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Padhi AK, Maurya S. Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:173-220. [PMID: 38448135 DOI: 10.1016/bs.apcsb.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Antimicrobial resistance (AMR) is a growing global concern with significant implications for infectious disease control and therapeutics development. This chapter presents a comprehensive overview of computational methods in the study of AMR. We explore the prevalence and statistics of AMR, underscoring its alarming impact on public health. The role of AMR in infectious disease outbreaks and its impact on therapeutics development are discussed, emphasizing the need for novel strategies. Resistance mutations are pivotal in AMR, enabling pathogens to evade antimicrobial treatments. We delve into their importance and contribution to the spread of AMR. Experimental methods for quantitatively evaluating resistance mutations are described, along with their limitations. To address these challenges, computational methods provide promising solutions. We highlight the advantages of computational approaches, including rapid analysis of large datasets and prediction of resistance profiles. A comprehensive overview of computational methods for studying AMR is presented, encompassing genomics, proteomics, structural bioinformatics, network analysis, and machine learning algorithms. The strengths and limitations of each method are briefly outlined. Additionally, we introduce ResScan-design, our own computational method, which employs a protein (re)design protocol to identify potential resistance mutations and adaptation signatures in pathogens. Case studies are discussed to showcase the application of ResScan in elucidating hotspot residues, understanding underlying mechanisms, and guiding the design of effective therapies. In conclusion, we emphasize the value of computational methods in understanding and combating AMR. Integration of experimental and computational approaches can expedite the discovery of innovative antimicrobial treatments and mitigate the threat posed by AMR.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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2
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Ayu Eka Pitaloka D, Izzati A, Rafa Amirah S, Abdan Syakuran L, Muhammad Irham L, Darumas Putri A, Adikusuma W. Bioinformatics Analysis to Uncover the Potential Drug Targets Responsible for Mycobacterium tuberculosis Peptidoglycan and Lysine Biosynthesis. Bioinform Biol Insights 2023; 17:11779322231171774. [PMID: 37187890 PMCID: PMC10176782 DOI: 10.1177/11779322231171774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Drug-resistant tuberculosis (TB), which results mainly from the selection of naturally resistant strains of Mycobacterium tuberculosis (MTB) due to mismanaged treatment, poses a severe challenge to the global control of TB. Therefore, screening novel and unique drug targets against this pathogen is urgently needed. The metabolic pathways of Homo sapiens and MTB were compared using the Kyoto Encyclopedia of Genes and Genomes tool, and further, the proteins that are involved in the metabolic pathways of MTB were subtracted and proceeded to protein-protein interaction network analysis, subcellular localization, drug ability testing, and gene ontology. The study aims to identify enzymes for the unique pathways for further screening to determine the feasibility of the therapeutic targets. The qualitative characteristics of 28 proteins identified as drug target candidates were studied. The results showed that 12 were cytoplasmic, 2 were extracellular, 12 were transmembrane, and 3 were unknown. Furthermore, druggability analysis revealed 14 druggable proteins, of which 12 were novel and responsible for MTB peptidoglycan and lysine biosynthesis. The novel targets obtained in this study are used to develop antimicrobial treatments against pathogenic bacteria. Future studies should further shed light on the clinical implementation to identify antimicrobial therapies against MTB.
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Affiliation(s)
- Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical
Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center for Translational Biomarker
Research, Universitas Padjadjaran, Sumedang, Indonesia
| | - Afifah Izzati
- Department of Pharmacology and Clinical
Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Siti Rafa Amirah
- Department of Pharmacology and Clinical
Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Luqman Abdan Syakuran
- Genetics and Molecular Laboratory,
Faculty of Biology, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Lalu Muhammad Irham
- Faculty of Pharmacy, Universitas Ahmad
Dahlan, Yogyakarta, Indonesia
- Research Center for Pharmaceutical
Ingrediensts and Traditional Medicine, National Research and Inovation Agency
(BRIN), South Tangerang, Indonesia
| | | | - Wirawan Adikusuma
- Department of Pharmacy, Faculty of
Health Science, Universitas Muhammadiyah Mataram, Mataram, Indonesia
- Research Center for Vaccine and Drugs,
National Research and Inovation Agency (BRIN), South Tangerang, Indonesia
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3
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Singh V, Dziwornu GA, Chibale K. The implication of Mycobacterium tuberculosis-mediated metabolism of targeted xenobiotics. Nat Rev Chem 2023; 7:340-354. [PMID: 37117810 PMCID: PMC10026799 DOI: 10.1038/s41570-023-00472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 03/29/2023]
Abstract
Drug metabolism is generally associated with liver enzymes. However, in the case of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), Mtb-mediated drug metabolism plays a significant role in treatment outcomes. Mtb is equipped with enzymes that catalyse biotransformation reactions on xenobiotics with consequences either in its favour or as a hindrance by deactivating or activating chemical entities, respectively. Considering the range of chemical reactions involved in the biosynthetic pathways of Mtb, information related to the biotransformation of antitubercular compounds would provide opportunities for the development of new chemical tools to study successful TB infections while also highlighting potential areas for drug discovery, host-directed therapy, dose optimization and elucidation of mechanisms of action. In this Review, we discuss Mtb-mediated biotransformations and propose a holistic approach to address drug metabolism in TB drug discovery and related areas. ![]()
Mycobacterium tuberculosis-mediated metabolism of xenobiotics poses an important research question for antitubercular drug discovery. Identification of the metabolic fate of compounds can inform requisite structure–activity relationship strategies early on in a drug discovery programme towards improving the properties of the compound.
