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Ge Y, Luo Q, Liu L, Shi Q, Zhang Z, Yue X, Tang L, Liang L, Hu J, Ouyang W. S288T mutation altering MmpL3 periplasmic domain channel and H-bond network: a novel dual drug resistance mechanism. J Mol Model 2024; 30:39. [PMID: 38224406 DOI: 10.1007/s00894-023-05814-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
CONTEXT Mycobacterial membrane proteins Large 3 (MmpL3) is responsible for the transport of mycobacterial acids out of cell membrane to form cell wall, which is essential for the survival of Mycobacterium tuberculosis (Mtb) and has become a potent anti-tuberculosis target. SQ109 is an ethambutol (EMB) analogue, as a novel anti-tuberculosis drug, can effectively inhibit MmpL3, and has completed phase 2b-3 clinical trials. Drug resistance has always been the bottleneck problem in clinical treatment of tuberculosis. The S288T mutant of MmpL3 shows significant resistance to the inhibitor SQ109, while the specific action mechanism remains unclear. The results show that MmpL3 S288T mutation causes local conformational change with little effect on the global structure. With MmpL3 bound by SQ109 inhibitor, the distance between D710 and R715 increases resulting in H-bond destruction, but their interactions and proton transfer function are still restored. In addition, the rotation of Y44 in the S288T mutant leads to an obvious bend in the periplasmic domain channel and an increased number of contact residues, reducing substrate transport efficiency. This work not only provides a possible dual drug resistance mechanism of MmpL3 S288T mutant but also aids the development of novel anti-tuberculosis inhibitors. METHODS In this work, molecular dynamics (MD) and quantum mechanics (QM) simulations both were performed to compare inhibitor (i.e., SQ109) recognition, motion characteristics, and H-bond energy change of MmpL3 after S288T mutation. In addition, the WT_SQ109 complex structure was obtained by molecular docking program (Autodock 4.2); Molecular Mechanics/ Poisson Boltzmann Surface Area (MM-PBSA) and Solvated Interaction Energy (SIE) methods were used to calculate the binding free energies (∆Gbind); Geometric criteria were used to analyze the changes of hydrogen bond networks.
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Affiliation(s)
- Yutong Ge
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Qing Luo
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, 999078, China
| | - Ling Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Quanshan Shi
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Zhigang Zhang
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Xinru Yue
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Lingkai Tang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
| | - Weiwei Ouyang
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
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Williams JT, Giletto M, Haiderer ER, Aleiwi B, Krieger-Burke T, Ellsworth E, Abramovitch RB. The Mycobacterium tuberculosis MmpL3 inhibitor MSU-43085 is active in a mouse model of infection. Microbiol Spectr 2024; 12:e0367723. [PMID: 38078724 PMCID: PMC10783087 DOI: 10.1128/spectrum.03677-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE MmpL3 is a protein that is required for the survival of bacteria that cause tuberculosis (TB) and nontuberculous mycobacterial (NTM) infections. This report describes the discovery and characterization of a new small molecule, MSU-43085, that targets MmpL3 and is a potent inhibitor of Mycobacterium tuberculosis (Mtb) and M. abscessus survival. MSU-43085 is shown to be orally bioavailable and efficacious in an acute model of Mtb infection. However, the analog is inactive against Mtb in chronically infected mice. Pharmacokinetic and metabolite identification studies identified in vivo metabolism of MSU-43085, leading to a short half-life in treated mice. These proof-of-concept studies will guide further development of the MSU-43085 series for the treatment of TB or NTM infections.
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Affiliation(s)
- John T. Williams
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Matthew Giletto
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Elizabeth R. Haiderer
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Bilal Aleiwi
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Teresa Krieger-Burke
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Edmund Ellsworth
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Robert B. Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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Boudehen YM, Tasrini Y, Aguilera-Correa JJ, Alcaraz M, Kremer L. Silencing essential gene expression in Mycobacterium abscessus during infection. Microbiol Spectr 2023; 11:e0283623. [PMID: 37831478 PMCID: PMC10714871 DOI: 10.1128/spectrum.02836-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Mycobacterium abscessus represents the most common rapidly growing mycobacterial pathogen in cystic fibrosis and is extremely difficult to eradicate. Essential genes are required for growth, often participate in pathogenesis, and encode valid drug targets for further chemotherapeutic developments. However, assessing the function of essential genes in M. abscessus remains challenging due to the limited spectrum of efficient genetic tools. Herein, we generated a Tet-OFF-based system allowing to knock down the expression of mmpL3, encoding the mycolic acid transporter in mycobacteria. Using this conditional mutant, we confirm the essentiality of mmpL3 in planktonic cultures, in biofilms, and during infection in zebrafish embryos. Thus, in this study, we developed a robust and reliable method to silence the expression of any M. abscessus gene during host infection.
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Affiliation(s)
- Yves-Marie Boudehen
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Yara Tasrini
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - John Jairo Aguilera-Correa
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
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Dhulap A, Banerjee P. Pharmacophore based virtual screening & molecular docking approach for identification of mycobacterial membrane protein large 3 ( MmpL3) inhibitors. J Biomol Struct Dyn 2023; 41:11062-11077. [PMID: 36571432 DOI: 10.1080/07391102.2022.2159876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 12/12/2022] [Indexed: 12/27/2022]
Abstract
Tuberculosis (TB) disease continues to remain one of the global threats for mankind. Till date many antibacterial compounds have been identified to target mycobacterium tuberculosis (MTB). However, the mutating nature of the mycobacteria has always posed a challenge for designing newer drugs which can target both the non-mutating and mutating forms of TB. In this process, Mycobacterial membrane protein Large 3 (MmpL3) transporter was identified as one of the key targets for inhibiting tuberculosis. Herein we have made an effort to find potential inhibitors against MmpL3 by using a pharmacophore-based virtual screening workflow, followed by molecular docking studies and molecular dynamic simulations. Based on a set of 220 compounds showing anti-tubercular activity proposed to target MmpL3 transporter with MIC values ranging from 0.003 to 737 μM, a 5-point pharmacophore ADHHR_2 model possessing one hydrogen acceptor, one hydrogen donor, two hydrophobic groups and an aromatic ring system was generated. The model validated by enrichment study was used to screen Asinex and DrugBank database to identify a potential lead compound such as DrugBank_6059 that was found to show better binding affinity (-11.36) and hydrophobic interactions with target protein in comparison to standard drug SQ109.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhijeet Dhulap
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Ghaziabad, Uttar Pradesh, India
- CSIR Unit for Research and Development of Information Products, Pune, Maharashtra, India
| | - Paromita Banerjee
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre, (CSIR-HRDC) Campus, Ghaziabad, Uttar Pradesh, India
- CSIR Unit for Research and Development of Information Products, Pune, Maharashtra, India
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Couston J, Guo Z, Wang K, Gourdon P, Blaise M. Cryo-EM structure of the trehalose monomycolate transporter, MmpL3, reconstituted into peptidiscs. Curr Res Struct Biol 2023; 6:100109. [PMID: 38034087 PMCID: PMC10682824 DOI: 10.1016/j.crstbi.2023.100109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Mycobacteria have an atypical thick and waxy cell wall. One of the major building blocks of such mycomembrane is trehalose monomycolate (TMM). TMM is a mycolic acid ester of trehalose that possesses long acyl chains with up to 90 carbon atoms. TMM represents an essential component of mycobacteria and is synthesized in the cytoplasm, and then flipped over the plasma membrane by a specific transporter known as MmpL3. Over the last decade, MmpL3 has emerged as an attractive drug target to combat mycobacterial infections. Recent three-dimensional structures of MmpL3 determined by X-ray crystallography and cryo-EM have increased our understanding of the TMM transport, and the mode of action of inhibiting compounds. These structures were obtained in the presence of detergent and/or in a lipidic environment. In this study, we demonstrate the possibility of obtaining a high-quality cryo-EM structure of MmpL3 without any presence of detergent through the reconstitution of the protein into peptidiscs. The structure was determined at an overall resolution of 3.2 Å and demonstrates that the overall structure of MmpL3 is preserved as compared to previous structures. Further, the study identified a new structural arrangement of the linker that fuses the two subdomains of the transmembrane domain, suggesting the feature may serve a role in the transport process.
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Affiliation(s)
- Julie Couston
- IRIM, CNRS, University of Montpellier, Montpellier, France
| | - Zongxin Guo
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen N, Denmark
| | - Kaituo Wang
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen N, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen N, Denmark
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, SE-22100, Lund, Sweden
| | - Mickaël Blaise
- IRIM, CNRS, University of Montpellier, Montpellier, France
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Sahoo SK, Ommi O, Maddipatla S, Singh P, Ahmad MN, Kaul G, Nanduri S, Dasgupta A, Chopra S, Yaddanapudi VM. Isoxazole carboxylic acid methyl ester-based urea and thiourea derivatives as promising antitubercular agents. Mol Divers 2023; 27:2037-2052. [PMID: 36282413 PMCID: PMC9592870 DOI: 10.1007/s11030-022-10543-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 11/01/2022]
Abstract
In our continued efforts to find potential chemotherapeutics active against drug-resistant (DR) Mycobacterium tuberculosis (Mtb), causative agent of Tuberculosis (TB) and to curb the current burdensome treatment regimen, herein we describe the synthesis and biological evaluation of urea and thiourea variants of 5-phenyl-3-isoxazolecarboxylic acid methyl esters as promising anti-TB agent. Majority of the tested compounds displayed potent in vitro activity not only against drug-susceptible (DS) Mtb H37Rv but also against drug-resistant (DR) Mtb. Cell viability test against Vero cells deemed these compounds devoid of significant toxicity. 3,4-Dichlorophenyl derivative (MIC 0.25 µg/mL) and 4-chlorophenyl congener (MIC 1 µg/mL) among urea and thiourea libraries respectively exhibited optimum potency. Lead optimization resulted in the identification of 1,4-linked analogue of 3,4-dichlorophenyl urea derivative demonstrating improved selectivity. Further, in silico study complemented with previously proposed prodrug like attributes of isoxazole esters. Taken together, this molecular hybridization approach presents a new chemotype having potential to be translated into an alternate anti-Mtb agent.
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Affiliation(s)
- Santosh Kumar Sahoo
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Ojaswitha Ommi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Sarvan Maddipatla
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Priti Singh
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Mohammad Naiyaz Ahmad
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Srinivas Nanduri
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India
| | - Arunava Dasgupta
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.
- AcSIR: Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana, 500037, India.
