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Wang K, Gong C, Xiao W, Abdukader A, Wang D. Accessing 1,8-Naphthyridone-3-carboxylic Acid Derivatives and Application to the Synthesis of Amfonelic Acid. J Org Chem 2024; 89:5811-5824. [PMID: 38602006 DOI: 10.1021/acs.joc.4c00415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
1,8-Naphthyridone-3-carboxyl is the core structure of several on-market antibacterial drugs. It has prompted significant interest from the synthetic community. Here, we report a practical synthesis of diversely functionalized 1,8-naphthyridone-3-carboxylic acid derivatives starting from readily available and inexpensive nicotinic acid derivatives. All key steps have been optimized. Furthermore, the usefulness of this protocol has been exemplified by the first synthesis of amfonelic acid.
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Affiliation(s)
- Kaijuan Wang
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, Xinjiang,China
| | - Chengcheng Gong
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, Xinjiang,China
| | - Weiwei Xiao
- School of Pharmaceutical Sciences and Institute of Materia Medica, Xinjiang University, Urumqi830017, Xinjiang,China
| | - Ablimit Abdukader
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, Xinjiang,China
| | - Dong Wang
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, Xinjiang,China
- School of Pharmaceutical Sciences and Institute of Materia Medica, Xinjiang University, Urumqi830017, Xinjiang,China
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2
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Chasák J, Oorts L, Dak M, Šlachtová V, Bazgier V, Berka K, De Vooght L, Smiejkowska N, Calster KV, Van Moll L, Cappoen D, Cos P, Brulíková L. Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation. Bioorg Med Chem 2023; 95:117504. [PMID: 37871508 DOI: 10.1016/j.bmc.2023.117504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Mycobacterial ATP synthase is a validated therapeutic target for combating drug-resistant tuberculosis. Inhibition of this enzyme has been featured as an efficient strategy for the development of new antimycobacterial agents against drug-resistant pathogens. In this study, we synthesised and explored two distinct series of squaric acid analogues designed to inhibit mycobacterial ATP synthase. Among the extensive array of compounds investigated, members of the phenyl-substituted sub-library emerged as primary hits. To gain deeper insights into their mechanisms of action, we conducted advanced biological studies, focusing on the compounds displaying a direct binding of a nitrogen heteroatom to the phenyl ring, resulting in the highest potency. Our investigations into spontaneous mutants led to the validation of a single point mutation within the atpB gene (Rv1304), responsible for encoding the ATP synthase subunit a. This genetic alteration sheds light on the molecular basis of resistance to squaramides. Furthermore, we explored the possibility of synergy between squaramides and the reference drug clofazimine using a checkerboard assay, highlighting the promising avenue for enhancing the effectiveness of existing treatments through combined therapeutic approaches. This study contributes to the expansion of investigating squaramides as promising drug candidates in the ongoing battle against drug-resistant tuberculosis.
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Affiliation(s)
- Jan Chasák
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Lauren Oorts
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Milan Dak
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Veronika Šlachtová
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Václav Bazgier
- Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Linda De Vooght
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Natalia Smiejkowska
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Kevin Van Calster
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Laurence Van Moll
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Lucie Brulíková
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic.
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3
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Guo K, Wang Y, Ma C. Characterization of stress degradation products of bedaquiline fumarate and bedaquiline by LC-PDA and LC-MS. J Pharm Biomed Anal 2023; 235:115658. [PMID: 37619292 DOI: 10.1016/j.jpba.2023.115658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Bedaquiline fumarate was a first-in-class diarylquinoline drug used for the treatment of M. tuberculosis and its main biologically active form was bedaquiline. This paper studied and compared the degradation products of bedaquiline fumarate and bedaquiline using LC-PDA, LC-MS, and NMR techniques under thermal, alkaline, acidic, oxidative, and photolytic conditions respectively. A LC method was established and optimized to separate all analytes of bedaquiline fumarate and bedaquiline. All degradation products were identified by LC-HRMS/MS and LC-MSn. Bedaquiline fumarate formed three degradation products (DP1, DP2, and DP3) related to fumarate under photolytic condition and formed demethylation product DP4 under acid condition. Bedaquiline formed four degradation products (IM1, IM2, IM3, and IM4) related to the side chains of tertiary alcohol and tertiary amine groups under photolytic condition and formed DP4 under acid condition. The two compounds were stable under thermal, alkaline, and oxidative conditions. DP1 and DP2 indicate that the fumarate could take cis-trans isomerization under light condition. DP3, IM3 and IM4 were first reported degradation products of bedaquiline fumarate and bedaquiline. Compared the degradation behavior of bedaquiline fumarate with bedaquiline, the fumarate form can make the side chain of bedaquiline more stable. It is better to avoid acid and light contact during their storage and manufacturing process.
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Affiliation(s)
- Kaijing Guo
- Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Yanan Wang
- Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Chen Ma
- Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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4
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Kelam LM, Wani MA, Dhaked DK. An update on ATP synthase inhibitors: A unique target for drug development in M. tuberculosis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:87-104. [PMID: 37105260 DOI: 10.1016/j.pbiomolbio.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
ATP synthase is a key protein in the oxidative phosphorylation process, as it aids in the effective production of ATP (Adenosine triphosphate) in all life's of kingdoms. ATP synthases have distinctive properties that contribute to efficient ATP synthesis. The ATP synthase of mycobacterium is of special relevance since it has been identified as a target for potential anti-TB molecules, especially Bedaquiline (BDQ). Better knowledge of how mycobacterial ATP synthase functions and its peculiar characteristics will aid in our understanding of bacterial energy metabolism adaptations. Furthermore, identifying and understanding the important distinctions between human ATP synthase and bacterial ATP synthase may provide insight into the design and development of inhibitors that target specific ATP synthase. In recent years, many potential candidates targeting the ATP synthase of mycobacterium have been developed. In this review, we discuss the druggable targets of the Electron transport chain (ETC) and recently identified potent inhibitors (including clinical molecules) from 2015 to 2022 of diverse classes that target ATP synthase of M. tuberculosis.
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Affiliation(s)
- Lakshmi Mounika Kelam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India
| | - Mushtaq Ahmad Wani
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India
| | - Devendra K Dhaked
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India.