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Affiliation(s)
- Vinayak Singh
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Godwin Akpeko Dziwornu
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Department of Chemistry, University of Cape Town, Rondebosch, South Africa
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4
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Progress Report: Antimicrobial Drug Discovery in the Resistance Era. Pharmaceuticals (Basel) 2022; 15:ph15040413. [PMID: 35455410 PMCID: PMC9030565 DOI: 10.3390/ph15040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.
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Isa MA, Abubakar MB, Mohammed MM, Ibrahim MM, Gubio FA. Identification of potent inhibitors of ATP synthase subunit c (AtpE) from Mycobacterium tuberculosis using in silico approach. Heliyon 2021; 7:e08482. [PMID: 34934830 PMCID: PMC8654640 DOI: 10.1016/j.heliyon.2021.e08482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/11/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022] Open
Abstract
ATP synthase subunit c (AtpE) is an enzyme that catalyzes the production of ATP from ADP in the presence of sodium or proton gradient from Mycobacterium tuberculosis (MTB). This enzyme considered an essential target for drug design and shares the same pathway with the target of Isoniazid. Thus, this enzyme would serve as an alternative target of the Isoniazid. The three dimensional (3D) model structure of the AtpE was constructed based on the principle of homology modeling using the Modeller9.16. The developed model was subjected to energy minimization and refinement using molecular dynamic (MD) simulation. The minimized model structure was searched against Zinc and PubChem database to determine ligands that bind to the enzyme with minimum binding energy using RASPD and PyRx tool. A total of 4776 compounds capable of bindings to AtpE with minimum binding energy were selected. These compounds further screened for physicochemical properties (Lipinski rule of five). All the compounds that possessed the desirable property selected and used for molecular docking analysis. Five (5) compounds with minimum binding energies ranged between ─8.69, and ─8.44 kcal/mol, less than the free binding energy of ATP were selected. These compounds further screened for the absorption, distribution, metabolism, excretion, and toxicity (ADME and toxicity) properties. Of the five compounds, three (ZINC14732869, ZINC14742188, and ZINC12205447) fitted all the ADME and toxicity properties and subjected to MD simulation and Molecular Mechanics Generalized Born and Surface Area (MM-GBSA) analyses. The results indicated that the ligands formed relatively stable complexes and had free binding energies, less than the binding energy of the ATP. Therefore, these ligands considered as prospective inhibitors of MTB after successful experimental validation.
