1
|
Sankar J, Chauhan A, Singh R, Mahajan D. Isoniazid-historical development, metabolism associated toxicity and a perspective on its pharmacological improvement. Front Pharmacol 2024; 15:1441147. [PMID: 39364056 PMCID: PMC11447295 DOI: 10.3389/fphar.2024.1441147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/30/2024] [Indexed: 10/05/2024] Open
Abstract
Despite the extraordinary anti-tubercular activity of isoniazid (INH), the drug-induced hepatotoxicity and peripheral neuropathy pose a significant challenge to its wider clinical use. The primary cause of INH-induced hepatotoxicity is in vivo metabolism involving biotransformation on its terminal -NH2 group owing to its high nucleophilic nature. The human N-acetyltransferase-2 enzyme (NAT-2) exploits the reactivity of INH's terminal -NH2 functional group and inactivates it by transferring the acetyl group, which subsequently converts to toxic metabolites. This -NH2 group also tends to react with vital endogenous molecules such as pyridoxine, leading to their deficiency, a major cause of peripheral neuropathy. The elevation of liver functional markers is observed in 10%-20% of subjects on INH treatment. INH-induced risk of fatal hepatitis is about 0.05%-1%. The incidence of peripheral neuropathy is 2%-6.5%. In this review, we discuss the genesis and historical development of INH, and different reported mechanisms of action of INH. This is followed by a brief review of various clinical trials in chronological order, highlighting treatment-associated adverse events and their occurrence rates, including details such as geographical location, number of subjects, dosing concentration, and regimen used in these clinical studies. Further, we elaborated on various known metabolic transformations highlighting the involvement of the terminal -NH2 group of INH and corresponding host enzymes, the structure of different metabolites/conjugates, and their association with hepatotoxicity or neuritis. Post this deliberation, we propose a hydrolysable chemical derivatives-based approach as a way forward to restrict this metabolism.
Collapse
Affiliation(s)
- Jishnu Sankar
- Centre for Drug Discovery, BRIC-Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Anjali Chauhan
- Centre for Drug Discovery, BRIC-Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Centre for Tuberculosis Research, BRIC-Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ramandeep Singh
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research, New Delhi, India
| | - Dinesh Mahajan
- Centre for Drug Discovery, BRIC-Translational Health Science and Technology Institute, Faridabad, Haryana, India
- Centre for Tuberculosis Research, BRIC-Translational Health Science and Technology Institute, Faridabad, Haryana, India
| |
Collapse
|
2
|
Dasoondi RS, Blundell TL, Pandurangan AP. In silico analyses of isoniazid and streptomycin resistance-associated mutations in Mycobacterium tuberculosis. Comput Struct Biotechnol J 2023; 21:1874-1884. [PMID: 36915381 PMCID: PMC10006719 DOI: 10.1016/j.csbj.2023.02.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023] Open
Abstract
Multi-drug resistant tuberculosis is categorised by the World Health Organisation (WHO) as a public health crisis. In silico techniques were used to probe the structural basis of Mycobacterium tuberculosis resistance to isoniazid and streptomycin. Isoniazid resistance-associated mutations in InhA were predicted to reduce the binding affinity of NADH to InhA, without affecting INH-NAD (competitive-inhibitor) binding. Perturbation of the mutated residues was predicted (with the AlloSigMA server) to modulate the free energy of allosteric modulation of key binding site residues F41, F149, Y158 and W222. These results suggest that allosteric modulation of the protein structure may be key to the mechanism by which isoniazid resistance-associated mutations act. Mutations in the methyltransferase glucose-inhibited division gene B (GidB) are associated with streptomycin resistance. Molecular docking was carried out to predict the structure of the GidB bound to its substrate (s-adenosyl methionine). The effects of streptomycin resistance-associated mutations in GidB on protein stability and substrate binding were predicted (using SDM and mCSM-lig). All GidB mutants were predicted to disfavour SAM binding.
Collapse
|
3
|
Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
Collapse
Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| |
Collapse
|
4
|
Li M, Patel HV, Cognetta AB, Smith TC, Mallick I, Cavalier JF, Previti ML, Canaan S, Aldridge BB, Cravatt BF, Seeliger JC. Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling. Cell Chem Biol 2022; 29:883-896.e5. [PMID: 34599873 PMCID: PMC8964833 DOI: 10.1016/j.chembiol.2021.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/08/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
The identification and validation of a small molecule's targets is a major bottleneck in the discovery process for tuberculosis antibiotics. Activity-based protein profiling (ABPP) is an efficient tool for determining a small molecule's targets within complex proteomes. However, how target inhibition relates to biological activity is often left unexplored. Here, we study the effects of 1,2,3-triazole ureas on Mycobacterium tuberculosis (Mtb). After screening ∼200 compounds, we focus on 4 compounds that form a structure-activity series. The compound with negligible activity reveals targets, the inhibition of which is functionally less relevant for Mtb growth and viability, an aspect not addressed in other ABPP studies. Biochemistry, computational docking, and morphological analysis confirms that active compounds preferentially inhibit serine hydrolases with cell wall and lipid metabolism functions and that disruption of the cell wall underlies biological activity. Our findings show that ABPP identifies the targets most likely relevant to a compound's antibacterial activity.
Collapse
Affiliation(s)
- Michael Li
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Hiren V Patel
- Department of Microbiology and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Armand B Cognetta
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Ivy Mallick
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | | | - Mary L Previti
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA.
| |
Collapse
|
5
|
Kreutzfeldt KM, Jansen RS, Hartman TE, Gouzy A, Wang R, Krieger IV, Zimmerman MD, Gengenbacher M, Sarathy JP, Xie M, Dartois V, Sacchettini JC, Rhee KY, Schnappinger D, Ehrt S. CinA mediates multidrug tolerance in Mycobacterium tuberculosis. Nat Commun 2022; 13:2203. [PMID: 35459278 PMCID: PMC9033802 DOI: 10.1038/s41467-022-29832-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/31/2022] [Indexed: 12/23/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to resist and tolerate antibiotics complicates the development of improved tuberculosis (TB) chemotherapies. Here we define the Mtb protein CinA as a major determinant of drug tolerance and as a potential target to shorten TB chemotherapy. By reducing the fraction of drug-tolerant persisters, genetic inactivation of cinA accelerated killing of Mtb by four antibiotics in clinical use: isoniazid, ethionamide, delamanid and pretomanid. Mtb ΔcinA was killed rapidly in conditions known to impede the efficacy of isoniazid, such as during nutrient starvation, during persistence in a caseum mimetic, in activated macrophages and during chronic mouse infection. Deletion of CinA also increased in vivo killing of Mtb by BPaL, a combination of pretomanid, bedaquiline and linezolid that is used to treat highly drug-resistant TB. Genetic and drug metabolism studies suggest that CinA mediates drug tolerance via cleavage of NAD-drug adducts.