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5
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Barbaro L, Nagalingam G, Triccas JA, Tan L, West NP, Priebbenow DL, Baell JB. Discovery of Anti-tubercular Analogues of Bedaquiline with Modified A-, B- and C-Ring Subunits. ChemMedChem 2023; 18:e202200533. [PMID: 36259365 DOI: 10.1002/cmdc.202200533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/16/2022] [Indexed: 01/24/2023]
Abstract
To date, the clinical use of the anti-tubercular therapy bedaquiline has been somewhat limited due to safety concerns. Recent investigations determined that modification of the B- and C-ring units of bedaquiline delivered new diarylquinolines (for example TBAJ-587) with potent anti-tubercular activity yet an improved safety profile due to reduced affinity for the hERG channel. Building on our recent discovery that substitution of the quinoline motif (the A-ring subunit) for C5-aryl pyridine groups within bedaquiline analogues led to retention of anti-tubercular activity, we investigated the concurrent modification of A-, B- and C-ring units within bedaquiline variants. This led to the discovery that 4-trifluoromethoxyphenyl and 4-chlorophenyl pyridyl analogues of TBAJ-587 retained relatively potent anti-tubercular activity and for the 4-chlorophenyl derivative in particular, a significant reduction in hERG inhibition relative to bedaquiline was achieved, demonstrating that modifications of the A-, B- and C-ring units within the bedaquiline structure is a viable strategy for the design of effective, yet safer (and less lipophilic) anti-tubercular compounds.
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Affiliation(s)
- Lisa Barbaro
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, 3052, Parkville, Victoria, Australia
| | - Gayathri Nagalingam
- School of Medical Sciences and Marie Bashir Institute, The University of Sydney, 2006, Sydney, NSW, Australia
| | - James A Triccas
- School of Medical Sciences and Marie Bashir Institute, The University of Sydney, 2006, Sydney, NSW, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, 4072, St Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, 4067 St., Lucia, Queensland, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Bioscience, The University of Queensland, 4072, St Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, 4067 St., Lucia, Queensland, Australia
| | - Daniel L Priebbenow
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, 3052, Parkville, Victoria, Australia.,School of Chemistry, The University of Melbourne, 3010, Parkville, Victoria, Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, 3052, Parkville, Victoria, Australia
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6
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Fischer G. The chemistry of citrazinic acid (2,6-dihydroxyisonicotinic acid). ADVANCES IN HETEROCYCLIC CHEMISTRY 2023. [DOI: 10.1016/bs.aihch.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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7
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New Quinoline-Urea-Benzothiazole Hybrids as Promising Antitubercular Agents: Synthesis, In Vitro Antitubercular Activity, Cytotoxicity Studies, and In Silico ADME Profiling. Pharmaceuticals (Basel) 2022; 15:ph15050576. [PMID: 35631402 PMCID: PMC9146500 DOI: 10.3390/ph15050576] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 01/30/2023] Open
Abstract
A series of 25 new benzothiazole−urea−quinoline hybrid compounds were synthesized successfully via a three-step synthetic sequence involving an amidation coupling reaction as a critical step. The structures of the synthesized compounds were confirmed by routine spectroscopic tools (1H and 13C NMR and IR) and by mass spectrometry (HRMS). In vitro evaluation of these hybrid compounds for their antitubercular inhibitory activity against the Mycobacterium tuberculosis H37Rv pMSp12::GPF bioreporter strain was undertaken. Of the 25 tested compounds, 17 exhibited promising anti-TB activities of less than 62.5 µM (MIC90). Specifically, 13 compounds (6b, 6g, 6i−j, 6l, 6o−p, 6r−t, and 6x−y) showed promising activity with MIC90 values in the range of 1−10 µM, while compound 6u, being the most active, exhibited sub-micromolar activity (0.968 µM) in the CAS assay. In addition, minimal cytotoxicity against the HepG2 cell line (cell viability above 75%) in 11 of the 17 compounds, at their respective MIC90 concentrations, was observed, with 6u exhibiting 100% cell viability. The hybridization of the quinoline, urea, and benzothiazole scaffolds demonstrated a synergistic relationship because the activities of resultant hybrids were vastly improved compared to the individual entities. In silico ADME predictions showed that the majority of these compounds have drug-like properties and are less likely to potentially cause cardiotoxicity (QPlogHERG > −5). The results obtained in this study indicate that the majority of the synthesized compounds could serve as valuable starting points for future optimizations as new antimycobacterial agents.
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8
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Synthetic studies towards isomeric pyrazolopyrimidines as potential ATP synthesis inhibitors of Mycobacterium tuberculosis. Structural correction of reported N-(6-(2-(dimethylamino)ethoxy)-5-fluoropyridin-3-yl)-2-(4-fluorophenyl)-5-(trifluoromethyl)pyrazolo[1,5-α]pyrimidin-7-amine. Tetrahedron Lett 2021; 90:None. [PMID: 35140452 PMCID: PMC8809387 DOI: 10.1016/j.tetlet.2021.153611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022]
Abstract
During our studies into preparing analogues of pyrazolopyrimidine as ATP synthesis inhibitors of Mycobacterium tuberculosis, a regiospecific condensation reaction between ethyl 4,4,4-trifluoroacetoacetate and 3-(4-fluorophenyl)-1H-pyrazol-5-amine was observed which was dependent on the specific reaction conditions employed. This work identifies optimized reaction conditions to access either the pyrazolo[3,4-β]pyridine or the pyrazolo[1,5-α]pyrimidine scaffold. This has led to the structural confirmation of the previously reported pyrazolopyrimidine 17b which was reported as pyrazolo[1,5-α]pyrimidine structure 2 which was corrected to pyrazolo[3,4-β]-pyrimidine 19.
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9
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Ohta K, Akatsuka A, Dan S, Iwasaki H, Yamashita M, Kojima N. Structure-Activity Relationships of Thiophene Carboxamide Annonaceous Acetogenin Analogs: Shortening the Alkyl Chain in the Tail Part Significantly Affects Their Growth Inhibitory Activity against Human Cancer Cell Lines. Chem Pharm Bull (Tokyo) 2021; 69:1029-1033. [PMID: 34602571 DOI: 10.1248/cpb.c21-00450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
In a previous study, we found that the thiophene carboxamide solamin analog, which is a mono-tetrahydrofuran annonaceous acetogenin, showed potent antitumor activity through the inhibition of mitochondrial complex I. In this study, we synthesized analogs with short alkyl chains instead of the n-dodecyl group in the tail part. We evaluated their growth inhibitory activities against human cancer cell lines. We found that the alkyl chain in the tail part plays an essential role in their activity.