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Wen Y, Lun S, Jiao Y, Zhang W, Liu T, Yang F, Tang J, Bishai WR, Yu LF. Structure-directed identification of pyridine-2-methylamine derivatives as MmpL3 inhibitors for use as antitubercular agents. Eur J Med Chem 2023; 255:115351. [PMID: 37116266 PMCID: PMC10239758 DOI: 10.1016/j.ejmech.2023.115351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
Mycobacterial membrane protein Large 3 (MmpL3), an inner membrane protein, plays a crucial role in the transport of mycolic acids that are essential for the viability of M. tuberculosis and has been a promising therapeutic target for new anti-TB agents. Herein, we report the discovery of pyridine-2-methylamine antitubercular compounds using a structure-based drug design strategy. Compound 62 stands out as the most potent compound with high activity against M. tb strain H37Rv (MIC = 0.016 μg/mL) as well as the clinically isolated strains of MDR/XDR-TB (MIC = 0.0039-0.0625 μg/mL), low Vero cell toxicity (IC50 ≥ 16 μg/mL), and moderate liver microsomal stability (CLint = 28 μL/min/mg). Furthermore, the resistant mutant of S288T due to single nucleotide polymorphism in mmpL3 was resistant to pyridine-2-methylamine 62, demonstrating compound 62 is likely target to MmpL3.
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Affiliation(s)
- Yu Wen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD, 21231-1044, United States
| | - Yuxue Jiao
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Wei Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Ting Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Fan Yang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Jie Tang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - William R Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD, 21231-1044, United States.
| | - Li-Fang Yu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.
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Alcaraz M, Edwards TE, Kremer L. New therapeutic strategies for Mycobacterium abscessus pulmonary diseases - untapping the mycolic acid pathway. Expert Rev Anti Infect Ther 2023; 21:813-829. [PMID: 37314394 PMCID: PMC10529309 DOI: 10.1080/14787210.2023.2224563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Treatment options against Mycobacterium abscessus infections are very limited. New compounds are needed to cure M. abscessus pulmonary diseases. While the mycolic acid biosynthetic pathway has been largely exploited for the treatment of tuberculosis, this metabolic process has been overlooked in M. abscessus, although it offers many potential drug targets for the treatment of this opportunistic pathogen. AREAS COVERED Herein, the authors review the role of the MmpL3 membrane protein and the enoyl-ACP reductase InhA involved in the transport and synthesis of mycolic acids, respectively. They discuss their importance as two major vulnerable drug targets in M. abscessus and report the activity of MmpL3 and InhA inhibitors. In particular, they focus on NITD-916, a direct InhA inhibitor against M. abscessus, particularly warranted in the context of multidrug resistance. EXPERT OPINION There is an increasing body of evidence validating the mycolic acid pathway as an attractive drug target to be further exploited for M. abscessus lung disease treatments. The NITD-916 studies provide a proof-of-concept that direct inhibitors of InhA are efficient in vitro, in macrophages and in zebrafish. Future work is now required to improve the activity and pharmacological properties of these inhibitors and their evaluation in pre-clinical models.
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Affiliation(s)
- Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Thomas E. Edwards
- UCB BioSciences, Bainbridge Island, WA 98109 USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109 USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
- INSERM, IRIM, 34293 Montpellier, France
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North EJ, Schwartz CP, Zgurskaya HI, Jackson M. Recent advances in mycobacterial membrane protein Large 3 inhibitor drug design for mycobacterial infections. Expert Opin Drug Discov 2023. [PMID: 37226498 DOI: 10.1080/17460441.2023.2218082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
INTRODUCTION Tuberculosis and nontuberculous mycobacterial infections are notoriously difficult to treat, requiring long-courses of intensive multi-drug therapies associated with adverse side effects. To identify better therapeutics, whole cell screens have identified novel pharmacophores, a surprisingly high number of which target an essential lipid transporter known as MmpL3. AREAS COVERED This paper summarizes what is known about MmpL3, its mechanism of lipid transport and therapeutic potential, and provides an overview of the different classes of MmpL3 inhibitors currently under development. It further describes the assays available to study MmpL3 inhibition by these compounds. EXPERT OPINION MmpL3 has emerged as a target of high therapeutic value. Accordingly, several classes of MmpL3 inhibitors are currently under development with one drug candidate (SQ109) having undergone a Phase 2b clinical study. The hydrophobic character of most MmpL3 series identified to date seem to drive antimycobacterial potency resulting in poor bioavailability, which is a significant impediment to their development. There is also a need for more high-throughput and informative assays to elucidate the precise mechanism of action of MmpL3 inhibitors and drive the rational optimization of analogues.
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Affiliation(s)
- E Jeffrey North
- Department of Pharmacy Sciences, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Chris P Schwartz
- Department of Pharmacy Sciences, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Kapp E, Calitz H, Streicher EM, Dippenaar A, Egieyeh S, Jordaan A, Warner DF, Joubert J, Malan SF, Sampson SL. Discovery and biological evaluation of an adamantyl-amide derivative with likely MmpL3 inhibitory activity. Tuberculosis (Edinb) 2023; 141:102350. [PMID: 37244249 DOI: 10.1016/j.tube.2023.102350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/29/2023]
Abstract
A series of molecules containing bulky lipophilic scaffolds was screened for activity against Mycobacterium tuberculosis and a number of compounds with antimycobacterial activity were identified. The most active compound, (2E)-N-(adamantan-1-yl)-3-phenylprop-2-enamide (C1), has a low micromolar minimum inhibitory concentration, low cytotoxicity (therapeutic index = 32.26), low mutation frequency and is active against intracellular Mycobacterium tuberculosis. Whole genome sequencing of mutants resistant to C1 showed a mutation in mmpL3 which may point to the involvement of MmpL3 in the antimycobacterial activity of the compound. In silico mutagenesis and molecular modelling studies were performed to better understand the binding of C1 within MmpL3 and the role that the specific mutation may play in the interaction at protein level. These analyses revealed that the mutation increases the energy required for binding of C1 within the protein translocation channel of MmpL3. The mutation also decreases the solvation energy of the protein, suggesting that the mutant protein might be more solvent-accessible, thereby restricting its interaction with other molecules. The results reported here describe a new molecule that may interact with the MmpL3 protein, providing insights into the effect of mutations on protein-ligand interactions and enhancing our understanding of this essential protein as a priority drug target.
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Affiliation(s)
- Erika Kapp
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Hanri Calitz
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
| | - Elizabeth M Streicher
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
| | - Anzaan Dippenaar
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa; Global Health Institute, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Gouverneur Kinsbergencentrum, Doornstraat 331, 2610, Wilrijk, Belgium.
| | - Samuel Egieyeh
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Audrey Jordaan
- Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa.
| | - Digby F Warner
- Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa.
| | - Jacques Joubert
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Sarel F Malan
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Samantha L Sampson
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town, 8000, South Africa.
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11
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Stampolaki M, Stylianakis I, Zgurskaya HI, Kolocouris A. Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations. J Comput Aided Mol Des 2023; 37:245-264. [PMID: 37129848 DOI: 10.1007/s10822-023-00504-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
N-geranyl-N΄-(2-adamantyl)ethane-1,2-diamine (SQ109) is a tuberculosis drug that has high potency against Mycobacterium tuberculosis (Mtb) and may function by blocking cell wall biosynthesis. After the crystal structure of MmpL3 from Mycobacterium smegmatis in complex with SQ109 became available, it was suggested that SQ109 inhibits Mmpl3 mycolic acid transporter. Here, we showed using molecular dynamics (MD) simulations that the binding profile of nine SQ109 analogs with inhibitory potency against Mtb and alkyl or aryl adducts at C-2 or C-1 adamantyl carbon to MmpL3 was consistent with the X-ray structure of MmpL3 - SQ109 complex. We showed that rotation of SQ109 around carbon-carbon bond in the monoprotonated ethylenediamine unit favors two gauche conformations as minima in water and lipophilic solvent using DFT calculations as well as inside the transporter's binding area using MD simulations. The binding assays in micelles suggested that the binding affinity of the SQ109 analogs was increased for the larger, more hydrophobic adducts, which was consistent with our results from MD simulations of the SQ109 analogues suggesting that sizeable C-2 adamantyl adducts of SQ109 can fill a lipophilic region between Y257, Y646, F260 and F649 in MmpL3. This was confirmed quantitatively by our calculations of the relative binding free energies using the thermodynamic integration coupled with MD simulations method with a mean assigned error of 0.74 kcal mol-1 compared to the experimental values.
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Affiliation(s)
- Marianna Stampolaki
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Ioannis Stylianakis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Norman, OK, 73019-5251, USA
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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12
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Kumar G, Kapoor S. Targeting mycobacterial membranes and membrane proteins: Progress and limitations. Bioorg Med Chem 2023; 81:117212. [PMID: 36804747 DOI: 10.1016/j.bmc.2023.117212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Among the various bacterial infections, tuberculosis continues to hold center stage. Its causative agent, Mycobacterium tuberculosis, possesses robust defense mechanisms against most front-line antibiotic drugs and host responses due to their complex cell membranes with unique lipid molecules. It is now well-established that bacteria change their membrane composition to optimize their environment to survive and elude drug action. Thus targeting membrane or membrane components is a promising avenue for exploiting the chemical space focussed on developing novel membrane-centric anti-bacterial small molecules. These approaches are more effective, non-toxic, and can attenuate resistance phenotype. We present the relevance of targeting the mycobacterial membrane as a practical therapeutic approach. The review highlights the direct and indirect targeting of membrane structure and function. Direct membrane targeting agents cause perturbation in the membrane potential and can cause leakage of the cytoplasmic contents. In contrast, indirect membrane targeting agents disrupt the function of membrane-associated proteins involved in cell wall biosynthesis or energy production. We discuss the chronological chemical improvements in various scaffolds targeting specific membrane-associated protein targets, their clinical evaluation, and up-to-date account of their ''mechanisms of action, potency, selectivity'' and limitations. The sources of anti-TB drugs/inhibitors discussed in this work have emerged from target-based identification, cell-based phenotypic screening, drug repurposing, and natural products. We believe this review will inspire the exploration of uncharted chemical space for informing the development of new scaffolds that can inhibit novel mycobacterial membrane targets.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Departemnt of Natural Products, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad 500037, India.
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan.
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13
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Abstract
Mycobacteria species include a large number of pathogenic organisms such as Mycobacterium tuberculosis, Mycobacterium leprae, and various non-tuberculous mycobacteria. Mycobacterial membrane protein large 3 (MmpL3) is an essential mycolic acid and lipid transporter required for growth and cell viability. In the last decade, numerous studies have characterized MmpL3 with respect to protein function, localization, regulation, and substrate/inhibitor interactions. This review summarizes new findings in the field and seeks to assess future areas of research in our rapidly expanding understanding of MmpL3 as a drug target. An atlas of known MmpL3 mutations that provide resistance to inhibitors is presented, which maps amino acid substitutions to specific structural domains of MmpL3. In addition, chemical features of distinct classes of Mmpl3 inhibitors are compared to provide insights into shared and unique features of varied MmpL3 inhibitors.