Collapse
Affiliation(s)
- Kaj M Kreutzfeldt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Robert S Jansen
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
- Department of Microbiology, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Travis E Hartman
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alexandre Gouzy
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08540, USA
| | - Inna V Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Jansy P Sarathy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Min Xie
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.
| |
Collapse
|
6
|
Mazen Mohammed Jwaid, Karima Fadhil Ali, Mayada Hadi Abd-alwahab. Synthesis, Antibacterial study and ADME Evaluation of Novel Isonicotinoyl Hydrazide Derivative Containing 1,3,4-Oxadiazole Moiety. AL MUSTANSIRIYAH JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 20:113-121. [DOI: 10.32947/ajps.v20i4.781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Novel derivative of isoniazid containing 1,3,4-oxadiazole pharmacophore has been synthesized. The chemical structure of the compound was characterized and confirmed by using FT-IR and 1H-NMR spectroscopy.
The desired compound was tested against gram-positive and gram-negative bacteria using agar well-diffusion technique for their ability as antibacterial agent and showed good antibacterial activity against gram-negative bacteria and gram-positive bacteria. In addition, ADME evaluations were performed using Swiss ADME to predict if the synthesized compound can be given orally, the bioavailability, topological polar surface area, and drug-likeness. The result showed that all tested compounds absorbed orally and fulfilled the Lipinski rule.
Collapse
|
7
|
Sangwan S, Yadav N, Kumar R, Chauhan S, Dhanda V, Walia P, Duhan A. A score years’ update in the synthesis and biological evaluation of medicinally important 2-pyridones. Eur J Med Chem 2022; 232:114199. [DOI: 10.1016/j.ejmech.2022.114199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/06/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022]
|
8
|
Sheikh BA, Bhat BA, Mehraj U, Mir W, Hamadani S, Mir MA. Development of New Therapeutics to Meet the Current Challenge of Drug Resistant Tuberculosis. Curr Pharm Biotechnol 2021; 22:480-500. [PMID: 32600226 DOI: 10.2174/1389201021666200628021702] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is a prominent infective disease and a major reason of mortality/ morbidity globally. Mycobacterium tuberculosis causes a long-lasting latent infection in a significant proportion of human population. The increasing burden of tuberculosis is mainly caused due to multi drug-resistance. The failure of conventional treatment has been observed in large number of cases. Drugs that are used to treat extensively drug-resistant tuberculosis are expensive, have limited efficacy, and have more side effects for a longer duration of time and are often associated with poor prognosis. To regulate the emergence of multidrug resistant tuberculosis, extensively drug-resistant tuberculosis and totally drug resistant tuberculosis, efforts are being made to understand the genetic/molecular basis of target drug delivery and mechanisms of drug resistance. Understanding the molecular approaches and pathology of Mycobacterium tuberculosis through whole genome sequencing may further help in the improvement of new therapeutics to meet the current challenge of global health. Understanding cellular mechanisms that trigger resistance to Mycobacterium tuberculosis infection may expose immune associates of protection, which could be an important way for vaccine development, diagnostics, and novel host-directed therapeutic strategies. The recent development of new drugs and combinational therapies for drug-resistant tuberculosis through major collaboration between industry, donors, and academia gives an improved hope to overcome the challenges in tuberculosis treatment. In this review article, an attempt was made to highlight the new developments of drug resistance to the conventional drugs and the recent progress in the development of new therapeutics for the treatment of drugresistant and non-resistant cases.
Collapse
Affiliation(s)
- Bashir A Sheikh
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Basharat A Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Wajahat Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Suhail Hamadani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Manzoor A Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| |
Collapse
|
9
|
Abo-Kadoum M, Dai Y, Asaad M, Hamdi I, Xie J. Differential Isoniazid Response Pattern Between Active and Dormant Mycobacterium tuberculosis. Microb Drug Resist 2021; 27:768-775. [DOI: 10.1089/mdr.2020.0179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- M.A. Abo-Kadoum
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, P.R. China
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assuit Branch, Assuit, Egypt
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, P.R. China
| | - Mohammed Asaad
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, P.R. China
| | - Insaf Hamdi
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, P.R. 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 Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, P.R. China
| |
Collapse
|
10
|
Atukuri D, Gunjal R, Holagundi N, Korlahalli B, Gangannavar S, Akkasali K. Contribution of N-heterocycles towards anti-tubercular drug discovery (2014-2019); predicted and reengineered molecular frameworks. Drug Dev Res 2021; 82:767-783. [PMID: 33660325 DOI: 10.1002/ddr.21809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 11/08/2022]
Abstract
Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis, responsible for high death frequency every year all over the world. In this regard, efficient drug-design and discovery towards the prevention of M.tb H37 Rv is of prime concern. Prevention of the infection may include vaccination, and the treatment comprises anti-TB drug regimen. However, the vaccine decreases the risk of tuberculosis infection only to some extent, while drug-resistance limits the efficacy of the existing anti-TB agents. Much improvement has to be achieved to overcome pitfalls such as side effects, high-toxicity, low bioavailability, pharmacokinetics and pharmacodynamics, and hence forth in clinical therapeutics. Amongst heterocyclic compounds, N-heterocycles played a pivotal role in drug-design and discovery. A wide range of microbial diseases are being treated by the N-heterocyclic drugs. The present review comprises description of anti-TB effects of the N-heterocycles such as indoles, triazoles, thiazoles, and pyrazoles. The potent anti-TB activity exerted by the derivatives of these heterocycles is evaluated critically alongside emphasizing structure-activity relationship. Besides, docking studies supporting anti-TB activity is supplemented. Alongside this, based on the potent heterocyclic molecules, the molecular frameworks are designed that would bring about enhanced M. tb H37 Rv inhibitory potencies.
Collapse
Affiliation(s)
- Dorababu Atukuri
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | - Rutu Gunjal
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | - Nagaraj Holagundi
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | | | | | - Kirankumar Akkasali
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| |
Collapse
|
11
|
Zarafu I, Matei L, Bleotu C, Ionita P, Tatibouët A, Păun A, Nicolau I, Hanganu A, Limban C, Nuta DC, Nemeș RM, Diaconu CC, Radulescu C. Synthesis, Characterization, and Biologic Activity of New Acyl Hydrazides and 1,3,4-Oxadiazole Derivatives. Molecules 2020; 25:E3308. [PMID: 32708236 PMCID: PMC7396991 DOI: 10.3390/molecules25143308] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/10/2020] [Accepted: 07/21/2020] [Indexed: 02/01/2023] Open
Abstract
Starting from isoniazid and carboxylic acids as precursors, thirteen new hydrazides and 1,3,4-oxadiazoles of 2-(4-substituted-phenoxymethyl)-benzoic acids were synthesized and characterized by appropriate means. Their biological properties were evaluated in terms of apoptosis, cell cycle blocking, and drug metabolism gene expression on HCT-8 and HT-29 cell lines. In vitro antimicrobial tests were performed by the microplate Alamar Blue assay for the anti-mycobacterial activities and an adapted agar disk diffusion technique for other non-tubercular bacterial strains. The best antibacterial activity (anti-Mycobacterium tuberculosis effects) was proved by 9. Compounds 7, 8, and 9 determined blocking of G1 phase. Compound 7 proved to be toxic, inducing apoptosis in 54% of cells after 72 h, an effect that can be predicted by the increased expression of mRNA caspases 3 and 7 after 24 h. The influence of compounds on gene expression of enzymes implicated in drug metabolism indicates that synthesized compounds could be metabolized via other pathways than NAT2, spanning adverse effects of isoniazid. Compound 9 had the best antibacterial activity, being used as a disinfectant agent. Compounds 7, 8, and 9, seemed to have antitumor potential. Further studies on the action mechanism of these compounds on the cell cycle may bring new information regarding their biological activity.