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Affiliation(s)
- Mustafa Alhaji Isa
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Nigeria
| | - Mustapha B Abubakar
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Maiduguri, Nigeria
| | - Mohammed Mustapha Mohammed
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Nigeria
| | - Muhammad Musa Ibrahim
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Nigeria
| | - Falmata Audu Gubio
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Nigeria
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6
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Cloete R, Shahbaaz M, Grobbelaar M, Sampson SL, Christoffels A. In silico repurposing of a Novobiocin derivative for activity against latency associated Mycobacterium tuberculosis drug target nicotinate-nucleotide adenylyl transferase (Rv2421c). PLoS One 2021; 16:e0259348. [PMID: 34727137 PMCID: PMC8562812 DOI: 10.1371/journal.pone.0259348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Nicotinamide-nucleotide adenylyl transferase (Rv2421c) was selected as a potential drug target, because it has been shown, in vitro, to be essential for Mycobacterium tuberculosis growth. It is conserved between mycobacterium species, is up-regulated during dormancy, has a known 3D crystal structure and has no known human homologs. A model of Rv2421c in complex with nicotinic acid adenine dinucleotide and magnesium ion was constructed and subject tovirtual ligand screening against the Prestwick Chemical Library and the ZINC database, which yielded 155 potential hit molecules. Of the 155 compounds identified five were pursued further using an IC50 based 3D-QSAR study. The 3D-QSAR model validated the inhibition properties of the five compounds based on R2 value of 0.895 and Q2 value of 0.944 compared to known inhibitors of Rv2421c. Higher binding affinities was observed for the novel ZINC13544129 and two FDA approved compounds (Novobiocin sodium salt, Sulfasalazine). Similarly, the total interaction energy was found to be the highest for Cromolyn disodium system (-418.88 kJ/mol) followed by Novobiocin (-379.19 kJ/mol) and Sulfasalazine with (-330.13 kJ/mol) compared to substrate DND having (-185.52 kJ/mol). Subsequent in vitro testing of the five compounds identified Novobiocin sodium salt with activity against Mycobacterium tuberculosis at 50 μM, 25μM and weakly at 10μM concentrations. Novobiocin salt interacts with a MG ion and active site residues His20, Thr86, Gly107 and Leu164 similar to substrate DND of Mycobacterium tuberculosis Rv2421c. Additional in silico structural analysis of known Novobiocin sodium salt derivatives against Rv2421c suggest Coumermycin as a promising alternative for the treatment of Mycobacterium tuberculosis based on large number of hydrogen bond interactions with Rv2421c similar in comparison to Novobiocin salt and substrate DND.
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Affiliation(s)
- Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Melanie Grobbelaar
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, Cape Town, South Africa
| | - Samantha L. Sampson
- Faculty of Medicine and Health Sciences, Division of Molecular Biology and Human Genetics, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, Cape Town, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
- * E-mail:
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7
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Lima RM, Freitas E Silva KS, Silva LDC, Ribeiro JFR, Neves BJ, Brock M, Soares CMDA, da Silva RA, Pereira M. A structure-based approach for the discovery of inhibitors against methylcitrate synthase of Paracoccidioides lutzii. J Biomol Struct Dyn 2021; 40:9361-9373. [PMID: 34060981 DOI: 10.1080/07391102.2021.1930584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Paracoccidioidomycosis (PCM) is a systemic mycosis, endemic in Latin America, caused by fungi of the genus Paracoccidioides. The treatment of PCM is complex, requiring a long treatment period, which often results in serious side effects. The aim of this study was to screen for inhibitors of a specific target of the fungus that is absent in humans. Methylcitrate synthase (MCS) is a unique enzyme of microorganisms and is responsible for the synthesis of methylcitrate at the beginning of the propionate degradation pathway. This pathway is essential for several microorganisms, since the accumulation of propionyl-CoA can impair virulence and prevent the development of the pathogen. We performed the modeling and molecular dynamics of the structure of Paracoccidioides lutzii MCS (PlMCS) and performed a virtual screening on 89,415 compounds against the active site of the enzyme. The compounds were selected according to the affinity and efficiency criteria of in vitro tests. Six compounds were able to inhibit the enzymatic activity of recombinant PlMCS but only the compound ZINC08964784 showed fungistatic and fungicidal activity against Paracoccidioides spp. cells. The analysis of the interaction profile of this compound with PlMCS showed its effectiveness in terms of specificity and stability when compared to the substrate (propionyl-CoA) of the enzyme. In addition, this compound did not show cytotoxicity in mammalian cells, with an excellent selectivity index. Our results suggest that the compound ZINC08964784 may become a promising alternative antifungal against Paracoccidioides spp. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Raisa Melo Lima
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goiás, Brazil.,Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
| | | | - Lívia do Carmo Silva
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
| | | | - Bruno Junior Neves
- Faculty of Pharmacy, Laboratory for Molecular Modeling and Drug Design, Federal University of Goiás, Goiânia, Brazil
| | - Matthias Brock
- School of Life Science, Fungal Biology Group, University of Nottingham, Nottingham, UK
| | | | - Roosevelt Alves da Silva
- Collaborative Nucleus of Biosystems, Institute of Exact Sciences, Federal University of Jataí, Jataí, Brazil
| | - Maristela Pereira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goiás, Brazil.,Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
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8
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Shahbaaz M, Cloete R, Grobbelaar M, Sampson S, Christoffels A. Structure based identification of novel inhibitors against ATP synthase of Mycobacterium tuberculosis: A combined in silico and in vitro study. Int J Biol Macromol 2019; 135:582-590. [DOI: 10.1016/j.ijbiomac.2019.05.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 11/29/2022]
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9
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Metabolite Profiling: A Tool for the Biochemical Characterisation of Mycobacterium sp. Microorganisms 2019; 7:microorganisms7050148. [PMID: 31130621 PMCID: PMC6560386 DOI: 10.3390/microorganisms7050148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/25/2019] [Indexed: 12/19/2022] Open
Abstract
Over the last decades, the prevalence of drug-resistance in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has increased. These findings have rekindled interest in elucidating the unique adaptive molecular and biochemistry physiology of Mycobacterium. The use of metabolite profiling independently or in combination with other levels of "-omic" analyses has proven an effective approach to elucidate key physiological/biochemical mechanisms associated with Mtb throughout infection. The following review discusses the use of metabolite profiling in the study of tuberculosis, future approaches, and the technical and logistical limitations of the methodology.