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Affiliation(s)
- John T Williams
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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14
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Chaitra R, Gandhi R, Jayanna N, Satyanath S, Pavadai P, Murahari M. Computational design of MmpL3 inhibitors for tuberculosis therapy. Mol Divers 2023; 27:357-69. [PMID: 35477825 DOI: 10.1007/s11030-022-10436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
Tuberculosis is a chronic communicable disease caused by Mycobacterium tuberculosis (Mtb) and spreads from lungs to lymphatic system. The cell wall of mycobacterium plays a prominent role in maintaining the virulence and pathogenicity and also acts as prime target for drug discovery. Hence, this study has put into emphasis with target MmpLs (Mycobacterial membrane proteins Large) which are significant for the growth and survival of Mycobacterium tuberculosis. MmpLs belongs to the resistance, nodulation and division (RND) protein superfamily. MmpL3 is the only MmpL deemed essential for the replication and viability of mycobacterial cells. For the study, we have selected SQ109 derivatives as Mmpl3 inhibitor, which holds non-covalent property. Structure-based pharmacophore model of MmpL3 target protein with SQ109 as co-crystallized ligand (PDB: 6AJG) was generated to screen the ligand database. Compounds with decent fitness score and pharmacophoric features were compared with standard drug and taken for molecular docking studies. Further prime molecular mechanics-Poisson-Boltzmann surface area (MM-GBSA) and induced fit calculations identified potential molecules for further drug-likeness screening. Overall computational calculations identified ZINC000000016638 and ZINC000000003594 as potential in silico MmpL3 inhibitors. Molecular dynamics simulations integrated with MM-PBSA free energy calculations identified that MmpL3-ZINC000000016638 complex was more stable. Study can be further extended for synthesis and biological evaluation, derivatization of active compound to identify potential and safe lead compounds for effective tuberculosis therapy.
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15
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Ochsner UA, De Groote MA, Jarvis TC, Liu H, Youmans T, Hoang T, Ribble W, Day J, Li W, Pearce C, Walz A, Panthi CM, Rimal B, Stevens CM, Zgurskaya HI, Jackson M, Ordway D, Gonzalez-Juarrero M, Sun X, Lamichhane G, Mason C. Microbiological profile, preclinical pharmacokinetics and efficacy of CRS0393, a novel antimycobacterial agent targeting MmpL3. Tuberculosis (Edinb) 2023; 138:102288. [PMID: 36470124 PMCID: PMC9892229 DOI: 10.1016/j.tube.2022.102288] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022]
Abstract
The benzothiazole amide CRS0393 demonstrated excellent in vitro activity against nontuberculous mycobacteria (NTM), including M. abscessus isolates from cystic fibrosis (CF) patients, with minimum inhibitory concentrations (MICs) of ≤0.03-0.5 μg/mL. The essential transport protein MmpL3 was confirmed as the target via analysis of spontaneous resistant mutants and further biological profiling. In mouse pharmacokinetic studies, intratracheal instillation of a single dose of CRS0393 resulted in high concentrations of drug in epithelial lining fluid (ELF) and lung tissue, which remained above the M. abscessus MIC for at least 9 hours post-dose. This exposure resulted in a penetration ratio of 261 for ELF and 54 for lung tissue relative to plasma. CRS0393 showed good oral bioavailability, particularly when formulated in kolliphor oil, with a lung-to-plasma penetration ratio ranging from 0.5 to 4. CRS0393 demonstrated concentration-dependent reduction of intracellular M. abscessus in a THP-1 macrophage infection model. CRS0393 was well tolerated following intranasal administration (8 mg/kg) or oral dosing (25 mg/kg) once daily for 28 days in dexamethasone-treated C3HeB/FeJ mice. Efficacy against M. abscessus strain 103 was achieved via the intranasal route, while oral dosing will need further optimization. CRS0393 holds promise for development as a novel agent with broad antimycobacterial activity.
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Affiliation(s)
| | | | | | - Hang Liu
- Crestone, Inc., 6075 Longbow Dr, Boulder, CO, USA
| | | | - Teresa Hoang
- Crestone, Inc., 6075 Longbow Dr, Boulder, CO, USA
| | - Wendy Ribble
- Crestone, Inc., 6075 Longbow Dr, Boulder, CO, USA
| | - Joshua Day
- Crestone, Inc., 6075 Longbow Dr, Boulder, CO, USA
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, 200 West Lake Street, Colorado State University, Fort Collins, CO, USA
| | - Camron Pearce
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, 200 West Lake Street, Colorado State University, Fort Collins, CO, USA
| | - Amanda Walz
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, 200 West Lake Street, Colorado State University, Fort Collins, CO, USA
| | - Chandra M Panthi
- Johns Hopkins University, 1550 Orleans Street, Baltimore, MD, USA
| | - Binayak Rimal
- Johns Hopkins University, 1550 Orleans Street, Baltimore, MD, USA
| | - Casey M Stevens
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK, USA
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, 200 West Lake Street, Colorado State University, Fort Collins, CO, USA
| | - Diane Ordway
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, 200 West Lake Street, Colorado State University, Fort Collins, CO, USA
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, 200 West Lake Street, Colorado State University, Fort Collins, CO, USA
| | - Xicheng Sun
- Crestone, Inc., 6075 Longbow Dr, Boulder, CO, USA
| | - Gyanu Lamichhane
- Johns Hopkins University, 1550 Orleans Street, Baltimore, MD, USA
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16
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Briffotaux J, Xu Y, Huang W, Hui Z, Wang X, Gicquel B, Liu S. A Hydrazine-Hydrazone Adamantine Compound Shows Antimycobacterial Activity and Is a Probable Inhibitor of MmpL3. Molecules 2022; 27:7130. [PMID: 36296721 DOI: 10.3390/molecules27207130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/03/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
Tuberculosis remains an important cause of morbidity and mortality throughout the world. Notably, an important number of multi drug resistant cases is an increasing concern. This problem points to an urgent need for novel compounds with antimycobacterial properties and to improve existing therapies. Whole-cell-based screening for compounds with activity against Mycobacterium tuberculosis complex strains in the presence of linezolid was performed in this study. A set of 15 bioactive compounds with antimycobacterial activity in vitro were identified with a minimal inhibitory concentration of less than 2 µg/mL. Among them, compound 1 is a small molecule with a chemical structure consisting of an adamantane moiety and a hydrazide–hydrazone moiety. Whole genome sequencing of spontaneous mutants resistant to the compounds suggested compound 1 to be a new inhibitor of MmpL3. This compound binds to the same pocket as other already published MmpL3 inhibitors, without disturbing the proton motive force of M. bovis BCG and M. smegmatis. Compound 1 showed a strong activity against a panel ofclinical strains of M. tuberculosis in vitro. This compound showed no toxicity against mammalian cells and protected Galleria mellonella larvae against M. bovis BCG infection. These results suggest that compound 1 is a promising anti-TB agent with the potential to improve TB treatment in combination with standard TB therapies.
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17
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Hu T, Yang X, Liu F, Sun S, Xiong Z, Liang J, Yang X, Wang H, Yang X, Guddat LW, Yang H, Rao Z, Zhang B. Structure-based design of anti-mycobacterial drug leads that target the mycolic acid transporter MmpL3. Structure 2022; 30:1395-1402.e4. [PMID: 35981536 DOI: 10.1016/j.str.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
New anti-tubercular agents are urgently needed to address the emerging threat of drug resistance to human tuberculosis. Here, we have used structure-assisted methods to develop compounds that target mycobacterial membrane protein large 3 (MmpL3). MmpL3 is essential for the transport of mycolic acids, an important cell-wall component of mycobacteria. We prepared compounds that potently inhibit the growth of Mycobacterium tuberculosis (Mtb) and other mycobacteria in cell culture. The cryoelectron microscopy (cryo-EM) structure of mycobacterial MmpL3 in complex with one of these compounds (ST004) was determined using lipid nanodiscs at an overall resolution of 3.36 Å. The structure reveals the binding mode of ST004 to MmpL3, with the S4 and S5 subsites of the inhibitor-binding pocket in the proton translocation channel playing vital roles. These data are a promising starting point for the development of anti-tuberculosis drugs that target MmpL3.
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Affiliation(s)
- Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolin Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Shan Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhiqi Xiong
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Xiaobao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201210, China.
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18
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Ray R, Das S, Lobo M, Birangal SR, Shenoy GG. A holistic molecular modelling approach to design novel indole-2-carboxamide derivatives as potential inhibitors of MmpL3. SAR QSAR Environ Res 2022; 33:551-581. [PMID: 35850557 DOI: 10.1080/1062936x.2022.2096691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Tuberculosis is an infectious air-borne disease and one of the leading causes of death globally among all infectious diseases. There is an urgent need to develop antitubercular drugs that would be highly efficient and less toxic than the presently available marketed drugs. Mycobacterium membrane protein large 3 (MmpL3) is an emerging drug target in tuberculosis with various classes of molecules that have been known to inhibit it. In this study, a dataset of indole-2-carboxamides showing antitubercular activity by inhibiting MmpL3 was utilized. Initially, a chimera-based homology model was developed and docking was performed with the filtered dataset to analyse the interactions. Thereafter, molecular dynamics simulations were run with representative molecules to gain a better insight on the binding patterns. To attain a more quantitative correlation, an atom-based 3D QSAR model was developed which complemented the results from the previous models. A library of novel indole-2-carboxamides was then generated using core hopping-based ligand enumeration and upon screening on our workflow model it predicted three molecules as potent antitubercular compounds. This work not only helps to gain new insights on the interactions at the MmpL3 binding site but also provides novel indole-2-carboxamides having the potential to become antitubercular drugs in future.
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Affiliation(s)
- R Ray
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - M Lobo
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S R Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - G G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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19
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Moorey AR, Cabanillas A, Batt SM, Ghidelli-Disse S, Urones B, Sanz O, Lelievre J, Bantscheff M, Cox LR, Besra GS. The multi-target aspect of an MmpL3 inhibitor: The BM212 series of compounds bind EthR2, a transcriptional regulator of ethionamide activation. Cell Surf 2021; 7:100068. [PMID: 34888432 PMCID: PMC8634040 DOI: 10.1016/j.tcsw.2021.100068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) ensures that drug discovery efforts remain at the forefront of TB research. There are multiple different experimental approaches that can be employed in the discovery of anti-TB agents. Notably, inhibitors of MmpL3 are numerous and structurally diverse in Mtb and have been discovered through the generation of spontaneous resistant mutants and subsequent whole genome sequencing studies. However, this approach is not always reliable and can lead to incorrect target assignment and requires orthogonal confirmatory approaches. In fact, many of these inhibitors have also been shown to act as multi-target agents, with secondary targets in Mtb, as well as in other non-MmpL3-containing pathogens. Herein, we have investigated further the cellular targets of the MmpL3-inhibitor BM212 and a number of BM212 analogues. To determine the alternative targets of BM212, which may have been masked by MmpL3 mutations, we have applied a combination of chemo-proteomic profiling using bead-immobilised BM212 derivatives and protein extracts, along with whole-cell and biochemical assays. The study identified EthR2 (Rv0078) as a protein that binds BM212 analogues. We further demonstrated binding of BM212 to EthR2 through an in vitro tryptophan fluorescence assay, which showed significant quenching of tryptophan fluorescence upon addition of BM212. Our studies have demonstrated the value of revisiting drugs with ambiguous targets, such as MmpL3, in an attempt to find alternative targets and the study of off-target effects to understand more precisely target engagement of new hits emerging from drug screening campaigns.