Collapse
Affiliation(s)
- Irina Zarafu
- Faculty of Chemistry, University of Bucharest, 050663 Bucharest, Romania; (P.I.); (A.P.); (I.N.)
| | - Lilia Matei
- “Stefan S Nicolau” Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (L.M.); (C.B.); (C.C.D.)
- Research Institute of the University of Bucharest (ICUB), Life, Environmental and Earth Sciences Division, University of Bucharest, 060023 Bucharest, Romania;
| | - Coralia Bleotu
- “Stefan S Nicolau” Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (L.M.); (C.B.); (C.C.D.)
- Research Institute of the University of Bucharest (ICUB), Life, Environmental and Earth Sciences Division, University of Bucharest, 060023 Bucharest, Romania;
| | - Petre Ionita
- Faculty of Chemistry, University of Bucharest, 050663 Bucharest, Romania; (P.I.); (A.P.); (I.N.)
| | - Arnaud Tatibouët
- Institute of Organic and Analytical Chemistry ICOA-UMR7311, University of Orleans, 45067 Orleans, France;
| | - Anca Păun
- Faculty of Chemistry, University of Bucharest, 050663 Bucharest, Romania; (P.I.); (A.P.); (I.N.)
| | - Ioana Nicolau
- Faculty of Chemistry, University of Bucharest, 050663 Bucharest, Romania; (P.I.); (A.P.); (I.N.)
| | - Anamaria Hanganu
- Research Institute of the University of Bucharest (ICUB), Life, Environmental and Earth Sciences Division, University of Bucharest, 060023 Bucharest, Romania;
- Institute of Organic Chemistry “C.D. Nenitescu” of the Romanian Academy, 060023 Bucharest, Romania
| | - Carmen Limban
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.L.); (D.C.N.)
| | - Diana Camelia Nuta
- Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.L.); (D.C.N.)
| | - Roxana Maria Nemeș
- National Institute of Pneumology Marius Nasta, 050152 Bucharest, Romania;
| | - Carmen Cristina Diaconu
- “Stefan S Nicolau” Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (L.M.); (C.B.); (C.C.D.)
| | - Cristiana Radulescu
- Faculty of Sciences and Arts, “Valahia” University of Targoviste, 130004 Targoviste, Romania
- Institute of Multidisciplinary Research for Science and Technology, Valahia University of Targoviste, 13004 Targoviste, Romania
| |
Collapse
|
12
|
Ribeiro JA, Chavez-Pacheco SM, de Oliveira GS, Silva CDS, Giudice JHP, Libreros-Zúñiga GA, Dias MVB. Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:682-693. [PMID: 31282477 DOI: 10.1107/s205979831900901x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 06/24/2019] [Indexed: 12/19/2022]
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis and is the leading cause of death from a single infectious pathogen, with a high prevalence in developing countries in Africa and Asia. There still is a need for the development or repurposing of novel therapies to combat this disease owing to the long-term nature of current therapies and because of the number of reported resistant strains. Here, structures of dihydrofolate reductase from M. tuberculosis (MtDHFR), which is a key target of the folate pathway, are reported in complex with four antifolates, pyrimethamine, cycloguanil, diaverdine and pemetrexed, and its substrate dihydrofolate in order to understand their binding modes. The structures of all of these complexes were obtained in the closed-conformation state of the enzyme and a fine structural analysis indicated motion in key regions of the substrate-binding site and different binding modes of the ligands. In addition, the affinities, through Kd measurement, of diaverdine and methotrexate have been determined; MtDHFR has a lower affinity (highest Kd) for diaverdine than pyrimethamine and trimethoprim, and a very high affinity for methotrexate, as expected. The structural comparisons and analysis described in this work provide new information about the plasticity of MtDHFR and the binding effects of different antifolates.
Collapse
Affiliation(s)
- João Augusto Ribeiro
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Sair Maximo Chavez-Pacheco
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Gabriel Stephani de Oliveira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Catharina Dos Santos Silva
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - João Henrique Pimenta Giudice
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Gerardo Andres Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo 05508-000, Brazil
| |
Collapse
|
13
|
Yadav R, Naik RM. Kinetics and mechanism of formation of the complex [Ru(CN)5INH]3− through the ligand substitution reaction between the aquapentacyanoruthenate(II) anion and isoniazid. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.1177/1468678319825737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The formation kinetics of the complex, [Ru(CN)5INH]3−, formed through the ligand substitution reaction between isoniazid (INH) and aquapentacyanoruthenate(II) ([Ru(CN)5H2O]3−), have been investigated, under pseudo first-order conditions, as a function of concentrations of [INH] and [Ru(CN)5H2O]3−, ionic strength and temperature at pH = 4.0 ± 0.02 in 0.2 M NaClO4 spectrophotometrically at 502 nm ( λmax of intense yellow colour product [Ru(CN)5INH]3−) corresponding to metal-to-ligand charge-transfer transitions, in aqueous medium. The pseudo first-order condition was maintained by taking at least 10% excess of [INH] over [Ru(CN)5H2O]3−. The stoichiometry of the reaction product was found to be 1:1 which was further supported and characterized using elemental analysis, infrared, nuclear magnetic resonance and mass spectrometric techniques. Thermodynamic and kinetic parameters have also been computed, using the Eyring equation, and the values of ΔH≠, Ea, ΔG≠ and ΔS≠ were found to be 47.3 kJ mol−1, 49.8 kJ mol−1, −8.62 kJ mol−1 and 187.6 J K−1mol−1, respectively. The reaction was found to obey first-order kinetics with respect to [INH]. It exhibited a negative salt effect on the rate upon variation of ionic strength of the medium. A tentative mechanistic scheme was proposed on the basis of experimental findings.
