1
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Khera H, Narang T, Sharma A, Malhotra S, Kumar V, Chhabra S, Khan AM, Suri V, Dogra S, Shafiq N. Exploring the therapeutic and prophylactic potential of bedaquiline in leprosy. Int J Dermatol 2024. [PMID: 39258824 DOI: 10.1111/ijd.17485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 08/28/2024] [Indexed: 09/12/2024]
Abstract
Leprosy remains a significant public health concern despite major strides in treatment and control efforts. The Global Leprosy Strategy 2021-2030 and the National Strategic Plan for Leprosy 2023-2027 majorly focus on facilitating action to reach the goal of zero leprosy. Exploration of new treatment regimens is emphasized as one of the verticals of the multipronged approach for reaching the aforementioned goals. This becomes particularly pertinent in the wake of growing evidence for resistance to the drugs currently being used in the management of leprosy. Repurposed molecules present a very good approach in this direction. The present review aims to explore the potential of bedaquiline, a drug used for multidrug-resistant tuberculosis, as a potential addition to the therapeutic armamentarium of leprosy. Through this narrative review, the authors attempt to look into the available proof of concept, clinical evidence, potential risks, and possible ways forward with bedaquiline in leprosy.
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Affiliation(s)
- Himanshi Khera
- Clinical Pharmacology Unit, Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tarun Narang
- Department of Dermatology, Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Apoorva Sharma
- Department of Dermatology, Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Samir Malhotra
- Clinical Pharmacology Unit, Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vimal Kumar
- ICMR-National JALMA Institute of Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Seema Chhabra
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - A M Khan
- ICMR-National JALMA Institute of Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Vikas Suri
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Dogra
- Department of Dermatology, Venereology and Leprology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nusrat Shafiq
- Clinical Pharmacology Unit, Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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2
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Ragunathan P, Shuyi Ng P, Singh S, Poh WH, Litty D, Kalia NP, Larsson S, Harikishore A, Rice SA, Ingham PW, Müller V, Moraski G, Miller MJ, Dick T, Pethe K, Grüber G. GaMF1.39's antibiotic efficacy and its enhanced antitubercular activity in combination with clofazimine, Telacebec, ND-011992, or TBAJ-876. Microbiol Spectr 2023; 11:e0228223. [PMID: 37982630 PMCID: PMC10715162 DOI: 10.1128/spectrum.02282-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE New drugs are needed to combat multidrug-resistant tuberculosis. The electron transport chain (ETC) maintains the electrochemical potential across the cytoplasmic membrane and allows the production of ATP, the energy currency of any living cell. The mycobacterial engine F-ATP synthase catalyzes the formation of ATP and has come into focus as an attractive and rich drug target. Recent deep insights into these mycobacterial F1FO-ATP synthase elements opened the door for a renaissance of structure-based target identification and inhibitor design. In this study, we present the GaMF1.39 antimycobacterial compound, targeting the rotary subunit γ of the biological engine. The compound is bactericidal, inhibits infection ex vivo, and displays enhanced anti-tuberculosis activity in combination with ETC inhibitors, which promises new strategies to shorten tuberculosis chemotherapy.
