1
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van der Klugt T, van den Biggelaar RHGA, Saris A. Host and bacterial lipid metabolism during tuberculosis infections: possibilities to synergise host- and bacteria-directed therapies. Crit Rev Microbiol 2024:1-21. [PMID: 38916142 DOI: 10.1080/1040841x.2024.2370979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative pathogen of tuberculosis, the most lethal infectious disease resulting in 1.3 million deaths annually. Treatments against Mtb are increasingly impaired by the growing prevalence of antimicrobial drug resistance, which necessitates the development of new antibiotics or alternative therapeutic approaches. Upon infecting host cells, predominantly macrophages, Mtb becomes critically dependent on lipids as a source of nutrients. Additionally, Mtb produces numerous lipid-based virulence factors that contribute to the pathogen's ability to interfere with the host's immune responses and to create a lipid rich environment for itself. As lipids, lipid metabolism and manipulating host lipid metabolism play an important role for the virulence of Mtb, this review provides a state-of-the-art overview of mycobacterial lipid metabolism and concomitant role of host metabolism and host-pathogen interaction therein. While doing so, we will emphasize unexploited bacteria-directed and host-directed drug targets, and highlight potential synergistic drug combinations that hold promise for the development of new therapeutic interventions.
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Affiliation(s)
- Teun van der Klugt
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Anno Saris
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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2
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Jowsey WJ, Cook GM, McNeil MB. Antibiotic resistance in Mycobacterium tuberculosis alters tolerance to cell wall-targeting inhibitors. JAC Antimicrob Resist 2024; 6:dlae086. [PMID: 38836195 PMCID: PMC11148391 DOI: 10.1093/jacamr/dlae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/11/2024] [Indexed: 06/06/2024] Open
Abstract
Background A limited ability to eliminate drug-resistant strains of Mycobacterium tuberculosis is a major contributor to the morbidity of TB. Complicating this problem, little is known about how drug resistance-conferring mutations alter the ability of M. tuberculosis to tolerate antibiotic killing. Here, we investigated if drug-resistant strains of M. tuberculosis have an altered ability to tolerate killing by cell wall-targeting inhibitors. Methods Bacterial killing and MIC assays were used to test for antibiotic tolerance and synergy against a panel of drug-resistant M. tuberculosis strains. Results Our results demonstrate that vancomycin and thioacetazone exhibit increased killing of diverse drug-resistant strains. Mutations in mmaA4 and mmpL3 increased vancomycin killing, which was consistent with vancomycin synergizing with thioacetazone and MmpL3-targeting inhibitors. In contrast, mutations in the mce1 operon conferred tolerance to vancomycin. Conclusions Overall, this work demonstrates how drug-resistant strains experience perturbations in cell-wall production that alters their tolerance to killing by cell wall-targeting inhibitors.
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Affiliation(s)
- William J Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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3
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Vasudevan N, Motiwala Z, Ramesh R, Wagh SB, Shingare RD, Katte R, Anand A, Choudhary S, Kumar A, Gokhale RS, Kulkarni KA, Reddy DS. Synthesis, biological evaluation and docking studies of silicon incorporated diarylpyrroles as MmpL3 inhibitors: An effective strategy towards development of potent anti-tubercular agents. Eur J Med Chem 2023; 259:115633. [PMID: 37524010 DOI: 10.1016/j.ejmech.2023.115633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 08/02/2023]
Abstract
Growing global demand for new molecules to treat tuberculosis has created an urgent need to develop novel strategies to combat the menace. BM212 related compounds were found to be potent anti-TB agents and they inhibit mycolic acid transporter, MmpL3, a known potent drug target from Mycobacterium tuberculosis. In order to enhance their inhibitory potency, several silicon analogues of diarylpyrroles related to BM212 were designed, synthesized, and evaluated for anti-tubercular activities. In Alamar blue assay, most of the silicon-incorporated compounds were found to be more potent than the parent compound (BM212), against Mycobacterium tuberculosis (MIC = 1.7 μM, H37Rv). Docking results from the crystal structure of MmpL3 and silicon analogues as pharmacophore model also strongly correlate with the biological assays and suggest that the incorporation of silicon in the inhibitor scaffold could enhance their potency by stabilizing the hydrophobic residues at the binding pocket. The best docking hit, compound 12 showed an MIC of 0.1 μM against H37Rv with an acceptable in vitro ADME profile and excellent selectivity index. Overall, the present study indicates that, the designed silicon analogues, especially compound 12 could be a good inhibitor for an intrinsically flexible drug-binding pocket of MmpL3 and has potential for further development as anti-tubercular agents.
