death worldwide. Although various virulence factors of M. tuberculosis have been identified, its pathogenesis remains incompletely understood. TlyA is a virulence factor in several bacterial infections and is evolutionarily conserved in many Gram-positive bacteria, but its function in M. tuberculosis pathogenesis has not been elucidated. Here, we report that TlyA significantly contributes to the pathogenesis of M. tuberculosis. We show that a TlyA mutant M. tuberculosis strain induces increased IL-12 and reduced IL-1β and IL-10 cytokine responses, which sharply contrasts with the immune responses induced by wild type M. tuberculosis. Furthermore, compared with wild type M. tuberculosis, TlyA-deficient M. tuberculosis bacteria are more susceptible to autophagy in macrophages. Consequently, animals infected with the TlyA mutant M. tuberculosis organisms exhibited increased host-protective immune responses, reduced bacillary load, and increased survival compared with animals infected with wild type M. tuberculosis. Thus, M. tuberculosis employs TlyA as a host evasion factor, thereby contributing to its virulence.
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Affiliation(s)
- Md Aejazur Rahman
- From the School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001 South Africa
| | - Parveen Sobia
- From the School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001 South Africa
| | - Ved Prakash Dwivedi
- From the School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001 South Africa
| | - Aakansha Bhawsar
- the Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dhiraj Kumar Singh
- the Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pawan Sharma
- the North Eastern Region Biotechnology Programme Management Cell, Defense Colony, New Delhi, India
| | - Prashini Moodley
- From the School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001 South Africa
| | - Luc Van Kaer
- the Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - William R Bishai
- the Center for Tuberculosis Research, Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland 21231-1001, and
| | - Gobardhan Das
- From the School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001 South Africa, the Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
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Sarangi AN, Lohani M, Aggarwal R. Proteome mining for drug target identification in Listeria monocytogenes strain EGD-e and structure-based virtual screening of a candidate drug target penicillin binding protein 4. J Microbiol Methods 2015; 111:9-18. [DOI: 10.1016/j.mimet.2015.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 12/27/2022]
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Li W, Fan X, Long Q, Xie L, Xie J. Mycobacterium tuberculosis effectors involved in host-pathogen interaction revealed by a multiple scales integrative pipeline. INFECTION GENETICS AND EVOLUTION 2015; 32:1-11. [PMID: 25709069 DOI: 10.1016/j.meegid.2015.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/02/2015] [Accepted: 02/14/2015] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter host immunity. Proteins are one important player in the host-pathogen interaction. A comprehensive list of such proteins will benefit our understanding of pathogenesis of Mtb. METHODS A genome-scale dataset was created from different sources of published data: global gene expression studies in disease models; genome-wide insertional mutagenesis defining gene essentiality under different conditions; genes lost in clinical isolates; subcellular localization analysis and non-homology analysis. Using data mining and meta-analysis, expressed proteins critical for intracellular survival of Mtb are first identified, followed by subcellular localization analysis, finally filtering a series of subtractive channel of analysis to find out promising drug target candidates. RESULTS The analysis found 54 potential candidates essential for the intracellular survival of the pathogen and non-homologous to host or gut flora, and might be promising drug targets. CONCLUSION Based on our meta-analysis and bioinformatics analysis, 54 hits were found from Mtb around 4000 open reading frames. These hits can be good candidates for further experimental investigation.
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Affiliation(s)
- Wu Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Shandong 250022, China
| | - Quanxin Long
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases of the Ministry of Education, Chongqing Medical University, 1 Medical Road, Yuzhong District, Chongqing 400016, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Uddin R, Saeed K, Khan W, Azam SS, Wadood A. Metabolic pathway analysis approach: Identification of novel therapeutic target against methicillin resistant Staphylococcus aureus. Gene 2015; 556:213-26. [DOI: 10.1016/j.gene.2014.11.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/18/2014] [Accepted: 11/25/2014] [Indexed: 12/31/2022]
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Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. BIOMED RESEARCH INTERNATIONAL 2015; 2015:139580. [PMID: 25705648 PMCID: PMC4325212 DOI: 10.1155/2015/139580] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 12/23/2022]
Abstract
Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.
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Sivashanmugam M, Nagarajan H, Vetrivel U, Ramasubban G, Therese KL, Narahari MH. In silico analysis and prioritization of drug targets in Fusarium solani. Med Hypotheses 2014; 84:81-4. [PMID: 25555413 DOI: 10.1016/j.mehy.2014.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 02/08/2023]
Abstract
Mycotic keratitis has emerged as a major ophthalmic problem and a leading cause of blindness, since its recognition in 1879. Filamentous fungi are major causative of mycotic keratitis. In India, the main etiological organism responsible for mycotic keratitis is Aspergillus species followed by Fusarium species. In South India, Fusarium based keratitis scales up to 43%. Nearly one-third of mycotic keratitis treatment results in failure, as fungal infections are highly resistant to antibiotic therapies. Therefore, there is need to determine novel and specific targets to constrain Fusarium infections in human eye. In this study, we implemented subtractive proteomics coupled with in silico functional annotation to prioritize potential and specific drug targets which can be used to modulate the virulence of Fusarium solani subsp.pisi (Nectria haematococca MPVI). The results infer that Thiamine thiazole synthase (Thi4), an intracellular membrane bound protein as the potential target, which is a core protein in biological and metabolic process of this pathogen. Moreover, this protein occurs in the thiamine thiazole biosynthesis pathway which is unique to F.solani and devoid in human. Hence, we predicted a plausible structure for this protein and also performed ligand-binding cavity analysis which can be for a strong base for drug designing studies. This study will pave way in better understanding of potential drug targets in F.solani and also leading to therapeutic interventions of fungal keratitis.