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Affiliation(s)
- Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Samsher Singh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Wee Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Dennis Litty
- Molecular Microbiology and Bioenergetics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Nitin Pal Kalia
- Department of Biological Sciences (Pharmacology & Toxicology), National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Simon Larsson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Philip W. Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute for Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Garrett Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Marvin J. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Jalan Tan Tock Seng, Singapore, Singapore
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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3
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Wong CF, Leow CY, Grüber G. Cryo-EM structure of the Mycobacterium abscessus F 1-ATPase. Biochem Biophys Res Commun 2023; 671:140-145. [PMID: 37302287 DOI: 10.1016/j.bbrc.2023.05.095] [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: 05/02/2023] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023]
Abstract
The cases of lung disease caused by non-tuberculous mycobacterium Mycobacterium abscessus (Mab) are increasing and not reliably curable. Repurposing of anti-tuberculosis inhibitors brought the oxidative phosphorylation pathway with its final product ATP, formed by the essential F1FO-ATP synthase (subunits α3:β3:γ:δ:ε:a:b:b':c9), into focus as an attractive inhibitor target against Mab. Because of the pharmacological attractiveness of this enzyme, we generated and purified a recombinant and enzymatically active Mab F1-ATPase complex, including subunits α3:β3:γ:δ:ε (MabF1-αβγδε) to achieve mechanistic, regulatory, and structural insights. The high purity of the complex enabled the first cryo-electron microscopy structure determination of the Mab F1-ATPase complex to 7.3 Å resolution. The enzyme showed low ATP hydrolysis activity, which was stimulated by trypsin treatment. No effect was observed in the presence of the detergent lauryldimethylamine oxide.
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Affiliation(s)
- Chui-Fann Wong
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Chen-Yen Leow
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Gerhard Grüber
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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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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F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:ijms24065417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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6
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Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors. Antimicrob Agents Chemother 2022; 66:e0105622. [PMID: 36445139 PMCID: PMC9764993 DOI: 10.1128/aac.01056-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The F1FO-ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the Mycobacterium smegmatis F1-ATPase and the F1FO-ATP synthase with different nucleotide occupation within the catalytic sites and visualize critical elements for latent ATP hydrolysis and efficient ATP synthesis. Mutational studies reveal that the extended C-terminal domain (αCTD) of subunit α is the main element for the self-inhibition mechanism of ATP hydrolysis for TB and NTM bacteria. Rotational studies indicate that the transition between the inhibition state by the αCTD and the active state is a rapid process. We demonstrate that the unique mycobacterial γ-loop and subunit δ are critical elements required for ATP formation. The data underline that these mycobacterium-specific elements of α, γ, and δ are attractive targets, providing a platform for the discovery of species-specific inhibitors.
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7
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Shin J, Harikishore A, Wong CF, Ragunathan P, Thomas D, Grüber G. Atomic solution structure of Mycobacterium abscessus F-ATP synthase subunit ε and identification of Ep1MabF1 as a targeted inhibitor. FEBS J 2022; 289:6308-6323. [PMID: 35612822 PMCID: PMC10609657 DOI: 10.1111/febs.16536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/27/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
Mycobacterium abscessus (Mab) is a nontuberculous mycobacterium of increasing clinical relevance. The rapidly growing opportunistic pathogen is intrinsically multi-drug-resistant and causes difficult-to-cure lung disease. Adenosine triphosphate, generated by the essential F1 FO ATP synthase, is the major energy currency of the pathogen, bringing this enzyme complex into focus for the discovery of novel antimycobacterial compounds. Coupling of proton translocation through the membrane-embedded FO sector and ATP formation in the F1 headpiece of the bipartite F1 FO ATP synthase occurs via the central stalk subunits γ and ε. Here, we used solution NMR spectroscopy to resolve the first atomic structure of the Mab subunit ε (Mabε), showing that it consists of an N-terminal β-barrel domain (NTD) and a helix-loop-helix motif in its C-terminal domain (CTD). NMR relaxation measurements of Mabε shed light on dynamic epitopes and amino acids relevant for coupling processes within the protein. We describe structural differences between other mycobacterial ε subunits and Mabε's lack of ATP binding. Based on the structural insights, we conducted an in silico inhibitor screen. One hit, Ep1MabF1, was shown to inhibit the growth of Mab and bacterial ATP synthesis. NMR titration experiments and docking studies described the binding epitopes of Ep1MabF1 on Mabε. Together, our data demonstrate the potential to develop inhibitors targeting the ε subunit of Mab F1 FO ATP synthase to interrupt the coupling process.