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Affiliation(s)
- N Vasudevan
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Zenia Motiwala
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Remya Ramesh
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sachin B Wagh
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Rahul D Shingare
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Revansiddha Katte
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Amitesh Anand
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sushil Choudhary
- CSIR-Indian Institute of Integrative Medicine, Post Bag No. 3, Canal Rd, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ajay Kumar
- CSIR-Indian Institute of Integrative Medicine, Post Bag No. 3, Canal Rd, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India; Immunometabolism Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kiran A Kulkarni
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - D Srinivasa Reddy
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Zhang L, Rao Z. Structural biology and inhibition of the Mtb cell wall glycoconjugates biosynthesis on the membrane. Curr Opin Struct Biol 2023; 82:102670. [PMID: 37542906 DOI: 10.1016/j.sbi.2023.102670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023]
Abstract
Glycoconjugates are the dominant components of the Mycobacterium tuberculosis cell wall. These glycoconjugates are essential for the viability of Mtb and attribute to drug resistance and virulence during infection. The assembly and maturation of the cell wall largely relies on the Mtb plasma membrane. A significant number of membrane-bound glycosyltransferases (GTs) and transporters play pivotal roles in forming the complex glycoconjugates and are targeted by the first-line anti-TB drug and potent drug candidates. Here we summarize the latest structural biology of mycobacterial GTs and transporters, and describe the modes of action of drug and drug candidates that are of substantial clinical value in anti-TB chemotherapeutics.
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Affiliation(s)
- Lu Zhang
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Zihe Rao
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
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5
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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] [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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6
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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] [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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7
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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; 18:707-724. [PMID: 37226498 PMCID: PMC10330604 DOI: 10.1080/17460441.2023.2218082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/22/2023] [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 seems 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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8
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Mahajan PS, Girigosavi P, Chauware V, Mokashi ND, Nema V. Issues with the current drugs for Mycobacterium tuberculosis cure and potential of cell envelope proteins for new drug discovery. Indian J Tuberc 2023; 70:286-296. [PMID: 37562902 DOI: 10.1016/j.ijtb.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 08/12/2023]
Abstract
Mycobacterium tuberculosis has been the smartest pathogen ever and a challenge to drug development. Its replicative machinery is unique, so targeting the same for killing the pathogen remains a challenge. Our body typically throws out the drugs before they see the bacterium multiply. The pathogen has also learned how to remove drugs from its internal chambers and not allow them to reach their targets. Another strategy for Mtb is the mutation of the targets to reject drug binding and bypass the drug's inhibitory actions. In this review, we tried to explore possible targets on the outer side of the bacterial cell. We have also explored if those targets are promising enough and if there are drugs or inhibitors available. We also discuss the essential proteins and why they remain to be a good target. We concluded that the cell envelope has got a few proteins that can be targeted in isolation or maybe along with other machinery while making the outer environment more conducive for penetration of current drugs or newly proposed drugs.
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Affiliation(s)
- Pratik S Mahajan
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Payal Girigosavi
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Vijay Chauware
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Nitin D Mokashi
- Postgraduate Institute, Yashwantrao Chavan Memorial Hospital, Pune, 411018, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India.
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9
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Berube B, Deshpande A, Bhagwat A, Parish T. Inoculum-dependent bactericidal activity of a Mycobacterium tuberculosis MmpL3 inhibitor. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37334886 DOI: 10.1099/mic.0.001345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Indolcarboxamides are a promising series of anti-tubercular agents, which target Mycobacterium tuberculosis MmpL3, the exporter of trehalose monomycolate, a key cell-wall component. We determined the kill kinetics of the lead indolcarboxamide NITD-349 and determined that while kill was rapid against low-density cultures, bactericidal activity was inoculum-dependent. A combination of NITD-349 with isoniazid (which inhibits mycolate synthesis) had an increased kill rate; this combination prevented the appearance of resistant mutants, even at higher inocula.