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Affiliation(s)
| | - Akinobu Akatsuka
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research
| | - Shingo Dan
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research
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10
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Dangi M, Khichi A, Jakhar R, Chhillar AK. Growing Preferences towards Analog-based Drug Discovery. Curr Pharm Biotechnol 2021; 22:1030-1045. [PMID: 32900347 DOI: 10.2174/1389201021666200908121409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/29/2020] [Accepted: 08/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The major concern of today's time is the developing resistance in most of the clinically derived pathogenic micro-organisms for available drugs through several mechanisms. Therefore, there is a dire need to develop novel molecules with drug-like properties that can be effective against the otherwise resistant micro-organisms. METHODS New drugs can be developed using several methods like structure-based drug design, ligandbased drug design, or by developing analogs of the available drugs to further improve their effects. However, the smartness is to opt for the techniques that have comparatively less expenditure, lower failure rates, and faster discovery rates. RESULTS Analog-Based Drug Design (ABDD) is one such technique that researchers worldwide are opting to develop new drug-like molecules with comparatively lower market values. They start by first designing the analogs sharing structural and pharmacological similarities to the existing drugs. This method embarks on scaffold structures of available drugs already approved by the clinical trials, but are left ineffective because of resistance developed by the pathogens. CONCLUSION In this review, we have discussed some recent examples of anti-fungal and anti-bacterial (antimicrobial) drugs that were designed based on the ABDD technique. Also, we have tried to focus on the in silico tools and techniques that can contribute to the designing and computational screening of the analogs, so that these can be further considered for in vitro screening to validate their better biological activities against the pathogens with comparatively reduced rates of failure.
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Affiliation(s)
- Mehak Dangi
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Alka Khichi
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Ritu Jakhar
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
| | - Anil K Chhillar
- Centre for Bioinformatics, M.D. University, Rohtak-124001, Haryana, India
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11
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Barbaro L, Nagalingam G, Triccas JA, Tan L, West NP, Baell JB, Priebbenow DL. Synthesis and evaluation of pyridine-derived bedaquiline analogues containing modifications at the A-ring subunit. RSC Med Chem 2021; 12:943-959. [PMID: 34223160 DOI: 10.1039/d1md00063b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
Despite promising efficacy, the clinical use of the anti-tubercular therapeutic bedaquiline has been restricted due to safety concerns. To date, limited SAR studies have focused on the quinoline ring (A-ring), and as such, we set out to explore modifications within this region in an attempt to discover new bedaquiline variants with an improved safety profile. We herein report the development of unique synthetic strategies that facilitated access to novel bedaquiline analogues leading to the discovery that anti-tubercular activity could be retained following replacement of the quinoline motif with pyridine heterocycles. This discovery is anticipated to open up multiple new avenues for exploration in the design of improved anti-tubercular therapeutics.
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Affiliation(s)
- Lisa Barbaro
- Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade Parkville Victoria 3052 Australia
| | - Gayathri Nagalingam
- School of Medical Sciences and Marie Bashir Institute, The University of Sydney Sydney NSW 2006 Australia
| | - James A Triccas
- School of Medical Sciences and Marie Bashir Institute, The University of Sydney Sydney NSW 2006 Australia
| | - Lendl Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland St Lucia Queensland 4072 Australia.,Australian Infectious Diseases Research Centre St. Lucia Queensland 4067 Australia
| | - Nicholas P West
- School of Chemistry and Molecular Bioscience, The University of Queensland St Lucia Queensland 4072 Australia.,Australian Infectious Diseases Research Centre St. Lucia Queensland 4067 Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade Parkville Victoria 3052 Australia
| | - Daniel L Priebbenow
- School of Chemistry, The University of Melbourne Parkville Victoria 3010 Australia
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12
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Inhibitors of F 1F 0-ATP synthase enzymes for the treatment of tuberculosis and cancer. Future Med Chem 2021; 13:911-926. [PMID: 33845594 DOI: 10.4155/fmc-2021-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The spectacular success of the mycobacterial F1F0-ATP synthase inhibitor bedaquiline for the treatment of drug-resistant tuberculosis has generated wide interest in the development of other inhibitors of this enzyme. Work in this realm has included close analogues of bedaquiline with better safety profiles and 'bedaquiline-like' compounds, some of which show potent antibacterial activity in vitro although none have yet progressed to clinical trials. The search has lately extended to a range of new scaffolds as potential inhibitors, including squaramides, diaminoquinazolines, chloroquinolines, dihydropyrazolo[1,5-a]pyrazin-4-ones, thiazolidinediones, diaminopyrimidines and tetrahydroquinolines. Because of the ubiquitous expression of ATP synthase enzymes, there has also been interest in inhibitors of other bacterial ATP synthases, as well as inhibitors of human mitochondrial ATP synthase for cancer therapy. The latter encompass both complex natural products and simpler small molecules. The review seeks to demonstrate the breadth of the structural types of molecules able to effectively inhibit the function of variants of this intriguing enzyme.
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13
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Chauhan A, Kumar M, Kumar A, Kanchan K. Comprehensive review on mechanism of action, resistance and evolution of antimycobacterial drugs. Life Sci 2021; 274:119301. [PMID: 33675895 DOI: 10.1016/j.lfs.2021.119301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
Tuberculosis is one of the deadliest infectious diseases existing in the world since ancient times and still possesses serious threat across the globe. Each year the number of cases increases due to high drug resistance shown by Mycobacterium tuberculosis (Mtb). Available antimycobacterial drugs have been classified as First line, Second line and Third line antibiotics depending on the time of their discoveries and their effectiveness in the treatment. These antibiotics have a broad range of targets ranging from cell wall to metabolic processes and their non-judicious and uncontrolled usage in the treatment for years has created a significant problem called multi-drug resistant (MDR) tuberculosis. In this review, we have summarized the mechanism of action of all the classified antibiotics currently in use along with the resistance mechanisms acquired by Mtb. We have focused on the new drug candidates/repurposed drugs, and drug in combinations, which are in clinical trials for either treating the MDR tuberculosis more effectively or involved in reducing the time required for the chemotherapy of drug sensitive TB. This information is not discussed very adequately on a single platform. Additionally, we have discussed the recent technologies that are being used to discover novel resistance mechanisms acquired by Mtb and for exploring novel drugs. The story of intrinsic resistance mechanisms and evolution in Mtb is far from complete. Therefore, we have also discussed intrinsic resistance mechanisms of Mtb and their evolution with time, emphasizing the hope for the development of novel antimycobacterial drugs for effective therapy of tuberculosis.