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10
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Shahbaaz M, Nkaule A, Christoffels A. Designing novel possible kinase inhibitor derivatives as therapeutics against Mycobacterium tuberculosis: An in silico study. Sci Rep 2019; 9:4405. [PMID: 30867456 PMCID: PMC6416319 DOI: 10.1038/s41598-019-40621-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/18/2019] [Indexed: 11/30/2022] Open
Abstract
Rv2984 is one of the polyphosphate kinases present in Mycobacterium tuberculosis involved in the catalytic synthesis of inorganic polyphosphate, which plays an essential role in bacterial virulence and drug resistance. Consequently, the structure of Rv2984 was investigated and an 18 membered compound library was designed by altering the scaffolds of computationally identified inhibitors. The virtual screening of these altered inhibitors was performed against Rv2984 and the top three scoring inhibitors were selected, exhibiting the free energy of binding between 8.2–9 kcal mol−1 and inhibition constants in the range of 255–866 nM. These selected molecules showed relatively higher binding affinities against Rv2984 compared to the first line drugs Isoniazid and Rifampicin. Furthermore, the docked complexes were further analyzed in explicit water conditions using 100 ns Molecular Dynamics simulations. Through the assessment of obtained trajectories, the interactions between the protein and selected inhibitors including first line drugs were evaluated using MM/PBSA technique. The results validated the higher efficiency of the designed molecules compared to 1st line drugs with total interaction energies observed between −100 kJ mol−1 and −1000 kJ mol−1. This study will facilitate the process of drug designing against M. tuberculosis and can be used in the development of potential therapeutics against drug-resistant strains of bacteria.
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Affiliation(s)
- Mohd Shahbaaz
- South African National Bioinformatics Institute (SANBI), SA Medical Research Council Bioinformatics Unit, University of the Western Cape, Private Bag X17, Bellville, 7535, Cape Town, South Africa
| | - Anati Nkaule
- South African National Bioinformatics Institute (SANBI), SA Medical Research Council Bioinformatics Unit, University of the Western Cape, Private Bag X17, Bellville, 7535, Cape Town, South Africa
| | - Alan Christoffels
- South African National Bioinformatics Institute (SANBI), SA Medical Research Council Bioinformatics Unit, University of the Western Cape, Private Bag X17, Bellville, 7535, Cape Town, South Africa.
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11
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Chen Y, Cao S, Liu Y, Zhang X, Wang W, Li C. Potential role for Rv2026c- and Rv2421c- specific antibody responses in diagnosing active tuberculosis. Clin Chim Acta 2018; 487:369-376. [PMID: 30195451 DOI: 10.1016/j.cca.2018.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 10/28/2022]
Abstract
The current diagnostic methods for tuberculosis (TB) have several limitations. Although commercial serological tests based on antibody detection are available, their variable accuracies limit their roles in the clinic. The aim of this study was to discover the improved biomarkers for TB disease by investigating the serum profiles of IgG and IgM antibodies against nearly all Mycobacterium tuberculosis (MTB) antigens in 36 active TB patients and 18 healthy controls (HCs) using proteome microarrays. Our results revealed that multiple antigens could induce stronger serum IgG or IgM responses in TB patients compared to HCs, among them, Rv2026c and Rv2421c were further validated by ELISA with sera from 221 samples and showed the moderate performance in diagnosing TB by receiver operating characteristic analysis. Moreover, logistic regression analysis was performed to establish a combined panel that provided better sensitivity and specificity at 82.5% and 88.12%, respectively, than single antigens in the diagnosis of active TB. Furthermore, the antibody reactivity against Rv2026c and Rv2421c was correlated with clinical backgrounds. These results suggest that the combination of different antigens and classes of antibodies could provide promise and encouragement in developing an efficient serological test for the diagnosis of active TB.