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Affiliation(s)
- Alice R Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Alejandro Cabanillas
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - Beatriz Urones
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Olalla Sanz
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Marcus Bantscheff
- Cellzome - a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Liam R Cox
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
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20
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Ung KL, Alsarraf H, Kremer L, Blaise M. MmpL3, the trehalose monomycolate transporter, is stable in solution in several detergents and can be reconstituted into peptidiscs. Protein Expr Purif 2021; 191:106014. [PMID: 34767949 DOI: 10.1016/j.pep.2021.106014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/04/2021] [Accepted: 11/07/2021] [Indexed: 11/24/2022]
Abstract
Mycobacteria possess a complex and waxy cell wall comprising a large panel of glycolipids. Among these, trehalose monomycolate (TMM) represents abundant and crucial components for the elaboration of the mycomembrane. TMM is synthesized in the cytoplasmic compartment and translocated across the inner membrane by the MmpL3 transporter. Inhibitors impeding TMM transport by targeting MmpL3 show great promises as new antimycobacterials. The recent X-ray or Cryo-EM structures of MmpL3 complexed to TMM or its inhibitors have shed light on the mechanisms of TMM transport and inhibition. So far, purification procedures mainly involved the use of n-Dodecyl-ß-d-Maltopyranoside to solubilize and stabilize MmpL3 from Mycobacterium smegmatis (MmpL3Msm) or Lauryl Maltose Neopentyl Glycol for MmpL3 from Mycobacterium tuberculosis. Herein, we explored the possibility to solubilize and stabilize MmpL3 with other detergents. We demonstrate that several surfactants from the ionic, non-ionic and zwitterionic classes are prone to solubilize MmpL3Msm expressed in Escherichia coli. The capacity of these detergents to stabilize MmpL3Msm was evaluated by size-exclusion chromatography and thermal stability. This study unraveled three new detergents DM, LDAO and sodium cholate that favor solubilization and stabilization of MmpL3Msm in solution. In addition, we report a protocol that allows reconstitution of MmpL3Msm into peptidiscs.
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Affiliation(s)
- Kien Lam Ung
- Université de Montpellier, IRIM, CNRS, Montpellier, France
| | - Husam Alsarraf
- Université de Montpellier, IRIM, CNRS, Montpellier, France; Department of Molecular Biology and Genetics, University of Aarhus, 8000, Aarhus, Denmark
| | - Laurent Kremer
- Université de Montpellier, IRIM, CNRS, Montpellier, France; INSERM, IRIM, Montpellier, France
| | - Mickaël Blaise
- Université de Montpellier, IRIM, CNRS, Montpellier, France.
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21
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Malwal SR, Oldfield E. Mycobacterial membrane protein Large 3-like-family proteins in bacteria, protozoa, fungi, plants, and animals: A bioinformatics and structural investigation. Proteins 2021; 90:776-790. [PMID: 34739144 DOI: 10.1002/prot.26273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 01/20/2023]
Abstract
Lipid transporters play an important role in most if not all organisms, ranging from bacteria to humans. For example, in Mycobacterium tuberculosis, the trehalose monomycolate transporter MmpL3 is involved in cell wall biosynthesis, while in humans, cholesterol transporters are involved in normal cell function as well as in disease. Here, using structural and bioinformatics information, we propose that there are proteins that also contain "MmpL3-like" (MMPL) transmembrane (TM) domains in many protozoa, including Trypanosoma cruzi, as well as in the bacterium Staphylococcus aureus, where the fatty acid transporter FarE has the same set of "active-site" residues as those found in the mycobacterial MmpL3s, and in T. cruzi. We also show that there are strong sequence and predicted structural similarities between the TM proton-translocation domain seen in the X-ray structures of mycobacterial MmpL3s and several human as well as fungal lipid transporters, leading to the proposal that there are similar proteins in apicomplexan parasites, and in plants. The animal, fungal, apicomplexan, and plant proteins have larger extra-membrane domains than are found in the bacterial MmpL3, but they have a similar TM domain architecture, with the introduction of a (catalytically essential) Phe > His residue change, and a Ser/Thr H-bond network, involved in H+ -transport. Overall, the results are of interest since they show that MMPL-family proteins are present in essentially all life forms: archaea, bacteria, protozoa, fungi, plants and animals and, where known, they are involved in "lipid" (glycolipid, phospholipid, sphingolipid, fatty acid, cholesterol, ergosterol) transport, powered by transmembrane molecular pumps having similar structures.
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Affiliation(s)
- Satish R Malwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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22
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Adams O, Deme JC, Parker JL, Fowler PW, Lea SM, Newstead S. Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target. Structure 2021; 29:1182-1191.e4. [PMID: 34242558 PMCID: PMC8752444 DOI: 10.1016/j.str.2021.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 11/09/2022]
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent and in 2019 an estimated 10 million people worldwide contracted the disease. Although treatments for TB exist, continual emergence of drug-resistant variants necessitates urgent development of novel antituberculars. An important new target is the lipid transporter MmpL3, which is required for construction of the unique cell envelope that shields Mycobacterium tuberculosis (Mtb) from the immune system. However, a structural understanding of the mutations in Mtb MmpL3 that confer resistance to the many preclinical leads is lacking, hampering efforts to circumvent resistance mechanisms. Here, we present the cryoelectron microscopy structure of Mtb MmpL3 and use it to comprehensively analyze the mutational landscape of drug resistance. Our data provide a rational explanation for resistance variants local to the central drug binding site, and also highlight a potential alternative route to resistance operating within the periplasmic domain.
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Affiliation(s)
- Oliver Adams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Justin C Deme
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford OX1 3RE, UK; Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK; National Institute of Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe, Oxford OX3 9DU, UK
| | - Susan M Lea
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford OX1 3RE, UK; Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK.
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Malwal SR, Zimmerman MD, Alvarez N, Sarathy JP, Dartois V, Nacy CA, Oldfield E. Structure, In Vivo Detection, and Antibacterial Activity of Metabolites of SQ109, an Anti-Infective Drug Candidate. ACS Infect Dis 2021; 7:2492-2507. [PMID: 34279904 DOI: 10.1021/acsinfecdis.1c00259] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SQ109 is a drug candidate for the treatment of tuberculosis (TB). It is thought to target primarily the protein MmpL3 in Mycobacterium tuberculosis, but it also inhibits the growth of some other bacteria. SQ109 is metabolized by the liver, and it has been proposed that some of its metabolites might be responsible for its activity against TB. Here, we synthesized six potential P450 metabolites of SQ109 and used these as well as 10 other likely metabolites as standards in a mass spectrometry study of M. tuberculosis-infected rabbits treated with SQ109, in addition to testing all 16 putative metabolites for antibacterial activity. We found that there were just two major metabolites in lung tissue: a hydroxy-adamantyl analog of SQ109 and N'-adamantylethylenediamine. Neither of these, or the other potential metabolites tested, inhibited the growth of M. tuberculosis or of M. smegmatis, Bacillus subtilis, or E. coli, making it unlikely that an SQ109 metabolite contributes to its antibacterial activity. In the rabbit TB model, it is thus the gradual accumulation of nonmetabolized SQ109 in tissues to therapeutic levels that leads to good efficacy. Our results also provide new insights into how SQ109 binds to its target MmpL3, based on our mass spectroscopy results which indicate that the charge in SQ109 is primarily localized on the geranyl nitrogen, explaining the very short distance to a key Asp found in the X-ray structure of SQ109 bound to MmpL3.
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Affiliation(s)
- Satish R. Malwal
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Matthew D. Zimmerman
- Center for Discovery and Innovation, 111 Ideation Way, Nutley, New Jersey 07110, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, 111 Ideation Way, Nutley, New Jersey 07110, United States
| | - Jansy P. Sarathy
- Center for Discovery and Innovation, 111 Ideation Way, Nutley, New Jersey 07110, United States
| | - Véronique Dartois
- Center for Discovery and Innovation, 111 Ideation Way, Nutley, New Jersey 07110, United States
- Hackensack School of Medicine, Department of Medical Sciences, 123, Metro Boulevard, Nutley, New Jersey 07110, United States
| | - Carol A. Nacy
- Sequella, Inc., 9610 Medical Center Drive, Suite 200, Rockville, Maryland 20850, United States
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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24
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Degiacomi G, Chiarelli LR, Recchia D, Petricci E, Gianibbi B, Fiscarelli EV, Fattorini L, Manetti F, Pasca MR. The Antimalarial Mefloquine Shows Activity against Mycobacterium abscessus, Inhibiting Mycolic Acid Metabolism. Int J Mol Sci 2021; 22:8533. [PMID: 34445239 DOI: 10.3390/ijms22168533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/17/2022] Open
Abstract
Some nontuberculous mycobacteria (NTM) are considered opportunistic pathogens. Nevertheless, NTM infections are increasing worldwide, becoming a major public health threat. Furthermore, there is no current specific drugs to treat these infections, and the recommended regimens generally lack efficacy, emphasizing the need for novel antibacterial compounds. In this paper, we focused on the essential mycolic acids transporter MmpL3, which is a well-characterized target of several antimycobacterial agents, to identify new compounds active against Mycobacterium abscessus (Mab). From the crystal structure of MmpL3 in complex with known inhibitors, through an in silico approach, we developed a pharmacophore that was used as a three-dimensional filter to identify new putative MmpL3 ligands within databases of known drugs. Among the prioritized compounds, mefloquine showed appreciable activity against Mab (MIC = 16 μg/mL). The compound was confirmed to interfere with mycolic acids biosynthesis, and proved to also be active against other NTMs, including drug-resistant clinical isolates. Importantly, mefloquine is a well-known antimalarial agent, opening the possibility of repurposing an already approved drug, which is a useful strategy to reduce the time and cost of disclosing novel drug candidates.