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Affiliation(s)
- Joon Shin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Chui Fann Wong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Dick Thomas
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Boulevard, Nutley, NJ 07110, USA
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road NW Medical-Dental Building, Washington, DC 20007, USA
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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8
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Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
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Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
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9
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Anti-Mycobacterium abscessus Activity of Tuberculosis F-ATP Synthase Inhibitor GaMF1. Antimicrob Agents Chemother 2022; 66:e0001822. [PMID: 35481752 PMCID: PMC9112937 DOI: 10.1128/aac.00018-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New drug targets and molecules with bactericidal activity are needed against the respiratory mycobacterial pathogen Mycobacterium abscessus. Employing a lead repurposing strategy, the antituberculosis compound GaMF1 was tested against M. abscessus. Whole-cell and ATP synthesis assays demonstrated that GaMF1 inhibits growth and kills M. abscessus by targeting the F-ATP synthase. GaMF1's anti-M. abscessus activity increased in combination with clofazimine, rifabutin, or amikacin. The study expands the repertoire of anti-M. abscessus compounds targeting oxidative phosphorylation.
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Harikishore A, Saw WG, Ragunathan P, Litty D, Dick T, Müller V, Grüber G. Mutational Analysis of Mycobacterial F-ATP Synthase Subunit δ Leads to a Potent δ Enzyme Inhibitor. ACS Chem Biol 2022; 17:529-535. [PMID: 35148057 DOI: 10.1021/acschembio.1c00766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While many bacteria are able to bypass the requirement for oxidative phosphorylation when grown on carbohydrates, Mycobacterium tuberculosis is unable to do so. Differences of amino acid composition and structural features of the mycobacterial F-ATP synthase (α3:β3:γ:δ:ε:a:b:b':c9) compared to its prokaryotic or human counterparts were recently elucidated and paved avenues for the discovery of molecules interfering with various regulative mechanisms of this essential energy converter. In this context, the mycobacterial peripheral stalk subunit δ came into focus, which displays a unique N-terminal 111-amino acid extension. Here, mutants of recombinant mycobacterial subunit δ were characterized, revealing significant reduction in ATP synthesis and demonstrating essentiality of this subunit for effective catalysis. These results provided the basis for the generation of a four-feature model forming a δ receptor-based pharmacophore and to identify a potent subunit δ inhibitor DeMF1 via in silico screening. The successful targeting of the δ subunit demonstrates the potential to advance δ's flexible coupling as a new area for the development of F-ATP synthase inhibitors.
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Affiliation(s)
- Amaravadhi Harikishore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Dennis Litty
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, New Jersey 07110, United States
- Medical Sciences, Hackensack Meridian School of Medicine, 123 Metro Boulevard, Nutley, New Jersey 07110, United States
- Department of Microbiology and Immunology, Georgetown University, 3900 Reservoir Road NW Medical-Dental Building, Washington, D.C. 20007, United States
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
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11
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Krah A, Grüber G, Bond PJ. Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase. Curr Res Struct Biol 2022; 4:278-284. [PMID: 36186842 PMCID: PMC9516385 DOI: 10.1016/j.crstbi.2022.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/13/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB), the deadly disease caused by Mycobacterium tuberculosis (Mtb), kills more people worldwide than any other bacterial infectious disease. There has been a recent resurgence of TB drug discovery activities, resulting in the identification of a number of novel enzyme inhibitors. Many of these inhibitors target the electron transport chain complexes and the F1FO-ATP synthase; these enzymes represent new target spaces for drug discovery, since the generation of ATP is essential for the bacterial pathogen's physiology, persistence, and pathogenicity. The anti-TB drug bedaquiline (BDQ) targets the Mtb F-ATP synthase and is used as salvage therapy against this disease. Medicinal chemistry efforts to improve the physio-chemical properties of BDQ resulted in the discovery of 3,5-dialkoxypyridine (DARQ) analogs to which TBAJ-876 belongs. TBAJ-876, a clinical development candidate, shows attractive in vitro and in vivo antitubercular activity. Both BDQ and TBAJ-876 inhibit the mycobacterial F1FO-ATP synthase by stopping rotation of the c-ring turbine within the FO domain, thereby preventing proton translocation and ATP synthesis to occur. While structural data for the BDQ bound state are available, no structural information about TBAJ-876 binding have been described. In this study, we show how TBAJ-876 binds to the FO domain of the M. smegmatis F1FO-ATP synthase. We further calculate the binding free energy of both drugs bound to their target and predict an increased affinity of TBAJ-876 for the FO domain. This approach will be useful in future efforts to design new and highly potent DARQ analogs targeting F-ATP synthases of Mtb, nontuberculosis mycobacteria (NTM) as well as the M. leprosis complex. BDQ inhibits mycobacterial F-ATP synthase. TBAJ-876 is a BDQ analogue with improved affinity for the enzyme. Simulations help to structurally clarify the FO domain binding sites of TBAJ-876. Insights will help guide development of multidrug-resistant tuberculosis drugs.