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Affiliation(s)
- Yanqing Chen
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China.; Department of Laboratory Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Shuhui Cao
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China.; Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yi Liu
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China
| | - Xuxia Zhang
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China
| | - Wei Wang
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China
| | - Chuanyou Li
- Institute for Geriatrics and Rehabilitation, Beijing Geriatric Hospital, Beijing University of Chinese Medicine, Beijing 100095, China..
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12
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Ramos PIP, Fernández Do Porto D, Lanzarotti E, Sosa EJ, Burguener G, Pardo AM, Klein CC, Sagot MF, de Vasconcelos ATR, Gales AC, Marti M, Turjanski AG, Nicolás MF. An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets. Sci Rep 2018; 8:10755. [PMID: 30018343 PMCID: PMC6050338 DOI: 10.1038/s41598-018-28916-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
Abstract
Klebsiella pneumoniae (Kp) is a globally disseminated opportunistic pathogen that can cause life-threatening infections. It has been found as the culprit of many infection outbreaks in hospital environments, being particularly aggressive towards newborns and adults under intensive care. Many Kp strains produce extended-spectrum β-lactamases, enzymes that promote resistance against antibiotics used to fight these infections. The presence of other resistance determinants leading to multidrug-resistance also limit therapeutic options, and the use of 'last-resort' drugs, such as polymyxins, is not uncommon. The global emergence and spread of resistant strains underline the need for novel antimicrobials against Kp and related bacterial pathogens. To tackle this great challenge, we generated multiple layers of 'omics' data related to Kp and prioritized proteins that could serve as attractive targets for antimicrobial development. Genomics, transcriptomics, structuromic and metabolic information were integrated in order to prioritize candidate targets, and this data compendium is freely available as a web server. Twenty-nine proteins with desirable characteristics from a drug development perspective were shortlisted, which participate in important processes such as lipid synthesis, cofactor production, and core metabolism. Collectively, our results point towards novel targets for the control of Kp and related bacterial pathogens.
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Affiliation(s)
- Pablo Ivan Pereira Ramos
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Darío Fernández Do Porto
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Germán Burguener
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Agustín M Pardo
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Cecilia C Klein
- Inria Grenoble Rhône-Alpes, Grenoble, France
- Université Claude Bernard Lyon 1, Lyon, France
- Centre for Genomic Regulation (CRG), Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marie-France Sagot
- Inria Grenoble Rhône-Alpes, Grenoble, France
- Université Claude Bernard Lyon 1, Lyon, France
| | | | - Ana Cristina Gales
- Laboratório Alerta. Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marcelo Marti
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Adrián G Turjanski
- Plataforma de Bioinformática Argentina (BIA), Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina.
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina.
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil.
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13
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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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14
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Khan S, Somvanshi P, Bhardwaj T, Mandal RK, Dar SA, Wahid M, Jawed A, Lohani M, Khan M, Areeshi MY, Haque S. Aspartate‐β‐semialdeyhyde dehydrogenase as a potential therapeutic target of
Mycobacterium tuberculosis
H37Rv: Evidence from in silico elementary mode analysis of biological network model. J Cell Biochem 2017; 119:2832-2842. [DOI: 10.1002/jcb.26458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Saif Khan
- Department of Clinical NutritionCollege of Applied Medical Sciences University of Ha'ilHa'ilSaudi Arabia
| | | | | | - Raju K. Mandal
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
| | - Sajad A. Dar
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
| | - Mohd Wahid
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
| | - Arshad Jawed
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
| | - Mohtashim Lohani
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
| | - Mahvish Khan
- Department of Clinical NutritionCollege of Applied Medical Sciences University of Ha'ilHa'ilSaudi Arabia
| | - Mohammed Y. Areeshi
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies UnitCollege of Nursing and Allied Health SciencesJazan UniversityJazanSaudi Arabia
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15
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Abstract
Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, uses various tactics to resist on antibiotics and evade host immunity. To control tuberculosis, antibiotics with novel mechanisms of action are urgently needed. Emerging new antibiotics and underlying novel drug targets are summarized in this paper.
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Affiliation(s)
- Nzungize Lambert
- a 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 , China
| | - Abualgasim Elgaili Abdalla
- a 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 , China.,b Department of Clinical Microbiology, College of Medical Laboratory Sciences, Omdurman , Islamic University , Omdurman , Sudan
| | - Xiangke Duan
- a 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 , China
| | - Jianping Xie
- a 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 , China
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