Collapse
Affiliation(s)
- Rupal Yadav
- Department of Chemistry, University of Lucknow, Lucknow, India
| | | |
Collapse
|
14
|
Aleksandrov A, Myllykallio H. Advances and challenges in drug design against tuberculosis: application of in silico approaches. Expert Opin Drug Discov 2018; 14:35-46. [PMID: 30477360 DOI: 10.1080/17460441.2019.1550482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains the deadliest infectious disease in the world with one-third of the world's population thought to be infected. Over the years, TB mortality rate has been largely reduced; however, this progress has been threatened by the increasing appearance of multidrug-resistant Mtb. Considerable recent efforts have been undertaken to develop new generation antituberculosis drugs. Many of these attempts have relied on in silico approaches, which have emerged recently as powerful tools complementary to biochemical attempts. Areas covered: The authors review the status of pharmaceutical drug development against TB with a special emphasis on computational work. They focus on those studies that have been validated by in vitro and/or in vivo experiments, and thus, that can be considered as successful. The major goals of this review are to present target protein systems, to highlight how in silico efforts compliment experiments, and to aid future drug design endeavors. Expert opinion: Despite having access to all of the gene and protein sequences of Mtb, the search for new optimal treatments against this deadly pathogen are still ongoing. Together with the geometric growth of protein structural and sequence databases, computational methods have become a powerful technique accelerating the successful identification of new ligands.
Collapse
Affiliation(s)
- Alexey Aleksandrov
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
| | - Hannu Myllykallio
- a Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182) , Ecole Polytechnique , Palaiseau , France
| |
Collapse
|
15
|
Sharma K, Tanwar O, Sharma S, Ali S, Alam M, Zaman M, Akhter M. Structural comparison of Mtb-DHFR and h-DHFR for design, synthesis and evaluation of selective non-pteridine analogues as antitubercular agents. Bioorg Chem 2018; 80:319-333. [DOI: 10.1016/j.bioorg.2018.04.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 11/29/2022]
|
16
|
|
17
|
de Oliveira Viana J, Scotti MT, Scotti L. Molecular Docking Studies in Multitarget Antitubercular Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
18
|
Kaur D, Mathew S, Nair CGS, Begum A, Jainanarayan AK, Sharma M, Brahmachari SK. Structure based drug discovery for designing leads for the non-toxic metabolic targets in multi drug resistant Mycobacterium tuberculosis. J Transl Med 2017; 15:261. [PMID: 29268770 PMCID: PMC5740895 DOI: 10.1186/s12967-017-1363-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/08/2017] [Indexed: 01/09/2023] Open
Abstract
Background The problem of drug resistance and bacterial persistence in tuberculosis is a cause of global alarm. Although, the UN’s Sustainable Development Goals for 2030 has targeted a Tb free world, the treatment gap exists and only a few new drug candidates are in the pipeline. In spite of large information from medicinal chemistry to ‘omics’ data, there has been a little effort from pharmaceutical companies to generate pipelines for the development of novel drug candidates against the multi drug resistant Mycobacterium tuberculosis. Methods In the present study, we describe an integrated methodology; utilizing systems level information to optimize ligand selection to lower the failure rates at the pre-clinical and clinical levels. In the present study, metabolic targets (Rv2763c, Rv3247c, Rv1094, Rv3607c, Rv3048c, Rv2965c, Rv2361c, Rv0865, Rv0321, Rv0098, Rv0390, Rv3588c, Rv2244, Rv2465c and Rv2607) in M. tuberculosis, identified using our previous Systems Biology and data-intensive genome level analysis, have been used to design potential lead molecules, which are likely to be non-toxic. Various in silico drug discovery tools have been utilized to generate small molecular leads for each of the 15 targets with available crystal structures. Results The present study resulted in identification of 20 novel lead molecules including 4 FDA approved drugs (droxidropa, tetroxoprim, domperidone and nemonapride) which can be further taken for drug repurposing. This comprehensive integrated methodology, with both experimental and in silico approaches, has the potential to not only tackle the MDR form of Mtb but also the most important persister population of the bacterium, with a potential to reduce the failures in the Tb drug discovery. Conclusion We propose an integrated approach of systems and structural biology for identifying targets that address the high attrition rate issue in lead identification and drug development We expect that this system level analysis will be applicable for identification of drug candidates to other pathogenic organisms as well. Electronic supplementary material The online version of this article (10.1186/s12967-017-1363-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Divneet Kaur
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shalu Mathew
- Centre for Open Innovation-Indian Centre for Social Transformation, Bengaluru, Karnataka, India
| | - Chinchu G S Nair
- Centre for Open Innovation-Indian Centre for Social Transformation, Bengaluru, Karnataka, India
| | - Azitha Begum
- Centre for Open Innovation-Indian Centre for Social Transformation, Bengaluru, Karnataka, India
| | - Ashwin K Jainanarayan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Indian Institute of Science Education and Research (IISER), Mohali, India
| | - Mukta Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Samir K Brahmachari
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India. .,Centre for Open Innovation-Indian Centre for Social Transformation, Bengaluru, Karnataka, India. .,Academy of Scientific and Innovative Research, New Delhi, India. .,CSIR-Open Source Drug Discovery Unit, New Delhi, India.
| |
Collapse
|
19
|
Laborde J, Deraeve C, Bernardes-Génisson V. Update of Antitubercular Prodrugs from a Molecular Perspective: Mechanisms of Action, Bioactivation Pathways, and Associated Resistance. ChemMedChem 2017; 12:1657-1676. [DOI: 10.1002/cmdc.201700424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/12/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Julie Laborde
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Céline Deraeve
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| | - Vania Bernardes-Génisson
- CNRS; LCC (Laboratoire de Chimie de Coordination); 205, route de Narbonne, BP 44099 31077 Toulouse, Cedex 4 France
- Université de Toulouse; UPS, INPT; 31077 Toulouse, Cedex 4 France
| |
Collapse
|
20
|
Drug development against tuberculosis: Past, present and future. ACTA ACUST UNITED AC 2017; 64:252-275. [DOI: 10.1016/j.ijtb.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/15/2017] [Indexed: 12/29/2022]
|
21
|
Dawadi S, Kordus SL, Baughn AD, Aldrich CC. Synthesis and Analysis of Bacterial Folate Metabolism Intermediates and Antifolates. Org Lett 2017; 19:5220-5223. [PMID: 28926267 DOI: 10.1021/acs.orglett.7b02487] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of action of para-aminosalicylic acid (PAS), a drug used to treat drug-resistant tuberculosis (TB), has been confirmed through the first synthesis and biochemical characterization of its active metabolite 7. The synthesis features the coupling of N2-acetyl-6-formylpterin obtained from the degradation of folic acid and appropriately functionalized arylamines to form Schiff bases. The sequential chemoselective reduction of the imine and pterin ring led to the formation of dihydrofolate analogue 7 and two other dihydropteroate species.