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Affiliation(s)
- Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
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14
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Small organic molecules targeting the energy metabolism of Mycobacterium tuberculosis. Eur J Med Chem 2020; 212:113139. [PMID: 33422979 DOI: 10.1016/j.ejmech.2020.113139] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/21/2022]
Abstract
Causing approximately 10 million incident cases and 1.3-1.5 million deaths every year, Mycobacterium tuberculosis remains a global health problem. The risk is further exacerbated with latent tuberculosis (TB) infection, the HIV pandemic, and increasing anti-TB drug resistance. Therefore, unexplored chemical scaffolds directed towards new molecular targets are increasingly desired. In this context, mycobacterial energy metabolism, particularly the oxidative phosphorylation (OP) pathway, is gaining importance. Mycobacteria possess primary dehydrogenases to fuel electron transport; aa3-type cytochrome c oxidase and bd-type menaquinol oxidase to generate a protonmotive force; and ATP synthase, which is essential for both growing mycobacteria as well as dormant mycobacteria because ATP is produced under both aerobic and hypoxic conditions. Small organic molecules targeting OP are active against latent TB as well as resistant TB strains. FDA approval of the ATP synthase inhibitor bedaquiline and the discovery of clinical candidate Q203, which both interfere with the cytochrome bc1 complex, have already confirmed mycobacterial energy metabolism to be a valuable anti-TB drug target. This review highlights both preferable molecular targets within mycobacterial OP and promising small organic molecules targeting OP. Progressive research in the area of mycobacterial OP revealed several highly potent anti-TB compounds with nanomolar-range MICs as low as 0.004 μM against Mtb H37Rv. Therefore, we are convinced that targeting the OP pathway can combat resistant TB and latent TB, leading to more efficient anti-TB chemotherapy.
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15
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The Unique C-Terminal Extension of Mycobacterial F-ATP Synthase Subunit α Is the Major Contributor to Its Latent ATP Hydrolysis Activity. Antimicrob Agents Chemother 2020; 64:AAC.01568-20. [PMID: 32988828 DOI: 10.1128/aac.01568-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 01/03/2023] Open
Abstract
Mycobacterial F1Fo-ATP synthases (α3:β3:γ:δ:ε:a:b:b':c9 ) are incapable of ATP-driven proton translocation due to their latent ATPase activity. This prevents wasting of ATP and altering of the proton motive force, whose dissipation is lethal to mycobacteria. We demonstrate that the mycobacterial C-terminal extension of nucleotide-binding subunit α contributes mainly to the suppression of ATPase activity in the recombinant mycobacterial F1-ATPase. Using C-terminal deletion mutants, the regions responsible for the enzyme's latency were mapped, providing a new compound epitope.
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Lu GL, Tong AST, Conole D, Sutherland HS, Choi PJ, Franzblau SG, Upton AM, Lotlikar MU, Cooper CB, Denny WA, Palmer BD. Synthesis and structure-activity relationships for tetrahydroisoquinoline-based inhibitors of Mycobacterium tuberculosis. Bioorg Med Chem 2020; 28:115784. [PMID: 33007562 PMCID: PMC7721589 DOI: 10.1016/j.bmc.2020.115784] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/05/2020] [Accepted: 09/18/2020] [Indexed: 11/15/2022]
Abstract
A series of 5,8-disubstituted tetrahydroisoquinolines were shown to be effective inhibitors of M. tb in culture and modest inhibitors of M. tb ATP synthase. There was a broad general trend of improved potency with higher lipophilicity. Large substituents (e.g., Bn) at the tetrahydroquinoline 5-position were well-tolerated, while N-methylpiperazine was the preferred 8-substituent. Structure-activity relationships for 7-linked side chains showed that the nature of the 7-linking group was important; –CO– and –COCH2– linkers were less effective than –CH2– or –CONH– ones. This suggests that the positioning of a terminal aromatic ring is important for target binding. Selected compounds showed much faster rates of microsomal clearance than did the clinical ATP synthase inhibitor bedaquiline, and modest inhibition of mycobacterial ATP synthase.
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Affiliation(s)
- Guo-Liang Lu
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand
| | - Amy S T Tong
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniel Conole
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand
| | - Hamish S Sutherland
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand
| | - Peter J Choi
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Anna M Upton
- Global Alliance for TB Drug Development, 40 Wall St, NY 10005, USA
| | | | | | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Brian D Palmer
- Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Moussa AY, Sobhy HA, Eldahshan OA, Singab ANB. Caspicaiene: a new kaurene diterpene with anti-tubercular activity from an Aspergillus endophytic isolate in Gleditsia caspia desf. Nat Prod Res 2020; 35:5653-5664. [PMID: 32954811 DOI: 10.1080/14786419.2020.1824222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A new kaurene derivative with a new 6/6/6/5/6 ring system structure, given the trivial name caspicaiene, was isolated from the fungal culture of the Aspergillus N830 isolate identified by ITS region DNA sequencing. The compound was characterized by 1, 2 D NMR, and HR-ESI-MS-MS and revealed a promising anti-tubercular effect using the Alamar Blue Assay (MABA), in a dose dependent manner, with MIC value of 124.5 µM. Furthermore, six known compounds were isolated and showed significant MIC values against Mycobacterium tuberculosis, ranging between 15.63 µg/mL (26.5 µM) to 125 µg/mL (500 µM), compared to the positive control isoniazid whose MIC value was 0.24 µg/mL (1.75 µM), which sets them forth as potentially natural anti-tubercular agents. To gain further insight of the underlying mechanism, in-silico molecular docking, using the C-Docker protocol, was conducted and demonstrated various interactions between the isolated compounds and three key mycobacterial enzymes. Additionally, the cytotoxic activity was reported and showed the safety of these molecules according to the calculated safety index in the human hepatic cancer cell line (HepG2) and Vero cell lines.