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Affiliation(s)
| | | | | | - Gayathri Ramasubban
- L&T Microbiology Research Centre, Vision Research Foundation, Chennai, India
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Hassan SS, Tiwari S, Guimarães LC, Jamal SB, Folador E, Sharma NB, de Castro Soares S, Almeida S, Ali A, Islam A, Póvoa FD, de Abreu VAC, Jain N, Bhattacharya A, Juneja L, Miyoshi A, Silva A, Barh D, Turjanski AG, Azevedo V, Ferreira RS. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014; 15 Suppl 7:S3. [PMID: 25573232 PMCID: PMC4243142 DOI: 10.1186/1471-2164-15-s7-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.
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Ghosh S, Prava J, Samal HB, Suar M, Mahapatra RK. Comparative genomics study for the identification of drug and vaccine targets in Staphylococcus aureus: MurA ligase enzyme as a proposed candidate. J Microbiol Methods 2014; 101:1-8. [DOI: 10.1016/j.mimet.2014.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/10/2014] [Accepted: 03/19/2014] [Indexed: 11/27/2022]
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Uddin R, Saeed K. Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. Comput Biol Chem 2014; 48:55-63. [DOI: 10.1016/j.compbiolchem.2013.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 01/18/2023]
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Comparative genomics study for identification of drug and vaccine targets in Vibrio cholerae: MurA ligase as a case study. Genomics 2013; 103:83-93. [PMID: 24368230 DOI: 10.1016/j.ygeno.2013.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/11/2013] [Accepted: 12/12/2013] [Indexed: 12/15/2022]
Abstract
A systematic workflow consisting of comparative genomics, metabolic pathways analysis and additional drug prioritization parameters identified 264 proteins of Vibrio cholerae which were predicted to be absent in Homo sapiens. Among these, 40 proteins were identified as essential proteins that could serve as potential drug and vaccine targets. Additional prioritization parameters characterized 11 proteins as vaccine candidates while druggability of each of the identified proteins as evaluated by the Drug Bank database which prioritized 16 proteins suitable for drug targets. As a case study, we built a homology model of one of the potential drug targets, MurA ligase, using MODELLER (9v12) software. The model has been further explored for in silico docking with inhibitors having druggability potential from the Drug Bank database. Results from this study could facilitate selecting V. cholerae proteins for drug design and vaccine production pipelines in future.
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Ravindranath BS, Krishnamurthy V, Krishna V, Vasudevanayaka KBL. in silico analyses of metabolic pathway and protein interaction network for identification of next gen therapeutic targets in Chlamydophila pneumoniae. Bioinformation 2013; 9:605-9. [PMID: 23904736 PMCID: PMC3725000 DOI: 10.6026/97320630009605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 06/03/2013] [Accepted: 06/07/2013] [Indexed: 12/02/2022] Open
Abstract
Chlamydophila pneumoniae, the causative agent of chronic obstructive pulmonary disease (COPD), is presently the fifth mortality causing chronic disease in the world. The understanding of disease and treatment options are limited represents a severe concern and a need for better therapeutics. With the advancements in the field of complete genome sequencing and computational approaches development have lead to metabolic pathway analysis and protein-protein interaction network which provides vital evidence to the protein function and has been appropriate to the fields such as systems biology and drug discovery. Protein interaction network analysis allows us to predict the most potential drug targets among large number of the non-homologous proteins involved in the unique metabolic pathway. A computational comparative metabolic pathway analysis of the host H. sapiens and the pathogen C pneumoniae AR39 has been carried out at three level analyses. Firstly, metabolic pathway analysis was performed to identify unique metabolic pathways and non-homologous proteins were identified. Secondly, essentiality of the proteins was checked, where these proteins contribute to the growth and survival of the organism. Finally these proteins were further subjected to predict protein interaction networks. Among the total 65 pathways in the C pneumoniae AR39 genome 10 were identified as the unique metabolic pathways which were not found in the human host, 32 enzymes were predicted as essential and these proteins were considered for protein interaction analysis, later using various criteria's we have narrowed down to prioritize ribonucleotide-diphosphate reductase subunit beta as a potential drug target which facilitate for the successful entry into drug designing.
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Affiliation(s)
- Bilachi S Ravindranath
- Department of Biotechnology, PES Institute of Technology (Recognized research centre of Kuvempu University), BSK III Stage, Bangalore - 560085, India
| | - Venkatappa Krishnamurthy
- Department of Biotechnology, PES Institute of Technology (Recognized research centre of Kuvempu University), BSK III Stage, Bangalore - 560085, India
| | - Venkatarangaiah Krishna
- Department of Biotechnology and Bioinformatics, Kuvempu University, Shankarghatta -577451, India
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