Collapse
Affiliation(s)
- Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Shannon L Kordus
- Department of Microbiology and Immunology, University of Minnesota Medical School , Minneapolis, Minnesota 55455, United States
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School , Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| |
Collapse
|
22
|
Angelova VT, Valcheva V, Pencheva T, Voynikov Y, Vassilev N, Mihaylova R, Momekov G, Shivachev B. Synthesis, antimycobacterial activity and docking study of 2-aroyl-[1]benzopyrano[4,3-c]pyrazol-4(1H)-one derivatives and related hydrazide-hydrazones. Bioorg Med Chem Lett 2017; 27:2996-3002. [PMID: 28512022 DOI: 10.1016/j.bmcl.2017.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/30/2022]
Abstract
A new convenient method for preparation of 2-aroyl-[1]benzopyrano[4,3-c]pyrazol-4(1H)-one derivatives 5b-g and coumarin containing hydrazide-hydrazone analogues 4a-e was presented. The antimycobacterial activity against reference strain Mycobacterium tuberculosis H37Rv and cytotoxicity against the human embryonic kidney cell line HEK-293 were tested in vitro. All compounds demonstrated significant minimum inhibitory concentrations (MIC) ranging 0.28-1.69μM, which were comparable to those of isoniazid. The cytotoxicity (IC50>200µM) to the "normal cell" model HEK-293T exhibited by 2-aroyl-[1]benzopyrano[4,3-c]pyrazol-4(1H)-one derivatives 5b-e, was noticeably milder compared to that of their hydrazone analogues 4a-e (IC50 33-403µM). Molecular docking studies on compounds 4a-e and 5b-g were also carried out to investigate their binding to the 2-trans-enoyl-ACP reductase (InhA) enzyme involved in M. tuberculosis cell wall biogenesis. The binding model suggested one or more hydrogen bonding and/or arene-H or arene-arene interactions between hydrazones or pyrazole-fused coumarin derivatives and InhA enzyme for all synthesized compounds.
Collapse
Affiliation(s)
- Violina T Angelova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria.
| | - Violeta Valcheva
- "Stefan Angelov" Institute of Microbiology, Bulgarian Academy of Sciences, 26 Acad. G. Bonchev Str., 1113 Sofia, Bulgaria
| | - Tania Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad. G. Bonchev Str, 1113 Sofia, Bulgaria
| | - Yulian Voynikov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Nikolay Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Rositsa Mihaylova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Georgi Momekov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Boris Shivachev
- Institute of Mineralogy and Crystallography, Bulgarian Academy of Sciences, 107 Acad. G. Bonchev Str., 1113 Sofia, Bulgaria
| |
Collapse
|
23
|
Marimuthu P, Singaravelu K, Namasivayam V. Probing the binding mechanism of mercaptoguanine derivatives as inhibitors of HPPK by docking and molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:3507-3521. [PMID: 27844507 DOI: 10.1080/07391102.2016.1260496] [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] [Indexed: 01/09/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a promising antimicrobial target involved in the folate biosynthesis pathway. Although, the results from crystallographic studies of HPPK have attracted a great interest in the design of novel HPPK inhibitors, the mechanism of action of HPPK due to inhibitor binding remains questionable. Recently, mercaptoguanine derivatives were reported to inhibit the pyrophosphoryl transfer mechanism of Staphylococcus aureus HPPK (SaHPPK). The present study is an attempt to understand the SaHPPK-inhibitors binding mechanism and to highlight the key residues that possibly involve in the complex formation. To decipher these questions, we used the state-of-the-art advanced insilico approach such as molecular docking, molecular dynamics (MD), molecular mechanics-generalized Born surface area approach. Domain cross correlation and principle component analysis were applied to the snapshots obtained from MD revealed that the compounds with high binding affinity stabilize the conformational dynamics of SaHPPK. The binding free energy estimation showed that the van der Waals and electrostatic interactions played a vital role for the binding mechanism. Additionally, the predicted binding free energy was in good agreement with the experimental values (R2 = .78). Moreover, the free energy decomposition on per-residue confirms the key residues that significantly contribute to the complex formation. These results are expected to be useful for rational design of novel SaHPPK inhibitors.
Collapse
Affiliation(s)
- Parthiban Marimuthu
- a Structural Bioinformatics Laboratory (SBL), Faculty of Science and Engineering , Åbo Akademi University , Turku FI-20520 , Finland
| | - Kalaimathy Singaravelu
- b Department of Information Technology, Turku Centre for Biotechnology , University of Turku , Turku FI-20520 , Finland
| | - Vigneshwaran Namasivayam
- c PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , An der Immenburg 4, Bonn D-53121 , Germany
| |
Collapse
|
24
|
Palomino JC, Martin A. The potential role of trimethoprim-sulfamethoxazole in the treatment of drug-resistant tuberculosis. Future Microbiol 2016; 11:539-47. [PMID: 27070731 DOI: 10.2217/fmb.16.2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Tuberculosis (TB) remains a serious public health threat worsened by emerging drug resistance. Mycobacterium tuberculosis has become resistant not only to front-line drugs but also to second-line antimicrobials directed at drug-resistant TB. Renewed efforts are devoted for the development of new antibiotics active against TB. Also, repurposing of other antibiotics is being explored to shorten the time to develop new drugs against M. tuberculosis. As a result, trimethoprim-sulfamethoxazole (SXT) has emerged as a potential new option to treat drug-resistant TB. SXT has been found to be surprisingly active against drug-resistant M. tuberculosis, not only in vitro but also in vivo. The potential role of SXT for the treatment of multidrug resistant/extensively drug resistant TB might be explored in further clinical evaluations.
Collapse
Affiliation(s)
- Juan Carlos Palomino
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, Ghent, Belgium
| | - Anandi Martin
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
25
|
Bhosle A, Chandra N. Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities. FEBS J 2016; 283:1139-67. [PMID: 26797763 DOI: 10.1111/febs.13662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/03/2015] [Accepted: 01/14/2016] [Indexed: 11/28/2022]
Abstract
Antifolates are competitive inhibitors of dihydrofolate reductase (DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the 'supersite' and classified supersites of DHFRs from 56 species into 16 'site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.
Collapse
Affiliation(s)
- Amrisha Bhosle
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| |
Collapse
|
26
|
Cheng YS, Sacchettini JC. Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance. Biochemistry 2016; 55:1107-19. [PMID: 26848874 PMCID: PMC6201685 DOI: 10.1021/acs.biochem.5b00993] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis (Mtb) Rv2671 is annotated as a 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate (AROPP) reductase (RibD) in the riboflavin biosynthetic pathway. Recently, a strain of Mtb with a mutation in the 5' untranslated region of Rv2671, which resulted in its overexpression, was found to be resistant to dihydrofolate reductase (DHFR) inhibitors including the anti-Mtb drug para-aminosalicylic acid (PAS). In this study, a biochemical analysis of Rv2671 showed that it was able to catalyze the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF), which explained why the overexpression of Rv2671 was sufficient to confer PAS resistance. We solved the structure of Rv2671 in complex with the NADP(+) and tetrahydrofolate (THF), which revealed the structural basis for the DHFR activity. The structures of Rv2671 complexed with two DHFR inhibitors, trimethoprim and trimetrexate, provided additional details of the substrate binding pocket and elucidated the differences between their inhibitory activities. Finally, Rv2671 was unable to catalyze the reduction of AROPP, which indicated that Rv2671 and its closely related orthologues are not involved in riboflavin biosynthesis.