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Affiliation(s)
- Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hagar A Sobhy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Omayma A Eldahshan
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Center for Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.,Center for Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt
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18
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Appetecchia F, Consalvi S, Scarpecci C, Biava M, Poce G. SAR Analysis of Small Molecules Interfering with Energy-Metabolism in Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:E227. [PMID: 32878317 PMCID: PMC7557483 DOI: 10.3390/ph13090227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis remains the world's top infectious killer: it caused a total of 1.5 million deaths and 10 million people fell ill with TB in 2018. Thanks to TB diagnosis and treatment, mortality has been falling in recent years, with an estimated 58 million saved lives between 2000 and 2018. However, the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains is a major concern that might reverse this progress. Therefore, the development of new drugs acting upon novel mechanisms of action is a high priority in the global health agenda. With the approval of bedaquiline, which targets mycobacterial energy production, and delamanid, which targets cell wall synthesis and energy production, the energy-metabolism in Mtb has received much attention in the last decade as a potential target to investigate and develop new antimycobacterial drugs. In this review, we describe potent anti-mycobacterial agents targeting the energy-metabolism at different steps with a special focus on structure-activity relationship (SAR) studies of the most advanced compound classes.
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Affiliation(s)
| | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy; (F.A.); (S.C.); (C.S.); (M.B.)
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19
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Villamizar-Mogotocoro AF, Vargas-Méndez LY, Kouznetsov VV. Pyridine and quinoline molecules as crucial protagonists in the never-stopping discovery of new agents against tuberculosis. Eur J Pharm Sci 2020; 151:105374. [DOI: 10.1016/j.ejps.2020.105374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022]
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20
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Wong CF, Lau AM, Harikishore A, Saw WG, Shin J, Ragunathan P, Bhushan S, Ngan SFC, Sze SK, Bates RW, Dick T, Grüber G. A systematic assessment of mycobacterial F 1 -ATPase subunit ε's role in latent ATPase hydrolysis. FEBS J 2020; 288:818-836. [PMID: 32525613 DOI: 10.1111/febs.15440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
In contrast to most bacteria, the mycobacterial F1 FO -ATP synthase (α3 :β3 :γ:δ:ε:a:b:b':c9 ) does not perform ATP hydrolysis-driven proton translocation. Although subunits α, γ and ε of the catalytic F1 -ATPase component α3 :β3 :γ:ε have all been implicated in the suppression of the enzyme's ATPase activity, the mechanism remains poorly defined. Here, we brought the central stalk subunit ε into focus by generating the recombinant Mycobacterium smegmatis F1 -ATPase (MsF1 -ATPase), whose 3D low-resolution structure is presented, and its ε-free form MsF1 αβγ, which showed an eightfold ATP hydrolysis increase and provided a defined system to systematically study the segments of mycobacterial ε's suppression of ATPase activity. Deletion of four amino acids at ε's N terminus, mutant MsF1 αβγεΔ2-5 , revealed similar ATP hydrolysis as MsF1 αβγ. Together with biochemical and NMR solution studies of a single, double, triple and quadruple N-terminal ε-mutants, the importance of the first N-terminal residues of mycobacterial ε in structure stability and latency is described. Engineering ε's C-terminal mutant MsF1 αβγεΔ121 and MsF1 αβγεΔ103-121 with deletion of the C-terminal residue D121 and the two C-terminal ɑ-helices, respectively, revealed the requirement of the very C terminus for communication with the catalytic α3 β3 -headpiece and its function in ATP hydrolysis inhibition. Finally, we applied the tools developed during the study for an in silico screen to identify a novel subunit ε-targeting F-ATP synthase inhibitor.
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Affiliation(s)
- Chui-Fann Wong
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Aik-Meng Lau
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Amaravadhi Harikishore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - So-Fong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Roderick W Bates
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore.,Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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21
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22
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Calvert MB, Furkert DP, Cooper CB, Brimble MA. Synthetic approaches towards bedaquiline and its derivatives. Bioorg Med Chem Lett 2020; 30:127172. [PMID: 32291133 DOI: 10.1016/j.bmcl.2020.127172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 01/11/2023]
Abstract
Bedaquiline is a diarylquinoline drug that demonstrates potent and selective inhibition of mycobacterial ATP synthase, and is clinically administered for the treatment of multi-drug resistant tuberculosis. Due to its excellent activity and novel mechanism of action, bedaquiline has been the focus of a number of synthetic studies. This review will discuss these synthetic approaches, as well as the synthesis and bioactivity of the numerous derivatives and molecular probes inspired by bedaquiline.
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Affiliation(s)
- Matthew B Calvert
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
| | - Christopher B Cooper
- Global Alliance for TB Drug Development, 40 Wall Street, New York, NY 10005, USA
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Symonds Street, Auckland 1010, New Zealand.
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23
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Oxidative Phosphorylation—an Update on a New, Essential Target Space for Drug Discovery in Mycobacterium tuberculosis. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072339] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New drugs with new mechanisms of action are urgently required to tackle the global tuberculosis epidemic. Following the FDA-approval of the ATP synthase inhibitor bedaquiline (Sirturo®), energy metabolism has become the subject of intense focus as a novel pathway to exploit for tuberculosis drug development. This enthusiasm stems from the fact that oxidative phosphorylation (OxPhos) and the maintenance of the transmembrane electrochemical gradient are essential for the viability of replicating and non-replicating Mycobacterium tuberculosis (M. tb), the etiological agent of human tuberculosis (TB). Therefore, new drugs targeting this pathway have the potential to shorten TB treatment, which is one of the major goals of TB drug discovery. This review summarises the latest and key findings regarding the OxPhos pathway in M. tb and provides an overview of the inhibitors targeting various components. We also discuss the potential of new regimens containing these inhibitors, the flexibility of this pathway and, consequently, the complexity in targeting it. Lastly, we discuss opportunities and future directions of this drug target space.