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Affiliation(s)
- Alexander Krah
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore
- Corresponding author.
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
- Corresponding author. Bioinformatics Institute, Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Str., #07-01 Matrix, 138671, Singapore.
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12
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Lee BS, Hards K, Engelhart CA, Hasenoehrl EJ, Kalia NP, Mackenzie JS, Sviriaeva E, Chong SMS, Manimekalai MSS, Koh VH, Chan J, Xu J, Alonso S, Miller MJ, Steyn AJC, Grüber G, Schnappinger D, Berney M, Cook GM, Moraski GC, Pethe K. Dual inhibition of the terminal oxidases eradicates antibiotic-tolerant Mycobacterium tuberculosis. EMBO Mol Med 2021; 13:e13207. [PMID: 33283973 PMCID: PMC7799364 DOI: 10.15252/emmm.202013207] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/09/2022] Open
Abstract
The approval of bedaquiline has placed energy metabolism in the limelight as an attractive target space for tuberculosis antibiotic development. While bedaquiline inhibits the mycobacterial F1 F0 ATP synthase, small molecules targeting other components of the oxidative phosphorylation pathway have been identified. Of particular interest is Telacebec (Q203), a phase 2 drug candidate inhibitor of the cytochrome bcc:aa3 terminal oxidase. A functional redundancy between the cytochrome bcc:aa3 and the cytochrome bd oxidase protects M. tuberculosis from Q203-induced death, highlighting the attractiveness of the bd-type terminal oxidase for drug development. Here, we employed a facile whole-cell screen approach to identify the cytochrome bd inhibitor ND-011992. Although ND-011992 is ineffective on its own, it inhibits respiration and ATP homeostasis in combination with Q203. The drug combination was bactericidal against replicating and antibiotic-tolerant, non-replicating mycobacteria, and increased efficacy relative to that of a single drug in a mouse model. These findings suggest that a cytochrome bd oxidase inhibitor will add value to a drug combination targeting oxidative phosphorylation for tuberculosis treatment.