Collapse
Affiliation(s)
- Yu-Shan Cheng
- Department of Chemistry, Texas A&M University,
College Station, Texas 77842, United States
| | - James C. Sacchettini
- Department of Chemistry, Texas A&M University,
College Station, Texas 77842, United States
- Department of Biochemistry and Biophysics, Texas
A&M University, College Station, Texas 77843, United States
| |
Collapse
|
27
|
Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis: Genes, Mutations, and Causalities. Microbiol Spectr 2016; 2:MGM2-0014-2013. [PMID: 26104204 DOI: 10.1128/microbiolspec.mgm2-0014-2013] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoniazid (INH) is the cornerstone of tuberculosis (TB) chemotherapy, used for both treatment and prophylaxis of TB. The antimycobacterial activity of INH was discovered in 1952, and almost as soon as its activity was published, the first INH-resistant Mycobacterium tuberculosis strains were reported. INH and its structural analog and second-line anti-TB drug ethionamide (ETH) are pro-drugs. INH is activated by the catalase-peroxidase KatG, while ETH is activated by the monooxygenase EthA. The resulting active species reacts with NAD+ to form an INH-NAD or ETH-NAD adduct, which inhibits the enoyl ACP reductase InhA, leading to mycolic acid biosynthesis inhibition and mycobacterial cell death. The major mechanism of INH resistance is mutation in katG, encoding the activator of INH. One specific KatG variant, S315T, is found in 94% of INH-resistant clinical isolates. The second mechanism of INH resistance is a mutation in the promoter region of inhA (c-15t), which results in inhA overexpression and leads to titration of the drug. Mutations in the inhA open reading frame and promoter region are also the major mechanism of resistance to ETH, found more often in ETH-resistant clinical isolates than mutations in the activator of ETH. Other mechanisms of resistance to INH and ETH include expression changes of the drugs' activators, redox alteration, drug inactivation, and efflux pump activation. In this article, we describe each known mechanism of resistance to INH and ETH and its importance in M. tuberculosis clinical isolates.
Collapse
|
28
|
Pereira MP, Shi J, Kelley SO. Peptide Targeting of an Antibiotic Prodrug toward Phagosome-Entrapped Mycobacteria. ACS Infect Dis 2015; 1:586-92. [PMID: 27623056 DOI: 10.1021/acsinfecdis.5b00099] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mycobacterial infections are difficult to treat due to the bacterium's slow growth, ability to reside in intracellular compartments within macrophages, and resistance mechanisms that limit the effectiveness of conventional antibiotics. Developing antibiotics that overcome these challenges is therefore critical to providing a pipeline of effective antimicrobial agents. Here, we describe the synthesis and testing of a unique peptide-drug conjugate that exhibits high levels of antimicrobial activity against M. smegmatis and M. tuberculosis as well as clearance of intracellular mycobacteria from cultured macrophages. Using an engineered peptide sequence, we deliver a potent DHFR inhibitor and target the intracellular phagosomes where mycobacteria reside and also incorporate a β-lactamase-cleavable cephalosporin linker to enhance the targeting of quiescent intracellular β-lactam-resistant mycobacteria. By using this type of prodrug approach to target intracellular mycobacterial infections, the emergence of antibacterial resistance mechanisms could be minimized.
Collapse
Affiliation(s)
- Mark P. Pereira
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, and Department of Biochemistry, Faculty
of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Julie Shi
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, and Department of Biochemistry, Faculty
of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shana O. Kelley
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, and Department of Biochemistry, Faculty
of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
29
|
In silico-based high-throughput screen for discovery of novel combinations for tuberculosis treatment. Antimicrob Agents Chemother 2015; 59:5664-74. [PMID: 26149995 PMCID: PMC4538536 DOI: 10.1128/aac.05148-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 06/27/2015] [Indexed: 11/20/2022] Open
Abstract
There are currently 18 drug classes for the treatment of tuberculosis, including those in the development pipeline. An in silico simulation enabled combing the innumerably large search space to derive multidrug combinations. Through the use of ordinary differential equations (ODE), we constructed an in silico kinetic platform in which the major metabolic pathways in Mycobacterium tuberculosis and the mechanisms of the antituberculosis drugs were integrated into a virtual proteome. The optimized model was used to evaluate 816 triplets from the set of 18 drugs. The experimentally derived cumulative fractional inhibitory concentration (∑FIC) value was within twofold of the model prediction. Bacterial enumeration revealed that a significant number of combinations that were synergistic for growth inhibition were also synergistic for bactericidal effect. The in silico-based screen provided new starting points for testing in a mouse model of tuberculosis, in which two novel triplets and five novel quartets were significantly superior to the reference drug triplet of isoniazid, rifampin, and ethambutol (HRE) or the quartet of HRE plus pyrazinamide (HREZ).
Collapse
|
30
|
E84G mutation in dihydrofolate reductase from drug resistant strains of Mycobacterium tuberculosis (Mumbai, India) leads to increased interaction with Trimethoprim. Int J Mycobacteriol 2015; 4:97-103. [DOI: 10.1016/j.ijmyco.2015.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/16/2015] [Indexed: 11/22/2022] Open
|
31
|
Gopal P, Dick T. Reactive dirty fragments: implications for tuberculosis drug discovery. Curr Opin Microbiol 2014; 21:7-12. [DOI: 10.1016/j.mib.2014.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/19/2014] [Accepted: 06/29/2014] [Indexed: 01/01/2023]
|
32
|
Anand P, Chandra N. Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection. Sci Rep 2014; 4:6356. [PMID: 25220818 PMCID: PMC5376175 DOI: 10.1038/srep06356] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/20/2014] [Indexed: 01/13/2023] Open
Abstract
Polypharmacology is beginning to emerge as an important concept in the field of drug discovery. However, there are no established approaches to either select appropriate target sets or design polypharmacological drugs. Here, we propose a structural-proteomics approach that utilizes the structural information of the binding sites at a genome-scale obtained through in-house algorithms to characterize the pocketome, yielding a list of ligands that can participate in various biochemical events in the mycobacterial cell. The pocket-type space is seen to be much larger than the sequence or fold-space, suggesting that variations at the site-level contribute significantly to functional repertoire of the organism. All-pair comparisons of binding sites within Mycobacterium tuberculosis (Mtb), pocket-similarity network construction and clustering result in identification of binding-site sets, each containing a group of similar binding sites, theoretically having a potential to interact with a common set of compounds. A polypharmacology index is formulated to rank targets by incorporating a measure of druggability and similarity to other pockets within the proteome. This study presents a rational approach to identify targets with polypharmacological potential along with possible drugs for repurposing, while simultaneously, obtaining clues on lead compounds for use in new drug-discovery pipelines.