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TBAJ-876, a 3,5-Dialkoxypyridine Analogue of Bedaquiline, Is Active against Mycobacterium abscessus. Antimicrob Agents Chemother 2020; 64:AAC.02404-19. [PMID: 31964791 PMCID: PMC7179298 DOI: 10.1128/aac.02404-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022] Open
Abstract
Lung disease caused by Mycobacterium abscessus is very difficult to cure, and treatment failure rates are high. The antituberculosis drug bedaquiline (BDQ) is used as salvage therapy against this dreadful disease. However, BDQ is highly lipophilic, displays a long terminal half-life, and presents a cardiotoxicity liability associated with QT interval prolongation. Recent medicinal chemistry campaigns resulted in the discovery of 3,5-dialkoxypyridine analogues of BDQ which are less lipophilic, have higher clearance, and display lower cardiotoxic potential. Lung disease caused by Mycobacterium abscessus is very difficult to cure, and treatment failure rates are high. The antituberculosis drug bedaquiline (BDQ) is used as salvage therapy against this dreadful disease. However, BDQ is highly lipophilic, displays a long terminal half-life, and presents a cardiotoxicity liability associated with QT interval prolongation. Recent medicinal chemistry campaigns resulted in the discovery of 3,5-dialkoxypyridine analogues of BDQ which are less lipophilic, have higher clearance, and display lower cardiotoxic potential. TBAJ-876, a clinical development candidate of this series, shows attractive in vitro antitubercular activity and efficacy in a murine tuberculosis model. Here, we asked whether TBAJ-876 is active against M. abscessus. TBAJ-876 displayed submicromolar in vitro activity against reference strains representing the three subspecies of M. abscessus and against a collection of clinical isolates. Drug-drug potency interaction studies with commonly used anti-M. abscessus antibiotics showed no antagonistic effects, suggesting that TBAJ-876 could be coadministered with currently used drugs. Efficacy studies, employing a mouse model of M. abscessus infection, demonstrated potent activity in vivo. In summary, we demonstrate that TBAJ-876 shows attractive in vitro and in vivo activities against M. abscessus, similar to its BDQ parent. This suggests that next-generation BDQ, with improved tolerability and pharmacological profiles, may be useful for the treatment of M. abscessus lung disease in addition to the treatment of tuberculosis.
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Choi PJ, Conole D, Sutherland HS, Blaser A, Tong AS, Cooper CB, Upton AM, Palmer BD, Denny WA. Synthetic Studies to Help Elucidate the Metabolism of the Preclinical Candidate TBAJ-876-A Less Toxic and More Potent Analogue of Bedaquiline. Molecules 2020; 25:molecules25061423. [PMID: 32245020 PMCID: PMC7144385 DOI: 10.3390/molecules25061423] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/12/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022] Open
Abstract
Bedaquiline is a novel drug approved in 2012 by the FDA for treatment of drug-resistant tuberculosis (TB). Although it shows high efficacy towards drug-resistant forms of TB, its use has been limited by the potential for significant side effects. In particular, bedaquiline is a very lipophilic compound with an associated long terminal half-life and shows potent inhibition of the cardiac potassium hERG channel, resulting in QTc interval prolongation in humans that may result in cardiac arrhythmia. To address these issues, we carried out a drug discovery programme to develop an improved second generation analogue of bedaquiline. From this medicinal chemistry program, a candidate (TBAJ-876) has been selected to undergo further preclinical evaluation. During this evaluation, three major metabolites arising from TBAJ-876 were observed in several preclinical animal models. We report here our synthetic efforts to unequivocally structurally characterize these three metabolites through their independent directed synthesis.
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Affiliation(s)
- Peter J. Choi
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
- Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Correspondence:
| | - Daniel Conole
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
| | - Hamish S. Sutherland
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
| | - Adrian Blaser
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
| | - Amy S.T. Tong
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
| | - Christopher B. Cooper
- Global Alliance for TB Drug Development, 40 Wall St, New York, NY 10005, USA; (C.B.C.); (A.M.U.)
| | - Anna M. Upton
- Global Alliance for TB Drug Development, 40 Wall St, New York, NY 10005, USA; (C.B.C.); (A.M.U.)
| | - Brian D. Palmer
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
- Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - William A. Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (D.C.); (H.S.S.); (A.B.); (A.S.T.T.); (B.D.P.); (W.A.D.)
- Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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26
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Matsumoto T, Akatsuka A, Dan S, Iwasaki H, Yamashita M, Kojima N. Synthesis and cancer cell growth inhibition effects of acetogenin analogs bearing ethylene glycol units for enhancing the water solubility. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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TBAJ-876 Displays Bedaquiline-Like Mycobactericidal Potency without Retaining the Parental Drug's Uncoupler Activity. Antimicrob Agents Chemother 2020; 64:AAC.01540-19. [PMID: 31712198 PMCID: PMC6985740 DOI: 10.1128/aac.01540-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/03/2019] [Indexed: 12/22/2022] Open
Abstract
The diarylquinoline F1FO-ATP synthase inhibitor bedaquiline (BDQ) displays protonophore activity. Thus, uncoupling electron transport from ATP synthesis appears to be a second mechanism of action of this antimycobacterial drug. Here, we show that the new BDQ analogue TBAJ-876 did not retain the parental drug’s protonophore activity. Comparative time-kill analyses revealed that both compounds exert the same bactericidal activity. The diarylquinoline F1FO-ATP synthase inhibitor bedaquiline (BDQ) displays protonophore activity. Thus, uncoupling electron transport from ATP synthesis appears to be a second mechanism of action of this antimycobacterial drug. Here, we show that the new BDQ analogue TBAJ-876 did not retain the parental drug’s protonophore activity. Comparative time-kill analyses revealed that both compounds exert the same bactericidal activity. These results suggest that the uncoupler activity is not required for the bactericidal activity of diarylquinolines.