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Umare MD, Khedekar PB, Chikhale RV. Mycobacterial Membrane Protein Large 3 ( MmpL3) Inhibitors: A Promising Approach to Combat Tuberculosis. ChemMedChem 2021; 16:3136-3148. [PMID: 34288519 DOI: 10.1002/cmdc.202100359] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/17/2021] [Indexed: 11/08/2022]
Abstract
Tuberculosis is a prominent aliment throughout the world and a leading cause of mortality among infectious diseases. Drug development for multi-drug resistance and reducing the current therapy time is the top priority. Mycobacterial membrane protein large 3 (MmpL3) is a promising target with high potential, however, it has not been explored to its greatest potential. It is a membrane transporter that translocates trehalose-monomycolate which is a precursor for the synthesis of mycolic acid that is essential for the synthesis of the bacterial cell wall and is pathogenic in nature. In this review, we have discussed the current development of MmpL3 inhibitors, different scaffolds, their derivatives, and their synthetic schemes and provide insight into the challenges in developing these inhibitors.
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Affiliation(s)
- Mohit D Umare
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, 440033, MS, India
| | - Pramod B Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, 440033, MS, India
| | - Rupesh V Chikhale
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1 N 1AX, UK
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26
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Luo Q, Duan H, Yan H, Liu X, Peng L, Hu Y, Liu W, Liang L, Shi H, Zhao G, Hu J. Specifically targeting Mtb cell-wall and TMM transporter: the development of MmpL3 inhibitors. Curr Protein Pept Sci 2021; 22:290-303. [PMID: 33882806 DOI: 10.2174/1389203722666210421105733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
Tuberculosis (TB) remains a serious threat to whole human health. In particular, the drug resistance of Mycobacterium tuberculosis (Mtb) has become a huge challenge in clinical medicine, and it is extremely urgent to develop effective inhibitors with novel structures and mechanisms. Belonging to the Resistance, Nodulation and Division (RND) superfamily, Mycobacterial membrane proteins Large 3 (MmpL3) is mainly responsible for transporting mycolic acid outside cell membrane to form cell wall, and plays critical roles in iron acquisition which is vital to the survival of Mtb. As a potential Mtb target in recent years, its inhibitor research has attracted wide attention. A series of inhibitors (such as SQ109, AU1235, BM212, etc.) through experimental screening have been reported in succession, especially SQ109 has entered the clinical stage. In this paper, the structural biology information of target MmpL3 was summarized, and the structure-activity relationship (SAR) of inhibitors reported in recent years and their inhibitory mechanism both were reviewed, aiming to provide help for the rational design of MmpL3 inhibitors in the future.
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Affiliation(s)
- Qing Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Huaichuan Duan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Hailian Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Xinyu Liu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Yichen Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Wei Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Li Liang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
| | - Jianping Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610106, China
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27
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Alsayed SSR, Lun S, Payne A, Bishai WR, Gunosewoyo H. Design, synthesis and antimycobacterial evaluation of novel adamantane and adamantanol analogues effective against drug-resistant tuberculosis. Bioorg Chem 2020; 106:104486. [PMID: 33276981 DOI: 10.1016/j.bioorg.2020.104486] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022]
Abstract
The treacherous nature of tuberculosis (TB) combined with the ubiquitous presence of the drug-resistant (DR) forms pose this disease as a growing public health menace. Therefore, it is imperative to develop new chemotherapeutic agents with a novel mechanism of action to circumvent the cross-resistance problems. The unique architecture of the Mycobacterium tuberculosis (M. tb) outer envelope plays a predominant role in its pathogenesis, contributing to its intrinsic resistance against available therapeutic agents. The mycobacterial membrane protein large 3 (MmpL3), which is a key player in forging the M. tb rigid cell wall, represents an emerging target for TB drug development. Several indole-2-carboxamides were previously identified in our group as potent anti-TB agents that act as inhibitor of MmpL3 transporter protein. Despite their highly potent in vitro activities, the lingering Achilles heel of these indoleamides can be ascribed to their high lipophilicity as well as low water solubility. In this study, we report our attempt to improve the aqueous solubility of these indole-2-carboxamides while maintaining an adequate lipophilicity to allow effective M. tb cell wall penetration. A more polar adamantanol moiety was incorporated into the framework of several indole-2-carboxamides, whereupon the corresponding analogues were tested for their anti-TB activity against drug-sensitive (DS) M. tb H37Rv strain. Three adamantanol derivatives 8i, 8j and 8l showed nearly 2- and 4-fold higher activity (MIC = 1.32 - 2.89 µM) than ethambutol (MIC = 4.89 µM). Remarkably, the most potent adamantanol analogue 8j demonstrated high selectivity towards DS and DR M. tb strains over mammalian cells [IC50 (Vero cells) ≥ 169 µM], evincing its lack of cytotoxicity. The top eight active compounds 8b, 8d, 8f, 8i, 8j, 8k, 8l and 10a retained their in vitro potency against DR M. tb strains and were docked into the MmpL3 active site. The most potent adamantanol/adamantane-based indoleamides 8j/8k displayed a two-fold surge in potency against extensively DR (XDR) M. tb strains with MIC values of 0.66 and 0.012 µM, respectively. The adamantanol-containing indole-2-carboxamides exhibited improved water solubility both in silico and experimentally, relative to the adamantane counterparts. Overall, the observed antimycobacterial and physicochemical profiles support the notion that adamantanol moiety is a suitable replacement to the adamantane scaffold within the series of indole-2-carboxamide-based MmpL3 inhibitors.
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Affiliation(s)
- Shahinda S R Alsayed
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, 1550, Orleans Street, Baltimore, MD 21231-1044, United States
| | - Alan Payne
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - William R Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, 1550, Orleans Street, Baltimore, MD 21231-1044, United States; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815-6789, United States.
| | - Hendra Gunosewoyo
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
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28
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Li M, Nyantakyi SA, Go ML, Dick T. Resistance against Membrane-Inserting MmpL3 Inhibitor through Upregulation of MmpL5 in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 64:e01100-20. [PMID: 32958714 DOI: 10.1128/AAC.01100-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022] Open
Abstract
Spiroketal indolyl Mannich bases (SIMBs) present a novel class of membrane-inserting antimycobacterials with efficacy in a tuberculosis mouse model. SIMBs exert their antibacterial activity by two mechanisms. The indolyl Mannich base scaffold causes permeabilization of bacteria, and the spiroketal moiety contributes to inhibition of the mycolic acid transporter MmpL3. Here, we show that low-level resistance to SIMBs arises by mutations in the transcriptional repressor MmpR5, resulting in upregulation of the efflux pump MmpL5. Spiroketal indolyl Mannich bases (SIMBs) present a novel class of membrane-inserting antimycobacterials with efficacy in a tuberculosis mouse model. SIMBs exert their antibacterial activity by two mechanisms. The indolyl Mannich base scaffold causes permeabilization of bacteria, and the spiroketal moiety contributes to inhibition of the mycolic acid transporter MmpL3. Here, we show that low-level resistance to SIMBs arises by mutations in the transcriptional repressor MmpR5, resulting in upregulation of the efflux pump MmpL5.
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29
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Sethiya JP, Sowards MA, Jackson M, North EJ. MmpL3 Inhibition: A New Approach to Treat Nontuberculous Mycobacterial Infections. Int J Mol Sci 2020; 21:E6202. [PMID: 32867307 PMCID: PMC7503588 DOI: 10.3390/ijms21176202] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/11/2022] Open
Abstract
Outside of Mycobacterium tuberculosis and Mycobacterium leprae, nontuberculous mycobacteria (NTM) are environmental mycobacteria (>190 species) and are classified as slow- or rapid-growing mycobacteria. Infections caused by NTM show an increased incidence in immunocompromised patients and patients with underlying structural lung disease. The true global prevalence of NTM infections remains unknown because many countries do not require mandatory reporting of the infection. This is coupled with a challenging diagnosis and identification of the species. Current therapies for treatment of NTM infections require multidrug regimens for a minimum of 18 months and are associated with serious adverse reactions, infection relapse, and high reinfection rates, necessitating discovery of novel antimycobacterial agents. Robust drug discovery processes have discovered inhibitors targeting mycobacterial membrane protein large 3 (MmpL3), a protein responsible for translocating mycolic acids from the inner membrane to periplasm in the biosynthesis of the mycobacterial cell membrane. This review focuses on promising new chemical scaffolds that inhibit MmpL3 function and represent interesting and promising putative drug candidates for the treatment of NTM infections. Additionally, agents (FS-1, SMARt-420, C10) that promote reversion of drug resistance are also reviewed.
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Affiliation(s)
- Jigar P. Sethiya
- Department of Pharmacy Sciences, School of Pharmacy & Health Professions, Creighton University, Omaha, NE 68178, USA; (J.P.S.); (M.A.S.)
| | - Melanie A. Sowards
- Department of Pharmacy Sciences, School of Pharmacy & Health Professions, Creighton University, Omaha, NE 68178, USA; (J.P.S.); (M.A.S.)
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Elton Jeffrey North
- Department of Pharmacy Sciences, School of Pharmacy & Health Professions, Creighton University, Omaha, NE 68178, USA; (J.P.S.); (M.A.S.)
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30
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Li M, Phua ZY, Xi Y, Xu Z, Nyantakyi SA, Li W, Jackson M, Wong MW, Lam Y, Chng SS, Go ML, Dick T. Potency Increase of Spiroketal Analogs of Membrane Inserting Indolyl Mannich Base Antimycobacterials Is Due to Acquisition of MmpL3 Inhibition. ACS Infect Dis 2020; 6:1882-1893. [PMID: 32413266 PMCID: PMC7875313 DOI: 10.1021/acsinfecdis.0c00121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chemistry campaigns identified amphiphilic indolyl Mannich bases as novel membrane-permeabilizing antimycobacterials. Spiroketal analogs of this series showed increased potency, and the lead compound 1 displayed efficacy in a mouse model of tuberculosis. Yet the mechanism by which the spiroketal moiety accomplished the potency "jump" remained unknown. Consistent with its membrane-permeabilizing mechanism, no resistant mutants could be isolated against indolyl Mannich base 2 lacking the spiroketal moiety. In contrast, mutations resistant against spiroketal analog 1 were obtained in mycobacterial membrane protein large 3 (MmpL3), a proton motive force (PMF)-dependent mycolate transporter. Thus, we hypothesized that the potency jump observed for 1 may be due to MmpL3 inhibition acquired by the addition of the spiroketal moiety. Here we showed that 1 inhibited MmpL3 flippase activity without loss of the PMF, colocalized with MmpL3tb-GFP in intact organisms, and yielded a consistent docking pose within the "common inhibitor binding pocket" of MmpL3. The presence of the spiroketal motif in 1 ostensibly augmented its interaction with MmpL3, an outcome not observed in the nonspiroketal analog 2, which displayed no cross-resistance to mmpL3 mutants, dissipated the PMF, and docked poorly in the MmpL3 binding pocket. Surprisingly, 2 inhibited MmpL3 flippase activity, which may be an epiphenomenon arising from its wider membrane disruptive effects. Hence, we conclude that the potency increase associated with the spiroketal analog 1 is linked to the acquisition of a second mechanism, MmpL3 inhibition. In contrast, the nonspiroketal analog 2 acts pleiotropically, affecting several cell membrane-embedded targets, including MmpL3, through its membrane permeabilizing and depolarizing effects.