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Affiliation(s)
- Bei Shi Lee
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Kiel Hards
- Department of Microbiology and ImmunologySchool of Biomedical SciencesUniversity of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryUniversity of AucklandAucklandNew Zealand
| | - Curtis A Engelhart
- Department of Microbiology and ImmunologyWeill Cornell Medical CollegeNew YorkNYUSA
| | - Erik J Hasenoehrl
- Department of Microbiology and ImmunologyAlbert Einstein College of MedicineBronxNYUSA
| | - Nitin P Kalia
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Ramalingaswami FellowClinical Microbiology DivisionCSIR‐IIIMJammu and KashmirIndia
| | - Jared S Mackenzie
- Africa Health Research InstituteNelson R. Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Ekaterina Sviriaeva
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Shi Min Sherilyn Chong
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Nanyang Institute of Technology in Health and MedicineInterdisciplinary Graduate SchoolNanyang Technological UniversitySingaporeSingapore
| | | | - Vanessa H Koh
- Department of MicrobiologyYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Infectious Disease ProgrammeDepartment of Microbiology and ImmunologyNational University of SingaporeSingaporeSingapore
| | - John Chan
- Department of MedicineAlbert Einstein College of MedicineBronxNYUSA
| | - Jiayong Xu
- Department of MedicineAlbert Einstein College of MedicineBronxNYUSA
| | - Sylvie Alonso
- Department of MicrobiologyYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Infectious Disease ProgrammeDepartment of Microbiology and ImmunologyNational University of SingaporeSingaporeSingapore
| | - Marvin J Miller
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameINUSA
| | - Adrie J C Steyn
- Africa Health Research InstituteNelson R. Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
- Department of MicrobiologyUniversity of AlabamaBirminghamALUSA
| | - Gerhard Grüber
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Dirk Schnappinger
- Department of Microbiology and ImmunologyWeill Cornell Medical CollegeNew YorkNYUSA
| | - Michael Berney
- Department of Microbiology and ImmunologyAlbert Einstein College of MedicineBronxNYUSA
| | - Gregory M Cook
- Department of Microbiology and ImmunologySchool of Biomedical SciencesUniversity of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryUniversity of AucklandAucklandNew Zealand
| | - Garrett C Moraski
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMTUSA
| | - Kevin Pethe
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
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13
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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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14
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Hotra A, Ragunathan P, Ng PS, Seankongsuk P, Harikishore A, Sarathy JP, Saw W, Lakshmanan U, Sae‐Lao P, Kalia NP, Shin J, Kalyanasundaram R, Anbarasu S, Parthasarathy K, Pradeep CN, Makhija H, Dröge P, Poulsen A, Tan JHL, Pethe K, Dick T, Bates RW, Grüber G. Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines. Angew Chem Int Ed Engl 2020; 59:13295-13304. [DOI: 10.1002/anie.202002546] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Adam Hotra
- 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 Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Pattarakiat Seankongsuk
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Amaravadhi Harikishore
- 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
| | - Jickky Palmae Sarathy
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
| | - Wuan‐Geok Saw
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Umayal Lakshmanan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Patcharaporn Sae‐Lao
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Nitin Pal Kalia
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Joon Shin
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Revathy Kalyanasundaram
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Sivaraj Anbarasu
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Krupakar Parthasarathy
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Chaudhari Namrata Pradeep
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Harshyaa Makhija
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Peter Dröge
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Jocelyn Hui Ling Tan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Kevin Pethe
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
- Center for Discovery and Innovation Hackensack Meridian Health 340 Kingsland Street Nutley NJ 07110 USA
| | - Roderick W. Bates
- 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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15
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Hotra A, Ragunathan P, Ng PS, Seankongsuk P, Harikishore A, Sarathy JP, Saw W, Lakshmanan U, Sae‐Lao P, Kalia NP, Shin J, Kalyanasundaram R, Anbarasu S, Parthasarathy K, Pradeep CN, Makhija H, Dröge P, Poulsen A, Tan JHL, Pethe K, Dick T, Bates RW, Grüber G. Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Adam Hotra
- 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 Republic of Singapore
| | - Priya Ragunathan
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Pearly Shuyi Ng
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Pattarakiat Seankongsuk
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Amaravadhi Harikishore
- 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
| | - Jickky Palmae Sarathy
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
| | - Wuan‐Geok Saw
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Umayal Lakshmanan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Patcharaporn Sae‐Lao
- School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371 Republic of Singapore
| | - Nitin Pal Kalia
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Joon Shin
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Revathy Kalyanasundaram
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Sivaraj Anbarasu