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Affiliation(s)
- Bryan Berube
- Center for Global Infectious Disease, Seattle Children's Research Institute, Seattle, WA, USA
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Aditi Deshpande
- Center for Global Infectious Disease, Seattle Children's Research Institute, Seattle, WA, USA
| | - Amala Bhagwat
- Center for Global Infectious Disease, Seattle Children's Research Institute, Seattle, WA, USA
| | - Tanya Parish
- Center for Global Infectious Disease, Seattle Children's Research Institute, Seattle, WA, USA
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
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10
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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] [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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Berube B, Deshpande A, Bhagwat A, Parish T. Inoculum-dependent bactericidal activity of a Mycobacterium tuberculosis MmpL3 inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529622. [PMID: 36865226 PMCID: PMC9980077 DOI: 10.1101/2023.02.22.529622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Indolcarboxamides are a promising series of anti-tubercular agents which target Mycobacterium tuberculosis MmpL3, the exporter of trehalose monomycolate, a key cell wall component. We determined the kill kinetics of the lead indolcarboxamide NITD-349 and determined that while kill was rapid against low density cultures, bactericidal activity was inoculum-dependent. A combination of NITD-349 with isoniazid (which inhibits mycolate synthesis) had an increased kill rate; this combination prevented the appearance of resistant mutants, even at higher inocula.
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12
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Computational design of MmpL3 inhibitors for tuberculosis therapy. Mol Divers 2023; 27:357-369. [PMID: 35477825 DOI: 10.1007/s11030-022-10436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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13
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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14
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Imran M, Arora MK, Chaudhary A, Khan SA, Kamal M, Alshammari MM, Alharbi RM, Althomali NA, Alzimam IM, Alshammari AA, Alharbi BH, Alshengeti A, Alsaleh AA, Alqahtani SA, Rabaan AA. MmpL3 Inhibition as a Promising Approach to Develop Novel Therapies against Tuberculosis: A Spotlight on SQ109, Clinical Studies, and Patents Literature. Biomedicines 2022; 10:2793. [PMID: 36359313 PMCID: PMC9687596 DOI: 10.3390/biomedicines10112793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/13/2023] Open
Abstract
Tuberculosis (TB) is accountable for considerable global morbidity and mortality. Effective TB therapy with multiple drugs completes in about six months. The longer duration of TB therapy challenges patient compliance and contributes to treatment collapse and drug resistance (DR) progress. Therefore, new medications with an innovative mechanism of action are desperately required to shorten the TB therapy's duration and effective TB control. The mycobacterial membrane protein Large 3 (MmpL3) is a novel, mycobacteria-conserved and recognized promiscuous drug target used in the development of better treatments for multi-drug resistance TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). This article spotlights MmpL3, the clinical studies of its inhibitor (SQ109), and the patent literature. The literature on MmpL3 inhibitors was searched on PubMed and freely available patent databases (Espacenet, USPTO, and PatentScope). SQ109, an analog of ethambutol (EMB), is an established MmpL3 inhibitor and has completed Phase 2b-3 clinical trials. Infectex and Sequella are developing orally active SQ109 in partnership to treat MDR pulmonary TB. SQ109 has demonstrated activity against drug-sensitive (DS) and drug-resistant (DR) Mycobacterium tuberculosis (Mtb) and a synergistic effect with isoniazid (INH), rifampicin (RIF), clofazimine (CFZ), and bedaquiline (BNQ). The combination of SQ109, clofazimine, bedaquiline, and pyrazinamide (PZA) has been patented due to its excellent anti-TB activity against MDR-TB, XDR-TB, and latent-TB. The combinations of SQ109 with other anti-TB drugs (chloroquine, hydroxychloroquine, and sutezolid) have also been claimed in the patent literature. SQ109 is more potent than EMB and could substitute EMB in the intensive stage of TB treatment with the three- or four-drug combination. Developing MmpL3 inhibitors is a promising approach to fighting the challenges associated with DS-TB and DR-TB. The authors foresee MmpL3 inhibitors such as SQ109 as future drugs for TB treatment.