Collapse
Affiliation(s)
- Praveen Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
| |
Collapse
|
33
|
An upstream truncation of the furA-katG operon confers high-level isoniazid resistance in a Mycobacterium tuberculosis clinical isolate with no known resistance-associated mutations. Antimicrob Agents Chemother 2014; 58:6093-100. [PMID: 25092698 DOI: 10.1128/aac.03277-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the major causes of isoniazid (INH) resistance in Mycobacterium tuberculosis are confined to structural mutations in katG and promoter mutations in the mabA-inhA operon, a significant proportion of INH-resistant strains have unknown resistance mechanisms. Recently, we identified a high-level INH-resistant M. tuberculosis clinical isolate, GB005, with no known resistance-associated mutations. A comprehensive study was performed to investigate the molecular basis of drug resistance in this strain. Although no mutations were found throughout the katG and furA-katG intergenic region, the katG expression and the catalase activity were greatly diminished compared to those in H37Rv (P < 0.01). Northern blotting revealed that the katG transcript from the isolate was smaller than that of H37Rv. Sequencing analysis of furA and upstream genes discovered a 7.2-kb truncation extended from the 96th base preceding the initiation codon of katG. Complementation of the M. tuberculosis Δ(furA-katG) strain with katG and different portions of the truncated region identified a 134-bp upstream fragment of furA that was essential for full catalase activity and INH susceptibility in M. tuberculosis. The promoter activity of this fragment was also shown to be stronger than that of the furA-katG intergenic region (P < 0.01). Collectively, these findings demonstrate that deletion of the 134-bp furA upstream fragment is responsible for the reduction in katG expression, resulting in INH resistance in GB005. To our knowledge, this is the first report showing that deletion of the upstream region preceding the furA-katG operon causes high-level INH resistance in a clinical isolate of M. tuberculosis.
Collapse
|
34
|
Drug Resistance Mechanisms in Mycobacterium tuberculosis. Antibiotics (Basel) 2014; 3:317-40. [PMID: 27025748 PMCID: PMC4790366 DOI: 10.3390/antibiotics3030317] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 01/16/2023] Open
Abstract
Tuberculosis (TB) is a serious public health problem worldwide. Its situation is worsened by the presence of multidrug resistant (MDR) strains of Mycobacterium tuberculosis, the causative agent of the disease. In recent years, even more serious forms of drug resistance have been reported. A better knowledge of the mechanisms of drug resistance of M. tuberculosis and the relevant molecular mechanisms involved will improve the available techniques for rapid drug resistance detection and will help to explore new targets for drug activity and development. This review article discusses the mechanisms of action of anti-tuberculosis drugs and the molecular basis of drug resistance in M. tuberculosis.
Collapse
|
35
|
Desai N, Shihory N, Kotadiya G, Desai P. Synthesis, antibacterial and antitubercular activities of benzimidazole bearing substituted 2-pyridone motifs. Eur J Med Chem 2014; 82:480-9. [DOI: 10.1016/j.ejmech.2014.06.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/05/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
|
36
|
Abstract
Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen's proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins, making up nearly 70% of the Mycobacterium tuberculosis proteome, are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of the M. tuberculosis genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site-based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.
Collapse
|
37
|
Encinas L, O'Keefe H, Neu M, Remuiñán MJ, Patel AM, Guardia A, Davie CP, Pérez-Macías N, Yang H, Convery MA, Messer JA, Pérez-Herrán E, Centrella PA, Alvarez-Gómez D, Clark MA, Huss S, O'Donovan GK, Ortega-Muro F, McDowell W, Castañeda P, Arico-Muendel CC, Pajk S, Rullás J, Angulo-Barturen I, Alvarez-Ruíz E, Mendoza-Losana A, Ballell Pages L, Castro-Pichel J, Evindar G. Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of Mycobacterium tuberculosis InhA. J Med Chem 2014; 57:1276-88. [PMID: 24450589 DOI: 10.1021/jm401326j] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Tuberculosis (TB) is one of the world's oldest and deadliest diseases, killing a person every 20 s. InhA, the enoyl-ACP reductase from Mycobacterium tuberculosis, is the target of the frontline antitubercular drug isoniazid (INH). Compounds that directly target InhA and do not require activation by mycobacterial catalase peroxidase KatG are promising candidates for treating infections caused by INH resistant strains. The application of the encoded library technology (ELT) to the discovery of direct InhA inhibitors yielded compound 7 endowed with good enzymatic potency but with low antitubercular potency. This work reports the hit identification, the selected strategy for potency optimization, the structure-activity relationships of a hundred analogues synthesized, and the results of the in vivo efficacy studies performed with the lead compound 65.
Collapse
Affiliation(s)
- Lourdes Encinas
- ELT Boston, Platform Technology & Science, GlaxoSmithKline , Waltham, Massachusetts 02451, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Dias M, Tyrakis P, Domingues R, Leme A, Blundell T. Mycobacterium tuberculosis Dihydrofolate Reductase Reveals Two Conformational States and a Possible Low Affinity Mechanism to Antifolate Drugs. Structure 2014; 22:94-103. [DOI: 10.1016/j.str.2013.09.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/14/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
|
39
|
In silico screening of chalcone derivatives as potential inhibitors of dihydrofolate reductase: Assessment using molecular docking, paired potential and molecular hydrophobic potential studies. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.dit.2013.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
40
|
Nerukh D, Okimoto N, Suenaga A, Taiji M. Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation. J Phys Chem Lett 2012; 3:3476-3479. [PMID: 26290975 DOI: 10.1021/jz301635h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein's surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.
Collapse
Affiliation(s)
- Dmitry Nerukh
- †Nonlinearity and Complexity Research Group, Aston University, Birmingham, B4 7ET, U.K
| | - Noriaki Okimoto
- ‡RIKEN Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | | | - Makoto Taiji
- ‡RIKEN Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| |
Collapse
|
41
|
Palomino JC, Martin A. Is repositioning of drugs a viable alternative in the treatment of tuberculosis? J Antimicrob Chemother 2012; 68:275-83. [DOI: 10.1093/jac/dks405] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
42
|
Inhibitors of fatty acid synthesis in prokaryotes and eukaryotes as anti-infective, anticancer and anti-obesity drugs. Future Med Chem 2012; 4:1113-51. [PMID: 22709254 DOI: 10.4155/fmc.12.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is a large range of diseases, such diabetes and cancer, which are connected to abnormal fatty acid metabolism in human cells. Therefore, inhibitors of human fatty acid synthase have great potential to manage or treat these diseases. In prokaryotes, fatty acid synthesis is important for signaling, as well as providing starting materials for the synthesis of phospholipids, which are required for the formation of the cell membrane. Recently, there has been renewed interest in the development of new molecules that target bacterial fatty acid synthases for the treatment of bacterial diseases. In this review, we look at the differences and similarities between fatty acid synthesis in humans and bacteria and highlight various small molecules that have been shown to inhibit either the mammalian or bacterial fatty acid synthase or both.