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Krupakar Parthasarathy
- Centre for Drug Discovery and Development Sathyabama Institute of Science and Technology Chennai 600119 India
| | - Chaudhari Namrata Pradeep
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Harshyaa Makhija
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Peter Dröge
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Jocelyn Hui Ling Tan
- Experimental Drug Development Centre Agency for Science Technology and Research, A*STAR 10 Biopolis Road Singapore 138670 Republic of Singapore
| | - Kevin Pethe
- School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Republic of Singapore
- Lee Kong Chian School of Medicine Nanyang Technological University Experimental Medicine Building Republic of Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology Yong Loo Lin School of Medicine National University of Singapore 14 Medical Drive Singapore 117599 Republic of Singapore
- Center for Discovery and Innovation Hackensack Meridian Health 340 Kingsland Street Nutley NJ 07110 USA
| | - Roderick W. Bates
- 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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16
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Chong SMS, Manimekalai MSS, Sarathy JP, Williams ZC, Harold LK, Cook GM, Dick T, Pethe K, Bates RW, Grüber G. Antituberculosis Activity of the Antimalaria Cytochrome bcc Oxidase Inhibitor SCR0911. ACS Infect Dis 2020; 6:725-737. [PMID: 32092260 DOI: 10.1021/acsinfecdis.9b00408] [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: 12/11/2022]
Abstract
The ability to respire and generate adenosine triphosphate (ATP) is essential for the physiology, persistence, and pathogenicity of Mycobacterium tuberculosis, which causes tuberculosis. By employing a lead repurposing strategy, the malarial cytochrome bc1 inhibitor SCR0911 was tested against mycobacteria. Docking studies were carried out to reveal potential binding and to understand the binding interactions with the target, cytochrome bcc. Whole-cell-based and in vitro assays demonstrated the potency of SCR0911 by inhibiting cell growth and ATP synthesis in both the fast- and slow-growing M. smegmatis and M. bovis bacillus Calmette-Guérin, respectively. The variety of biochemical assays and the use of a cytochrome bcc deficient mutant strain validated the cytochrome bcc oxidase as the direct target of the drug. The data demonstrate the broad-spectrum activity of SCR0911 and open the door for structure-activity relationship studies to improve the potency of new mycobacteria specific SCR0911 analogues.
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Affiliation(s)
- Shi Min Sherilyn Chong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Republic of Singapore
- Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Republic of Singapore
| | | | - Jickky Palmae Sarathy
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Zoe C. Williams
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Liam K. Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Gregory M. Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street Building 102, Nutley, New Jersey 07110, United States
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore
| | - Roderick W. Bates
- 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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17
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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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18
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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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19
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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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20
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Unique structural and mechanistic properties of mycobacterial F-ATP synthases: Implications for drug design. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 152:64-73. [PMID: 31743686 DOI: 10.1016/j.pbiomolbio.2019.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/25/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
The causative agent of Tuberculosis (TB) Mycobacterium tuberculosis (Mtb) encounters unfavourable environmental conditions in the lungs, including nutrient limitation, low oxygen tensions and/or low/high pH values. These harsh conditions in the host triggers Mtb to enter a dormant state in which the pathogen does not replicate and uses host-derived fatty acids instead of carbohydrates as an energy source. Independent to the energy source, the bacterium's energy currency ATP is generated by oxidative phosphorylation, in which the F1FO-ATP synthase uses the proton motive force generated by the electron transport chain. This catalyst is essential in Mtb and inhibition by the diarylquinoline class of drugs like Bedaquilline, TBAJ-587, TBAJ-876 or squaramides demonstrated that this engine is an attractive target in TB drug discovery. A special feature of the mycobacterial F-ATP synthase is its inability to establish a significant proton gradient during ATP hydrolysis, and its latent ATPase activity, to prevent energy waste and to control the membrane potential. Recently, unique epitopes of mycobacterial F1FO-ATP synthase subunits absent in their prokaryotic or mitochondrial counterparts have been identified to contribute to the regulation of the low ATPase activity. Most recent structural insights into individual subunits, the F1 domain or the entire mycobacterial enzyme added to the understanding of mechanisms, regulation and differences of the mycobacterial F1FO-ATP synthase compared to other bacterial and eukaryotic engines. These novel insights provide the basis for the design of new compounds targeting this engine and even novel regimens for multidrug resistant TB.
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21
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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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