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Affiliation(s)
- Ming Li
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zheng Yen Phua
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Yu Xi
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Zhujun Xu
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Samuel A. Nyantakyi
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Ming Wah Wong
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Yulin Lam
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Shu Sin Chng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
- Singapore Centre for Environmental Life Science Engineering (SCELSE), National University of Singapore, Singapore
| | - Mei Lin Go
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
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Raynaud C, Daher W, Roquet-Banères F, Johansen MD, Stec J, Onajole OK, Ordway D, Kozikowski AP, Kremer L. Synergistic Interactions of Indole-2-Carboxamides and β-Lactam Antibiotics against Mycobacterium abscessus. Antimicrob Agents Chemother 2020; 64:e02548-19. [PMID: 32041716 DOI: 10.1128/AAC.02548-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/06/2020] [Indexed: 11/20/2022] Open
Abstract
New drugs or therapeutic combinations are urgently needed against Mycobacterium abscessus Previously, we demonstrated the potent activity of indole-2-carboxamides 6 and 12 against M. abscessus We show here that these compounds act synergistically with imipenem and cefoxitin in vitro and increase the bactericidal activity of the β-lactams against M. abscessus In addition, compound 12 also displays synergism with imipenem and cefoxitin within infected macrophages. The clinical potential of these new drug combinations requires further evaluation.
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32
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Raynaud C, Daher W, Johansen MD, Roquet-Banères F, Blaise M, Onajole OK, Kozikowski AP, Herrmann JL, Dziadek J, Gobis K, Kremer L. Active Benzimidazole Derivatives Targeting the MmpL3 Transporter in Mycobacterium abscessus. ACS Infect Dis 2020; 6:324-337. [PMID: 31860799 DOI: 10.1021/acsinfecdis.9b00389] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The prevalence of pulmonary infections due to nontuberculous mycobacteria such as Mycobacterium abscessus has been increasing and surpassing tuberculosis (TB) in some industrialized countries. Because of intrinsic resistance to most antibiotics that drastically limits conventional chemotherapeutic treatment options, new anti-M. abscessus therapeutics are urgently needed against this emerging pathogen. Extensive screening of a library of benzimidazole derivatives that were previously shown to be active against Mycobacterium tuberculosis led to the identification of a lead compound exhibiting very potent in vitro activity against a wide panel of M. abscessus clinical strains. Designated EJMCh-6, this compound, a 2-(2-cyclohexylethyl)-5,6-dimethyl-1H-benzo[d]imidazole), also exerted very strong activity against intramacrophage-residing M. abscessus. Moreover, the treatment of infected zebrafish embryos with EJMCh-6 was correlated with significantly increased embryo survival and a decrease in the bacterial burden as compared to those for untreated fish. Insights into the mechanism of action were inferred from the generation of spontaneous benzimidazole-resistant strains and the identification of a large set of missense mutations in MmpL3, the mycolic acid transporter in mycobacteria. Overexpression of the mutated mmpL3 alleles in a susceptible M. abscessus strain was associated with high resistance levels to EJMCh-6 and to other known MmpL3 inhibitors. Mapping the mutations conferring resistance on an MmpL3 three-dimensional homology model defined a potential EJMCh-6-binding cavity. These data emphasize a yet unexploited chemical structure class against M. abscessus with promising translational development for the treatment of M. abscessus lung diseases.
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Affiliation(s)
- Clément Raynaud
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Wassim Daher
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Matt D. Johansen
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Mickael Blaise
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Oluseye K. Onajole
- Department of Biological, Physical and Health Sciences, Roosevelt University, 425 S. Wabash Avenue, Chicago, Illinois 60605, United States
| | - Alan P. Kozikowski
- StarWise Therapeutics LLC, 2020 N. Lincoln Park West, Chicago, Illinois 60614, United States
| | - Jean-Louis Herrmann
- 2I, UVSQ, INSERM UMR1173, Université Paris-Saclay, 2 avenue de la Source de la Bièvre, 78180 Montigny-Le-Bretonneux, France
- APHP, GHU-Paris Saclay, Hôpital Raymond Poincaré, Garches, France
| | - Jaroslaw Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Lodowa 106, Łódź 93-232, Poland
| | - Katarzyna Gobis
- Department of Organic Chemistry, Medical University of Gdansk, 107 Gen. Hallera Avenue, 80-416 Gdansk, Poland
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
- INSERM, IRIM, 34293 Montpellier, France
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33
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Ung KL, Alsarraf HMAB, Kremer L, Blaise M. The crystal structure of the mycobacterial trehalose monomycolate transport factor A, TtfA, reveals an atypical fold. Proteins 2019; 88:809-815. [PMID: 31833106 DOI: 10.1002/prot.25863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022]
Abstract
Trehalose monomycolate (TMM) represents an essential element of the mycobacterial envelope. While synthesized in the cytoplasm, TMM is transported across the inner membrane by MmpL3 but, little is known regarding the MmpL3 partners involved in this process. Recently, the TMM transport factor A (TtfA) was found to form a complex with MmpL3 and to participate in TMM transport, although its biological role remains to be established. Herein, we report the crystal structure of the Mycobacterium smegmatis TtfA core domain. The phylogenetic distribution of TtfA homologues in non-mycolate containing bacteria suggests that TtfA may exert additional functions.
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Affiliation(s)
- Kien Lam Ung
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
| | - Husam M A B Alsarraf
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France.,Institut de Recherche en Infectiologie de Montpellier (IRIM), INSERM, Montpellier, France
| | - Mickaël Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, Montpellier, France
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Dal Molin M, Selchow P, Schäfle D, Tschumi A, Ryckmans T, Laage-Witt S, Sander P. Identification of novel scaffolds targeting Mycobacterium tuberculosis. J Mol Med (Berl) 2019; 97:1601-1613. [PMID: 31728550 DOI: 10.1007/s00109-019-01840-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/13/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Drug resistance in Mycobacterium tuberculosis is relentlessly progressing while only a handful of novel drug candidates are developed. Here we describe a GFP-based high-throughput screening of 386,496 diverse compounds to identify putative tuberculosis drug candidates. In an exploratory analysis of the model organism M. bovis BCG and M. smegmatis and the subsequent screening of the main library, we identified 6354 compounds with anti-mycobacterial activity. These hit compounds were predominantly selective for mycobacteria while dozens had activity in the low μM range. We tested toxicity against the human monocyte/macrophage cell line THP-1 and elaborated activity against M. tuberculosis growing in liquid broth, under unique conditions such as non-replicating persistence or inhibition of M. tuberculosis residing in macrophages. Finally, spontaneous compound-resistant M. tuberculosis mutants were selected and subsequently analyzed by whole genome sequencing. In addition to compounds targeting the well-described proteins Pks13 and MmpL3, we identified two novel scaffolds targeting the bifunctional guanosine pentaphosphate synthetase/ polyribonucleotide nucleotidyltransferase GpsI, or interacting with the aminopeptidase PepB, a probable pro-drug activator. KEY MESSAGES: A newly identified scaffold targets the bifunctional enzyme GpsI. The aminopeptidase PepB is interacting with a second novel scaffold. Phenotypic screenings regularly identify novel compounds targeting Pks13 and MmpL3.
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Affiliation(s)
- Michael Dal Molin
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland
| | - Petra Selchow
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland
| | - Daniel Schäfle
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland
| | - Andreas Tschumi
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland
| | - Thomas Ryckmans
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland
| | - Stephan Laage-Witt
- Roche Pharma Research and Early Development, Infectious Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070, Basel, Switzerland
| | - Peter Sander
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006, Zürich, Switzerland. .,Nationales Zentrum für Mykobakterien, 8006, Zürich, Switzerland.
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35
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Dupont C, Chen Y, Xu Z, Roquet-Banères F, Blaise M, Witt AK, Dubar F, Biot C, Guérardel Y, Maurer FP, Chng SS, Kremer L. A piperidinol-containing molecule is active against Mycobacterium tuberculosis by inhibiting the mycolic acid flippase activity of MmpL3. J Biol Chem 2019; 294:17512-17523. [PMID: 31562241 DOI: 10.1074/jbc.ra119.010135] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/25/2019] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a major human pathogen, and current treatment options to combat this disease are under threat because of the emergence of multidrug-resistant and extensively drug-resistant tuberculosis. High-throughput whole-cell screening of an extensive compound library has recently identified a piperidinol-containing molecule, PIPD1, as a potent lead compound against M. tuberculosis Herein, we show that PIPD1 and related analogs exert in vitro bactericidal activity against the M. tuberculosis strain mc26230 and also against a panel of multidrug-resistant and extensively drug-resistant clinical isolates of M. tuberculosis, suggesting that PIPD1's mode of action differs from those of most first- and second-line anti-tubercular drugs. Selection and DNA sequencing of PIPD1-resistant mycobacterial mutants revealed the presence of single-nucleotide polymorphisms in mmpL3, encoding an inner membrane-associated mycolic acid flippase in M. tuberculosis Results from functional assays with spheroplasts derived from a M. smegmatis strain lacking the endogenous mmpL3 gene but harboring the M. tuberculosis mmpL3 homolog indicated that PIPD1 inhibits the MmpL3-driven translocation of trehalose monomycolate across the inner membrane without altering the proton motive force. Using a predictive structural model of MmpL3 from M. tuberculosis, docking studies revealed a PIPD1-binding cavity recently found to accommodate different inhibitors in M. smegmatis MmpL3. In conclusion, our findings have uncovered bactericidal activity of a new chemical scaffold. Its anti-tubercular activity is mediated by direct inhibition of the flippase activity of MmpL3 rather than by inhibition of the inner membrane proton motive force, significantly advancing our understanding of MmpL3-targeted inhibition in mycobacteria.