Collapse
|
43
|
Wolff KA, Nguyen L. Strategies for potentiation of ethionamide and folate antagonists against Mycobacterium tuberculosis. Expert Rev Anti Infect Ther 2012; 10:971-81. [PMID: 23106273 PMCID: PMC3971469 DOI: 10.1586/eri.12.87] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antifolates inhibit de novo folate biosynthesis, whereas ethionamide targets the mycolate synthetic pathway in Mycobacterium tuberculosis. These antibiotics are effective against M. tuberculosis but their use has been hampered by concerns over toxicity and low therapeutic indexes. With the increasing spread of drug-resistant forms, interest in using old drugs for tuberculosis treatment has been renewed. Specific inhibitors targeting resistance mechanisms could sensitize M. tuberculosis to these available, clinically approved drugs. This review discusses recently developed strategies to boost the antituberculous activity of ethionamide and antifolates. These approaches might help broaden the currently limited chemotherapeutic options of not only drug-resistant but also drug-susceptible tuberculosis, which still remains one of the most common infectious diseases in the developing world.
Collapse
Affiliation(s)
- Kerstin A Wolff
- Case Western Reserve University School of Medicine, Department of Molecular Biology and Microbiology, Cleveland, OH 44106, USA
| | - Liem Nguyen
- Case Western Reserve University School of Medicine, Department of Molecular Biology and Microbiology, Cleveland, OH 44106, USA
| |
Collapse
|
44
|
Brown-Elliott BA, Nash KA, Wallace RJ. Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 2012; 25:545-82. [PMID: 22763637 PMCID: PMC3416486 DOI: 10.1128/cmr.05030-11] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Within the past 10 years, treatment and diagnostic guidelines for nontuberculous mycobacteria have been recommended by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). Moreover, the Clinical and Laboratory Standards Institute (CLSI) has published and recently (in 2011) updated recommendations including suggested antimicrobial and susceptibility breakpoints. The CLSI has also recommended the broth microdilution method as the gold standard for laboratories performing antimicrobial susceptibility testing of nontuberculous mycobacteria. This article reviews the laboratory, diagnostic, and treatment guidelines together with established and probable drug resistance mechanisms of the nontuberculous mycobacteria.
Collapse
|
45
|
Kumar A, Zhang M, Zhu L, Liao RP, Mutai C, Hafsat S, Sherman DR, Wang MW. High-throughput screening and sensitized bacteria identify an M. tuberculosis dihydrofolate reductase inhibitor with whole cell activity. PLoS One 2012; 7:e39961. [PMID: 22768185 PMCID: PMC3386958 DOI: 10.1371/journal.pone.0039961] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 05/30/2012] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is a bacterial pathogen that claims roughly 1.4 million lives every year. Current drug regimens are inefficient at clearing infection, requiring at least 6 months of chemotherapy, and resistance to existing agents is rising. There is an urgent need for new drugs that are more effective and faster acting. The folate pathway has been successfully targeted in other pathogens and diseases, but has not yielded a lead drug against tuberculosis. We developed a high-throughput screening assay against Mtb dihydrofolate reductase (DHFR), a critical enzyme in the folate pathway, and screened a library consisting of 32,000 synthetic and natural product-derived compounds. One potent inhibitor containing a quinazoline ring was identified. This compound was active against the wild-type laboratory strain H37Rv (MIC99 = 207 µM). In addition, an Mtb strain with artificially lowered DHFR levels showed increased sensitivity to this compound (MIC99 = 70.7 µM), supporting that the inhibition was target-specific. Our results demonstrate the potential to identify Mtb DHFR inhibitors with activity against whole cells, and indicate the power of using a recombinant strain of Mtb expressing lower levels of DHFR to facilitate the discovery of antimycobacterial agents. With these new tools, we highlight the folate pathway as a potential target for new drugs to combat the tuberculosis epidemic.
Collapse
Affiliation(s)
- Anuradha Kumar
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Meng Zhang
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Linyun Zhu
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Reiling P. Liao
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Charles Mutai
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - Shittu Hafsat
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
| | - David R. Sherman
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- * E-mail: (DRS); (MWW)
| | - Ming-Wei Wang
- The National Center for Drug Screening and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
- * E-mail: (DRS); (MWW)
| |
Collapse
|
46
|
Weeken D, Schlitzer M. [Accidental discoveries, different mechanisms of action. Active agents against Mycobacterium tuberculosis in clinical application]. PHARMAZIE IN UNSERER ZEIT 2012; 41:35-47. [PMID: 22470917 DOI: 10.1002/pauz.201100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Daniela Weeken
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, Marburg
| | | |
Collapse
|
47
|
Prediction of residues involved in inhibitor specificity in the dihydrofolate reductase family. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1870-9. [DOI: 10.1016/j.bbapap.2011.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 12/11/2022]
|
48
|
Brossier F. Mécanismes d’action et de résistance de l’isoniazide, un antituberculeux de première ligne. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.antinf.2011.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
49
|
A novel metabolite of antituberculosis therapy demonstrates host activation of isoniazid and formation of the isoniazid-NAD+ adduct. Antimicrob Agents Chemother 2011; 56:28-35. [PMID: 22037847 DOI: 10.1128/aac.05486-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the most effective and widely used antituberculosis (anti-TB) drugs is isoniazid (INH), a prodrug activated via oxidation that forms an adduct with NAD(+) to inhibit NADH-dependent targets of Mycobacterium tuberculosis, such as enoyl-acyl carrier protein reductase (InhA). The metabolic by-products and potentially toxic intermediates resulting from INH therapy have been identified through a large body of work. However, an INH-NAD adduct or structures related to this adduct have not been identified in specimens from human TB patients or animal models of TB. Analyses by mass spectrometry of urine collected from TB patients in a study conducted by the NIAID-funded Tuberculosis Research Unit identified 4-isonicotinoylnicotinamide (C(12)H(9)N(3)O(2)) as a novel metabolite of INH therapy. This compound was formed by M. tuberculosis strains in a KatG-dependent manner but could also be produced by mice treated with INH independent of an M. tuberculosis infection. Thus, the 4-isonicotinoylnicotinamide observed in human urine samples is likely derived from the degradation of oxidized INH-NAD adducts and provides direct evidence of host INH activation.
Collapse
|
50
|
Barry CE. Lessons from seven decades of antituberculosis drug discovery. Curr Top Med Chem 2011; 11:1216-25. [PMID: 21401509 DOI: 10.2174/156802611795429158] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 11/25/2010] [Indexed: 12/31/2022]
Abstract
Despite massive global efforts tuberculosis rates continue to climb and drug-resistance rates are rising to alarming levels. Discovering new agents for treating this bacterial pathogen poses unique challenges, but these challenges have been faced throughout the entire modern history of research into anti-infectives. This review looks back at every decade since the 1940s and summarizes the most important drugs developed during each decade highlighting the lessons learned during these successful medicinal chemistry programs. Looking forward we must accelerate the integration of these past lessons with the impressive advances that have been made in the basic understanding of the biology of this disease.
Collapse
Affiliation(s)
- Clifton E Barry
- Tuberculosis Research Section, LCID, NIAID, NIH, Bethesda, MD, USA.
| |
Collapse
|