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28
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Harikishore A, Chong SSM, Ragunathan P, Bates RW, Grüber G. Targeting the menaquinol binding loop of mycobacterial cytochrome bd oxidase. Mol Divers 2020; 25:517-524. [PMID: 31939065 DOI: 10.1007/s11030-020-10034-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/06/2020] [Indexed: 12/27/2022]
Abstract
Mycobacteria have shown enormous resilience to survive and persist by remodeling and altering metabolic requirements. Under stringent conditions or exposure to drugs, mycobacteria have adapted to rescue themselves by shutting down their major metabolic activity and elevate certain survival factor levels and efflux pathways to survive and evade the effects of drug treatments. A fundamental feature in this adaptation is the ability of mycobacteria to vary the enzyme composition of the electron transport chain (ETC), which generates the proton motive force for the synthesis of adenosine triphosphate via oxidative phosphorylation. Mycobacteria harbor dehydrogenases to fuel the ETC, and two terminal respiratory oxidases, an aa3-type cytochrome c oxidase (cyt-bcc-aa3) and a bacterial specific cytochrome bd-type menaquinol oxidase (cyt-bd). In this study, we employed homology modeling and structure-based virtual screening studies to target mycobacteria-specific residues anchoring the b558 menaquinol binding region of Mycobacterium tuberculosis cyt-bd oxidase to obtain a focused library. Furthermore, ATP synthesis inhibition assays were carried out. One of the ligands MQL-H2 inhibited both NADH2- and succinate-driven ATP synthesis inhibition of Mycobacterium smegmatis inside-out vesicles in micromolar potency. Similarly, MQL-H2 also inhibited NADH2-driven ATP synthesis in inside-out vesicles of the cytochrome-bcc oxidase deficient M. smegmatis strain. Since neither varying the electron donor substrates nor deletion of the cyt-bcc oxidase, a major source of protons, hindered the inhibitory effects of the MQL-H2, reflecting that MQL-H2 targets the terminal oxidase cytochrome bd oxidase, which was consistent with molecular docking studies. Characterization of novel cytochrome bd oxidase Menaquinol binding domain inhibitor (MQL-H2) using virtual screening and ATP synthesis inhibition assays.
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Affiliation(s)
- Amaravadhi Harikishore
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Republic of Singapore
| | - Sherilyn Shi Min Chong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Republic of Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
- Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Roderick W Bates
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Republic of Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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Re-Understanding the Mechanisms of Action of the Anti-Mycobacterial Drug Bedaquiline. Antibiotics (Basel) 2019; 8:antibiotics8040261. [PMID: 31835707 PMCID: PMC6963887 DOI: 10.3390/antibiotics8040261] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022] Open
Abstract
Bedaquiline (BDQ) inhibits ATP generation in Mycobacterium tuberculosis by interfering with the F-ATP synthase activity. Two mechanisms of action of BDQ are broadly accepted. A direct mechanism involves BDQ binding to the enzyme’s c-ring to block its rotation, thus inhibiting ATP synthesis in the enzyme’s catalytic α3β3-headpiece. An indirect mechanism involves BDQ uncoupling electron transport in the electron transport chain from ATP synthesis at the F-ATP synthase. In a recently uncovered second direct mechanism, BDQ binds to the enzyme’s ε-subunit to disrupt its ability to link c-ring rotation to ATP synthesis at the α3β3-headpiece. However, this mechanism is controversial as the drug’s binding affinity for the isolated ε-subunit protein is moderate and spontaneous resistance mutants in the ε-subunit cannot be isolated. Recently, the new, structurally distinct BDQ analogue TBAJ-876 was utilized as a chemical probe to revisit BDQ’s mechanisms of action. In this review, we first summarize discoveries on BDQ’s mechanisms of action and then describe the new insights derived from the studies of TBAJ-876. The TBAJ-876 investigations confirm the c-ring as a target, while also supporting a functional role for targeting the ε-subunit. Surprisingly, the new findings suggest that the uncoupler mechanism does not play a key role in BDQ’s anti-mycobacterial activity.
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Sutherland HS, Tong AST, Choi PJ, Blaser A, Franzblau SG, Cooper CB, Upton AM, Lotlikar M, Denny WA, Palmer BD. Variations in the C-unit of bedaquiline provides analogues with improved biology and pharmacology. Bioorg Med Chem 2019; 28:115213. [PMID: 31810890 DOI: 10.1016/j.bmc.2019.115213] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 11/25/2022]
Abstract
Analogues of the anti-tuberculosis drug bedaquiline, bearing a 3,5-dimethoxy-4-pyridyl C-unit, retain high anti-bacterial potency yet exert less inhibition of the hERG potassium channel, in vitro, than the parent compound. Two of these analogues (TBAJ-587 and TBAJ-876) are now in preclinical development. The present study further explores structure-activity relationships across a range of related 3,5-disubstituted-4-pyridyl C-unit bedaquiline analogues of greatly varying lipophilicity (clogP from 8.16 to 1.89). This broader class shows similar properties to the 3,5-dimethoxy-4-pyridyl series, being substantially more potent in vitro and equally active in an in vivo (mouse) model than bedaquiline, while retaining a lower cardiovascular risk profile through greatly attenuated hERG inhibition.
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Key Words
- CFU, colony-forming units
- HPLC, high-peformance liquid chromatography
- LDA, lithium diisopropylamide
- LORA, low oxygen recovery assay
- LiTMP, lithium tetramethylpiperidide
- M.tb, Mycobacterium tuberculosis
- MABA, microplate alamar blue assay
- MIC(90), minimum concentration for 90% inhibition
- TB, tuberculosis
- hERG, the alpha subunit of a K+ channel that contributes to the electrical activity of the heart
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Affiliation(s)
- Hamish S Sutherland
- Auckland Cancer Society Research Centre, School of Medical Sciences, and Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Amy S T Tong
- Auckland Cancer Society Research Centre, School of Medical Sciences, and Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Peter J Choi
- Auckland Cancer Society Research Centre, School of Medical Sciences, and Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Adrian Blaser
- Auckland Cancer Society Research Centre, School of Medical Sciences, and Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | | | - Anna M Upton
- Global Alliance for TB Drug Development, 40 Wall St, New York, NY 10005, USA
| | - Manisha Lotlikar
- Global Alliance for TB Drug Development, 40 Wall St, New York, NY 10005, USA
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, and Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Brian D Palmer
- Auckland Cancer Society Research Centre, School of Medical Sciences, and Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Saw WG, Wong CF, Dick T, Grüber G. Overexpression, purification, enzymatic and microscopic characterization of recombinant mycobacterial F-ATP synthase. Biochem Biophys Res Commun 2019; 522:374-380. [PMID: 31761325 DOI: 10.1016/j.bbrc.2019.11.098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 01/16/2023]
Abstract
The F-ATP synthase is an essential enzyme in mycobacteria, including the pathogenic Mycobacterium tuberculosis. Several new compounds in the TB-drug pipeline target the F-ATP synthase. In light of the importance and pharmacological attractiveness of this novel antibiotic target, tools have to be developed to generate a recombinant mycobacterial F1FO ATP synthase to achieve atomic insight and mutants for mechanistic and regulatory understanding as well as structure-based drug design. Here, we report the first genetically engineered, purified and enzymatically active recombinant M. smegmatis F1FO ATP synthase. The projected 2D- and 3D structures of the recombinant enzyme derived from negatively stained electron micrographs are presented. Furthermore, the first 2D projections from cryo-electron images are revealed, paving the way for an atomic resolution structure determination.