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Affiliation(s)
- Christian Dupont
- Centre National de la Recherche Scientifique UMR9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
| | - Yushu Chen
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Zhujun Xu
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
| | - Mickaël Blaise
- Centre National de la Recherche Scientifique UMR9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France
| | - Anne-Kathrin Witt
- National Reference Center for Mycobacteria, Research Center Borstel-Leibniz Lung Center, D-23845 Borstel, Germany
| | - Faustine Dubar
- University of Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Christophe Biot
- University of Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Yann Guérardel
- University of Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Florian P Maurer
- National Reference Center for Mycobacteria, Research Center Borstel-Leibniz Lung Center, D-23845 Borstel, Germany
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore 117543
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 34293 Montpellier, France .,INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
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36
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Korycka-Machała M, Viljoen A, Pawełczyk J, Borówka P, Dziadek B, Gobis K, Brzostek A, Kawka M, Blaise M, Strapagiel D, Kremer L, Dziadek J. 1 H-Benzo[ d]Imidazole Derivatives Affect MmpL3 in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:e00441-19. [PMID: 31332069 DOI: 10.1128/AAC.00441-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022] Open
Abstract
1H-benzo[d]imidazole derivatives exhibit antitubercular activity in vitro at a nanomolar range of concentrations and are not toxic to human cells, but their mode of action remains unknown. Here, we showed that these compounds are active against intracellular Mycobacterium tuberculosis To identify their target, we selected drug-resistant M. tuberculosis mutants and then used whole-genome sequencing to unravel mutations in the essential mmpL3 gene, which encodes the integral membrane protein that catalyzes the export of trehalose monomycolate, a precursor of the mycobacterial outer membrane component trehalose dimycolate (TDM), as well as mycolic acids bound to arabinogalactan. The drug-resistant phenotype was also observed in the parental strain overexpressing the mmpL3 alleles carrying the mutations identified in the resistors. However, no cross-resistance was observed between 1H-benzo[d]imidazole derivatives and SQ109, another MmpL3 inhibitor, or other first-line antitubercular drugs. Metabolic labeling and quantitative thin-layer chromatography (TLC) analysis of radiolabeled lipids from M. tuberculosis cultures treated with the benzoimidazoles indicated an inhibition of trehalose dimycolate (TDM) synthesis, as well as reduced levels of mycolylated arabinogalactan, in agreement with the inhibition of MmpL3 activity. Overall, this study emphasizes the pronounced activity of 1H-benzo[d]imidazole derivatives in interfering with mycolic acid metabolism and their potential for therapeutic application in the fight against tuberculosis.
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37
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Li W, Stevens CM, Pandya AN, Darzynkiewicz Z, Bhattarai P, Tong W, Gonzalez-Juarrero M, North EJ, Zgurskaya HI, Jackson M. Direct Inhibition of MmpL3 by Novel Antitubercular Compounds. ACS Infect Dis 2019; 5:1001-1012. [PMID: 30882198 PMCID: PMC6580365 DOI: 10.1021/acsinfecdis.9b00048] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MmpL3, an essential transporter involved in the export of mycolic acids, is the proposed target of a number of antimycobacterial inhibitors under development. Whether MmpL3 serves as the direct target of these compounds, however, has been called into question after the discovery that some of them dissipated the proton motive force from which MmpL transporters derive their energy. Using a combination of in vitro and whole-cell-based approaches, we here provide evidence that five structurally distinct MmpL3 inhibitor series, three of which impact proton motive force in Mycobacterium tuberculosis, directly interact with MmpL3. Medium- to high-throughput assays based on these approaches were developed to facilitate the future screening and optimization of MmpL3 inhibitors. The promiscuity of MmpL3 as a drug target and the mechanisms through which missense mutations located in a transmembrane region of this transporter may confer cross-resistance to a variety of chemical scaffolds are discussed in light of the exquisite vulnerability of MmpL3, its apparent mechanisms of interaction with inhibitors, and evidence of conformational changes induced both by the inhibitors and one of the most commonly identified resistance mutations in MmpL3.
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Affiliation(s)
- Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Casey M. Stevens
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Amitkumar N. Pandya
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, United States
| | - Zbigniew Darzynkiewicz
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Pankaj Bhattarai
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, United States
| | - Weiwei Tong
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - E. Jeffrey North
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, Colorado 80523, United States
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Pandya AN, Prathipati PK, Hegde P, Li W, Graham KF, Mandal S, Drescher KM, Destache CJ, Ordway D, Jackson M, North EJ. Indole-2-Carboxamides Are Active against Mycobacterium abscessus in a Mouse Model of Acute Infection. Antimicrob Agents Chemother 2019; 63:e02245-18. [PMID: 30602519 DOI: 10.1128/AAC.02245-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/14/2018] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) pathogens particularly infect patients with structural lung disorders. We previously reported novel indole-2-carboxamides (ICs) that are active against a wide panel of NTM pathogens. This study discloses in vivo data for two lead molecules (compounds 5 and 25) that were advanced for efficacy studies in Mycobacterium abscessus-infected mouse models. Oral administration of the lead molecules showed a statistically significant reduction in the bacterial loads in lung and spleen of M. abscessus-infected mice.
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39
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Pal R, Hameed S, Fatima Z. Altered drug efflux under iron deprivation unveils abrogated MmpL3 driven mycolic acid transport and fluidity in mycobacteria. Biometals 2018; 32:49-63. [PMID: 30430296 DOI: 10.1007/s10534-018-0157-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is a global threat to human health hence better understanding of the MTB pathogenesis for improved therapeutics requires immediate attention. Emergence of drug-resistant strains has stimulated an urgent need for adopting new strategies that could be implemented to control TB. One of the contributing mechanisms by which MTB evades drug doses is overexpression of drug efflux pumps. Thus blocking or modulating the functionality of efflux pumps represents an attractive approach to combat drug resistance. Iron is a critical micronutrient required for MTB survival and not freely available inside the host. In this study, we demonstrated that iron deprivation impairs drug efflux pump activity and confers synergism for anti-TB drugs in presence of efflux pump inhibitors against MTB. Mechanistic insights revealed that iron deprivation inhibit resistance nodulation division superfamily transporter activity. This was evident from enhanced Nile red accumulation and reduced expression of MmpL3, a transmembrane promising target involved in mycolic acid transport across membrane. Furthermore, iron deprivation led to abrogated MA transport particularly of class methoxy-MA which was confirmed by TLC and mass spectrometry based lipidome analysis. Additionally, iron deprivation leads to enhanced membrane fluidity in MTB. Together, MmpL3 being a promiscuous anti-TB target, metal chelation strategy could be adopted to boost the effectiveness of current anti-TB drug regimes to combat drug resistance TB.
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Affiliation(s)
- Rahul Pal
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
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40
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De Groote MA, Jarvis TC, Wong C, Graham J, Hoang T, Young CL, Ribble W, Day J, Li W, Jackson M, Gonzalez-Juarrero M, Sun X, Ochsner UA. Optimization and Lead Selection of Benzothiazole Amide Analogs Toward a Novel Antimycobacterial Agent. Front Microbiol 2018; 9:2231. [PMID: 30294313 PMCID: PMC6158578 DOI: 10.3389/fmicb.2018.02231] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria remain an important problem worldwide, especially drug resistant human pathogens. Novel therapeutics are urgently needed to tackle both drug-resistant tuberculosis (TB) and difficult-to-treat infections with nontuberculous mycobacteria (NTM). Benzothiazole adamantyl amide had previously emerged as a high throughput screening hit against M. tuberculosis (Mtb) and was subsequently found to be active against NTM as well. For lead optimization, we applied an iterative process of design, synthesis and screening of several 100 analogs to improve antibacterial potency as well as physicochemical and pharmacological properties to ultimately achieve efficacy. Replacement of the adamantyl group with cyclohexyl derivatives, including bicyclic moieties, resulted in advanced lead compounds that showed excellent potency and a mycobacteria-specific spectrum of activity. MIC values ranged from 0.03 to 0.12 μg/mL against M. abscessus (Mabs) and other rapid- growing NTM, 1–2 μg/mL against M. avium complex (MAC), and 0.12–0.5 μg/mL against Mtb. No pre-existing resistance was found in a collection of n = 54 clinical isolates of rapid-growing NTM. Unlike many antibacterial agents commonly used to treat mycobacterial infections, benzothiazole amides demonstrated bactericidal effects against both Mtb and Mabs. Metabolic labeling provided evidence that the compounds affect the transfer of mycolic acids to their cell envelope acceptors in mycobacteria. Mapping of resistance mutations pointed to the trehalose monomycolate transporter (MmpL3) as the most likely target. In vivo efficacy and tolerability of a benzothiazole amide was demonstrated in a mouse model of chronic NTM lung infection with Mabs. Once daily dosing over 4 weeks by intrapulmonary microspray administration as 5% corn oil/saline emulsion achieved statistically significant CFU reductions compared to vehicle control and non-inferiority compared to azithromycin. The benzothiazole amides hold promise for development of a novel therapeutic agent with broad antimycobacterial activity, though further work is needed to develop drug formulations for direct intrapulmonary delivery via aerosol.
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Affiliation(s)
- Mary A De Groote
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | | | | | | | - Joshua Day
- Crestone, Inc., Boulder, CO, United States
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
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41
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Li W, Yazidi A, Pandya AN, Hegde P, Tong W, Calado Nogueira de Moura V, North EJ, Sygusch J, Jackson M. MmpL3 as a Target for the Treatment of Drug-Resistant Nontuberculous Mycobacterial Infections. Front Microbiol 2018; 9:1547. [PMID: 30042757 PMCID: PMC6048240 DOI: 10.3389/fmicb.2018.01547] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Nontuberculous mycobacterial (NTM) pulmonary infections are emerging as a global health problem and pose a threat to susceptible individuals with structural or functional lung conditions such as cystic fibrosis, chronic obstructive pulmonary disease and bronchiectasis. Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABSC) species account for 70–95% of the pulmonary NTM infections worldwide. Treatment options for these pathogens are limited, involve lengthy multidrug regimens of 12–18 months with parenteral and oral drugs, and their outcome is often suboptimal. Development of new drugs and improved regimens to treat NTM infections are thus greatly needed. In the last 2 years, the screening of compound libraries against M. abscessus in culture has led to the discovery of a number of different chemotypes that target MmpL3, an essential inner membrane transporter involved in the export of the building blocks of the outer membrane of all mycobacteria known as the mycolic acids. This perspective reflects on the therapeutic potential of MmpL3 in Mycobacterium tuberculosis and NTM and the possible reasons underlying the outstanding promiscuity of this target. It further analyzes the physiological and structural factors that may account for the apparent looser structure-activity relationship of some of these compound series against M. tuberculosis compared to NTM.
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Affiliation(s)
- Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Amira Yazidi
- Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada.,Groupe d'Étude des Protéines Membranaires, Université de Montréal, Montréal, QC, Canada
| | - Amitkumar N Pandya
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, NE, United States
| | - Pooja Hegde
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, NE, United States
| | - Weiwei Tong
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Vinicius Calado Nogueira de Moura
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - E Jeffrey North
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, NE, United States
| | - Jurgen Sygusch
- Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada.,Groupe d'Étude des Protéines Membranaires, Université de Montréal, Montréal, QC, Canada
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
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Zheng H, Williams JT, Coulson GB, Haiderer ER, Abramovitch RB. HC2091 Kills Mycobacterium tuberculosis by Targeting the MmpL3 Mycolic Acid Transporter. Antimicrob Agents Chemother 2018; 62:e02459-17. [PMID: 29661875 DOI: 10.1128/AAC.02459-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, is a deadly disease that requires a long course of treatment. The emergence of drug-resistant strains has driven efforts to discover new small molecules that can kill the bacterium. Here, we report characterizations of the compound HC2091, which kills M. tuberculosis in a time- and dose-dependent manner in vitro and inhibits M. tuberculosis growth in macrophages. Whole-genome sequencing of spontaneous HC2091-resistant mutants identified single-nucleotide variants in the mmpL3 mycolic acid transporter gene. HC2091-resistant mutants do not exhibit cross-resistance with the well-characterized Mycobacterium membrane protein large 3 (MmpL3) inhibitor SQ109, suggesting a distinct mechanism of interaction with MmpL3. Additionally, HC2091 does not modulate bacterial membrane potential or kill nonreplicating M. tuberculosis, thus acting differently from other known MmpL3 inhibitors. RNA sequencing (RNA-seq) transcriptional profiling and lipid profiling of M. tuberculosis treated with HC2091 or SQ109 show that the two compounds target a similar pathway. HC2091 has a chemical structure dissimilar to those of previously described MmpL3 inhibitors, supporting the notion that HC2091 is a new class of MmpL3 inhibitor.
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Viljoen A, Herrmann JL, Onajole OK, Stec J, Kozikowski AP, Kremer L. Controlling Extra- and Intramacrophagic Mycobacterium abscessus by Targeting Mycolic Acid Transport. Front Cell Infect Microbiol 2017; 7:388. [PMID: 28920054 PMCID: PMC5585149 DOI: 10.3389/fcimb.2017.00388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium abscessus is a rapidly growing mycobacterium (RGM) causing serious infections especially among cystic fibrosis patients. Extremely limited therapeutic options against M. abscessus and a rise in infections with this mycobacterium require novel chemotherapies and a better understanding of how the bacterium causes infection. Different from most RGM, M. abscessus can survive inside macrophages and persist for long durations in infected tissues. We recently delineated differences in the infective programs followed by smooth (S) and rough (R) variants of M. abscessus. Unexpectedly, we found that the S variant behaves like pathogenic slow growing mycobacteria, through maintaining a block on the phagosome maturation process and by inducing phagosome-cytosol communications. On the other hand, R variant infection triggers autophagy and apoptosis, reminiscent of the way that macrophages control RGM. However, the R variant has an exquisite capacity to form extracellular cords, allowing these bacteria to rapidly divide and evade phagocytosis. Therefore, new chemotherapeutic interventions against M. abscessus need to efficiently deal with both the reservoir of intracellular bacilli and the extracellular cords. In this context, we recently identified two chemical entities that were very effective against both M. abscessus populations. Although being structurally unrelated these two chemotypes inhibit the activity of the essential mycolic acid transporter, MmpL3. In this Perspective, we aimed to highlight recent insights into how M. abscessus interacts with phagocytic cells and how the inhibition of mycolic acid transport in this pathogenic RGM could be an efficient means to control both intracellular and extracellular populations of the bacterium.
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Affiliation(s)
- Albertus Viljoen
- Centre National de la Recherche Scientifique UMR9004, Institut de Recherche en Infectiologie de Montpellier, Université de MontpellierMontpellier, France
| | - Jean-Louis Herrmann
- UMR1173, INSERM and UFR Des Sciences de la Santé Simone Veil, Université de Versailles Saint QuentinMontigny-le-Bretonneux, France
| | - Oluseye K Onajole
- Department of Biological, Chemical and Physical Sciences, Roosevelt UniversityChicago, IL, United States
| | - Jozef Stec
- Department of Pharmaceutical Sciences, College of Pharmacy, Marshall B. Ketchum UniversityFullerton, CA, United States
| | - Alan P Kozikowski
- StarWise Therapeutics LLC, University Research ParkMadison, WI, United States
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR9004, Institut de Recherche en Infectiologie de Montpellier, Université de MontpellierMontpellier, France.,INSERM, IRIM, 34293Montpellier, France
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Li W, Sanchez-Hidalgo A, Jones V, de Moura VC, North EJ, Jackson M. Synergistic Interactions of MmpL3 Inhibitors with Antitubercular Compounds In Vitro. Antimicrob Agents Chemother 2017; 61:e02399-16. [PMID: 28115355 DOI: 10.1128/AAC.02399-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/16/2017] [Indexed: 01/06/2023] Open
Abstract
A number of inhibitors of the essential Mycobacterium tuberculosis mycolic acid transporter, MmpL3, are currently under development as potential novel antituberculosis agents. Using the checkerboard method to study the interaction profiles of various antituberculosis drugs or experimental compounds with two different chemotypes inhibiting this transporter (indolcarboxamides and adamantyl ureas), we showed that MmpL3 inhibitors act synergistically with rifampin, bedaquiline, clofazimine, and β-lactams.
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Poce G, Consalvi S, Cocozza M, Fernandez-Menendez R, Bates RH, Ortega Muro F, Barros Aguirre D, Ballell L, Biava M. Pharmaceutical salt of BM635 with improved bioavailability. Eur J Pharm Sci 2016; 99:17-23. [PMID: 27939618 DOI: 10.1016/j.ejps.2016.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 12/01/2016] [Accepted: 12/03/2016] [Indexed: 11/18/2022]
Abstract
BM635 is a small molecule endowed with outstanding anti-mycobacterial activity (minimum inhibitory concentration of 0.12μM against M. tuberculosis H37Rv) identified during a hit-to-lead campaign. Its poor aqueous solubility together with its high lipophilicity led to low exposure in vivo. Indeed, the half-life in vivo of BM635 was 1h, allowing a reasonable maximum concentration (Cmax=1.62μM) and a moderate bioavailability (46%). The present study aimed to develop salt forms of BM635 with pharmaceutically accepted hydrochloric, methanesulphonic, phosphoric, tartaric, and citric acids to overcome these drawbacks. BM635 salts (BM635-HCl, BM635-Mes, BM635-PA, BM635-TA and BM635-CA) were evaluated for physicochemical as well as biopharmaceutical attributes.
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Affiliation(s)
- Giovanna Poce
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy.
| | - Sara Consalvi
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy
| | - Martina Cocozza
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy
| | - Raquel Fernandez-Menendez
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GSK, Tres Cantos, Madrid, Spain
| | - Robert H Bates
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GSK, Tres Cantos, Madrid, Spain
| | - Fátima Ortega Muro
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GSK, Tres Cantos, Madrid, Spain
| | - David Barros Aguirre
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GSK, Tres Cantos, Madrid, Spain
| | - Lluis Ballell
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GSK, Tres Cantos, Madrid, Spain
| | - Mariangela Biava
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy
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Belardinelli JM, Yazidi A, Yang L, Fabre L, Li W, Jacques B, Angala SK, Rouiller I, Zgurskaya HI, Sygusch J, Jackson M. Structure-Function Profile of MmpL3, the Essential Mycolic Acid Transporter from Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:702-713. [PMID: 27737557 DOI: 10.1021/acsinfecdis.6b00095] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The MmpL family of proteins translocates complex (glyco)lipids and siderophores across the cell envelope of mycobacteria and closely related Corynebacteriaceae and plays important roles in the biogenesis of the outer membrane of these organisms. Despite their significance in the physiology and virulence of Mycobacterium tuberculosis, and from the perspective of developing novel antituberculosis agents, little is known about their structure and mechanism of translocation. In this study, the essential mycobacterial mycolic acid transporter, MmpL3, and its orthologue in Corynebacterium glutamicum, CmpL1, were investigated as prototypical MmpL proteins to gain insight into the transmembrane topology, tertiary and quaternary structures, and functional regions of this transporter family. The combined genetic, biochemical, and biophysical studies indicate that MmpL3 and CmpL1 are structurally similar to Gram-negative resistance-nodulation and division efflux pumps. They harbor 12 transmembrane segments interrupted by two large soluble periplasmic domains and function as homotrimers to export long-chain (C22-C90) mycolic acids, possibly in their acetylated form, esterified to trehalose. The mapping of a number of functional residues within the middle region of the transmembrane domain of MmpL3 shows a striking overlap with mutations associated with resistance to MmpL3 inhibitors. The results suggest that structurally diverse inhibitors of MmpL3 all target the proton translocation path of the transporter and that multiresistance to these inhibitors is enabled by conformational changes in MmpL3.
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Affiliation(s)
- Juan Manuel Belardinelli
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Amira Yazidi
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Lucien Fabre
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, Quebec H3A 2B2, Canada
| | - Wei Li
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Benoit Jacques
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | - Shiva kumar Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Isabelle Rouiller
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, Quebec H3A 2B2, Canada
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jurgen Sygusch
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
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Foss MH, Pou S, Davidson PM, Dunaj JL, Winter RW, Pou S, Licon MH, Doh JK, Li Y, Kelly JX, Dodean RA, Koop DR, Riscoe MK, Purdy GE. Diphenylether-Modified 1,2-Diamines with Improved Drug Properties for Development against Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:500-8. [PMID: 27626102 DOI: 10.1021/acsinfecdis.6b00052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
New treatments for tuberculosis infection are critical to combat the emergence of multidrug- and extensively drug-resistant Mycobacterium tuberculosis (Mtb). We report the characterization of a diphenylether-modified adamantyl 1,2-diamine that we refer to as TBL-140, which has a minimal inhibitory concentration (MIC99) of 1.2 μg/mL. TBL-140 is effective against drug-resistant Mtb and nonreplicating bacteria. In addition, TBL-140 eliminates expansion of Mtb in cell culture infection assays at its MIC. To define the mechanism of action of this compound, we performed a spontaneous mutant screen and biochemical assays. We determined that TBL-140 treatment affects the proton motive force (PMF) by perturbing the transmembrane potential (ΔΨ), consistent with a target in the electron transport chain (ETC). As a result, treated bacteria have reduced intracellular ATP levels. We show that TBL-140 exhibits greater metabolic stability than SQ109, a structurally similar compound in clinical trials for treatment of MDR-TB infections. Combined, these results suggest that TBL-140 should be investigated further to assess its potential as an improved therapeutic lead against Mtb.
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Affiliation(s)
- Marie H. Foss
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Sovitj Pou
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Patrick M. Davidson
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Jennifer L. Dunaj
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Rolf W. Winter
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Sovijja Pou
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Meredith H. Licon
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Julia K. Doh
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Yuexin Li
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Jane X. Kelly
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Rozalia A. Dodean
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Dennis R. Koop
- Department of Physiology and Pharmacology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Michael K. Riscoe
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
- Portland VA Medical Center, 3710 S.W. U.S. Veterans Hospital
Road, Portland, Oregon 97239, United States
| | - Georgiana E. Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
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