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Affiliation(s)
- Wuan-Geok Saw
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Chui-Fann Wong
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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Narang R, Kumar R, Kalra S, Nayak SK, Khatik GL, Kumar GN, Sudhakar K, Singh SK. Recent advancements in mechanistic studies and structure activity relationship of FoF1 ATP synthase inhibitor as antimicrobial agent. Eur J Med Chem 2019; 182:111644. [DOI: 10.1016/j.ejmech.2019.111644] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/17/2022]
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TBAJ-876 Retains Bedaquiline's Activity against Subunits c and ε of Mycobacterium tuberculosis F-ATP Synthase. Antimicrob Agents Chemother 2019; 63:AAC.01191-19. [PMID: 31358589 PMCID: PMC6761534 DOI: 10.1128/aac.01191-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/25/2019] [Indexed: 12/18/2022] Open
Abstract
The antituberculosis drug bedaquiline (BDQ) inhibits Mycobacterium tuberculosis F-ATP synthase by interfering with two subunits. Drug binding to the c subunit stalls the rotation of the c ring, while binding to the ε subunit blocks coupling of c ring rotation to ATP synthesis at the catalytic α3:β3 headpiece. BDQ is used for the treatment of drug-resistant tuberculosis. The antituberculosis drug bedaquiline (BDQ) inhibits Mycobacterium tuberculosis F-ATP synthase by interfering with two subunits. Drug binding to the c subunit stalls the rotation of the c ring, while binding to the ε subunit blocks coupling of c ring rotation to ATP synthesis at the catalytic α3:β3 headpiece. BDQ is used for the treatment of drug-resistant tuberculosis. However, the drug is highly lipophilic, displays a long terminal half-life, and has a cardiotoxicity liability by causing QT interval prolongation. Recent medicinal chemistry campaigns have resulted in the discovery of 3,5-dialkoxypyridine analogues of BDQ that are less lipophilic, have higher clearance, and display lower cardiotoxic potential. TBAJ-876, which is a new developmental compound of this series, shows attractive antitubercular activity and efficacy in a murine tuberculosis model. Here, we asked whether TBAJ-876 and selected analogues of the compound retain BDQ’s mechanism of action. Biochemical assays showed that TBAJ-876 is a potent inhibitor of mycobacterial F-ATP synthase. Selection of spontaneous TBAJ-876-resistant mutants identified missense mutations at BDQ’s binding site on the c subunit, suggesting that TBAJ-876 retains BDQ’s targeting of the c ring. Susceptibility testing against a strain overexpressing the ε subunit and a strain harboring an engineered mutation in BDQ’s ε subunit binding site suggest that TBAJ-876 retains BDQ’s activity on the ε subunit. Nuclear magnetic resonance (NMR) titration studies confirmed that TBAJ-876 binds to the ε subunit at BDQ’s binding site. We show that TBAJ-876 retains BDQ’s antimycobacterial mode of action. The developmental compound inhibits the mycobacterial F-ATP synthase via a dual-subunit mechanism of interfering with the functions of both the enzyme’s c and ε subunits.
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Cohen K, Maartens G. A safety evaluation of bedaquiline for the treatment of multi-drug resistant tuberculosis. Expert Opin Drug Saf 2019; 18:875-882. [DOI: 10.1080/14740338.2019.1648429] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karen Cohen
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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Nesci S, Trombetti F, Algieri C, Pagliarani A. A Therapeutic Role for the F 1F O-ATP Synthase. SLAS DISCOVERY 2019; 24:893-903. [PMID: 31266411 DOI: 10.1177/2472555219860448] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recently, the F1FO-ATP synthase, due to its dual role of life enzyme as main adenosine triphosphate (ATP) maker and of death enzyme, as ATP dissipator and putative structural component of the mitochondrial permeability transition pore (mPTP), which triggers cell death, has been increasingly considered as a drug target. Accordingly, the enzyme offers new strategies to counteract the increased antibiotic resistance. The challenge is to find or synthesize compounds able to discriminate between prokaryotic and mitochondrial F1FO-ATP synthase, exploiting subtle structural differences to kill pathogens without affecting the host. From this perspective, the eukaryotic enzyme could also be made refractory to macrolide antibiotics by chemically produced posttranslational modifications. Moreover, because the mitochondrial F1FO-ATPase activity stimulated by Ca2+ instead of by the natural modulator Mg2+ is most likely involved in mPTP formation, effectors preferentially targeting the Ca2+-activated enzyme may modulate the mPTP. If the enzyme involvement in the mPTP is confirmed, Ca2+-ATPase inhibitors may counteract conditions featured by an increased mPTP activity, such as neurodegenerative and cardiovascular diseases and physiological aging. Conversely, mPTP opening could be pharmacologically stimulated to selectively kill unwanted cells. On the basis of recent literature and promising lab findings, the action mechanism of F1 and FO inhibitors is considered. These molecules may act as enzyme modifiers and constitute new drugs to kill pathogens, improve compromised enzyme functions, and limit the deathly enzyme role in pathologies. The enzyme offers a wide spectrum of therapeutic strategies to fight at the molecular level diseases whose treatment is still insufficient or merely symptomatic.
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Affiliation(s)
- Salvatore Nesci
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Bologna, Italy
| | - Fabiana Trombetti
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Bologna, Italy
| | - Cristina Algieri
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Bologna, Italy
| | - Alessandra Pagliarani
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Bologna, Italy
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