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Affiliation(s)
- Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Mandeep Kumar Arora
- School of Pharmaceutical and Population Health Informatics, DIT University, Dehradun 248009, India
| | - Anurag Chaudhary
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut 250005, India
| | - Shah Alam Khan
- Department of Pharmaceutical Chemistry, College of Pharmacy, National University of Science and Technology, Muscat 130, Oman
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Manal Mutlaq Alshammari
- Pharmacy Department, Hotat Bani Tamim General Hospital, Hotat Bani Tamim 16631, Saudi Arabia
| | | | | | | | | | | | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | | | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
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15
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A Hydrazine-Hydrazone Adamantine Compound Shows Antimycobacterial Activity and Is a Probable Inhibitor of MmpL3. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27207130. [PMID: 36296721 PMCID: PMC9610904 DOI: 10.3390/molecules27207130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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16
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Novel chemical entities inhibiting Mycobacterium tuberculosis growth identified by phenotypic high-throughput screening. Sci Rep 2022; 12:14879. [PMID: 36050506 PMCID: PMC9435431 DOI: 10.1038/s41598-022-19192-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
We performed a high-throughput phenotypic whole cell screen of Mycobacterium tuberculosis against a diverse chemical library of approximately 100,000 compounds from the AbbVie corporate collection and identified 24 chemotypes with anti-tubercular activity. We selected two series for further exploration and conducted structure-activity relationship studies with new analogs for the 4-phenyl piperidines (4PP) and phenylcyclobutane carboxamides (PCB). Strains with mutations in MmpL3 demonstrated resistance to both compound series. We isolated resistant mutants for the two series and found mutations in MmpL3. These data suggest that MmpL3 is the target, or mechanism of resistance for both series.
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The driving force for mycolic acid export by mycobacterial MmpL3 is proton translocation. Proc Natl Acad Sci U S A 2022; 119:e2211130119. [PMID: 35939679 PMCID: PMC9388100 DOI: 10.1073/pnas.2211130119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Zhao H, Gao Y, Li W, Sheng L, Cui K, Wang B, Fu L, Gao M, Lin Z, Zou X, Jackson M, Huang H, Lu Y, Zhang D. Design, Synthesis, and Biological Evaluation of Pyrrole-2-carboxamide Derivatives as Mycobacterial Membrane Protein Large 3 Inhibitors for Treating Drug-Resistant Tuberculosis. J Med Chem 2022; 65:10534-10553. [PMID: 35915958 PMCID: PMC9379527 DOI: 10.1021/acs.jmedchem.2c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, pyrrole-2-carboxamides were designed with a structure-guided strategy based on the crystal structure of MmpL3 and a pharmacophore model. The structure-activity relationship studies revealed that attaching phenyl and pyridyl groups with electron-withdrawing substituents to the pyrrole ring and attaching bulky substituents to the carboxamide greatly improved anti-TB activity. Most compounds showed potent anti-TB activity (MIC < 0.016 μg/mL) and low cytotoxicity (IC50 > 64 μg/mL). Compound 32 displayed excellent activity against drug-resistant tuberculosis, good microsomal stability, almost no inhibition of the hERG K+ channel, and good in vivo efficacy. Furthermore, the target of the pyrrole-2-carboxamides was identified by measuring their potency against M. smegmatis expressing wild-type and mutated variants of the mmpL3 gene from M. tuberculosis (mmpL3tb) and determining their effect on mycolic acid biosynthesis using a [14C] acetate metabolic labeling assay. The present study provides new MmpL3 inhibitors that are promising anti-TB agents.
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Affiliation(s)
- Hongyi Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yongxin Gao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Li Sheng
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Keli Cui
- College of Life Science and Bio-engineering, Beijing University of Technology, 100 Ping Le Yuan, Beijing 100124, P. R. China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Lei Fu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Meng Gao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Ziyun Lin
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Xiaowen Zou
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Dongfeng Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
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19
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Bhakhar KA, Vaghela PV, Varakala SD, Chudasma SJ, Gajjar ND, Nagar PR, Sriram D, Dhameliya TM. Indole‐2‐carboxamides as New Anti‐Mycobacterial Agents: Design, Synthesis, Biological Evaluation and Molecular Modeling against mmpL3. ChemistrySelect 2022. [DOI: 10.1002/slct.202201813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kaushikkumar A. Bhakhar
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Punit V. Vaghela
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Saiprasad D. Varakala
- Department of Pharmacy Birla Institute of Technology & Science - Pilani Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 India
| | - Shrdhhaba J. Chudasma
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Normi D. Gajjar
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Prinsa R. Nagar
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Dharmarajan Sriram
- Department of Pharmacy Birla Institute of Technology & Science - Pilani Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 India
| | - Tejas M. Dhameliya
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
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20
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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 AND QSAR IN ENVIRONMENTAL RESEARCH 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] [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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21
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Belete TM. Recent Progress in the Development of Novel Mycobacterium Cell Wall Inhibitor to Combat Drug-Resistant Tuberculosis. Microbiol Insights 2022; 15:11786361221099878. [PMID: 35645569 PMCID: PMC9131376 DOI: 10.1177/11786361221099878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Despite decades of research in drug development against TB, it is still the leading cause of death due to infectious diseases. The long treatment duration, patient noncompliance coupled with the ability of the tuberculosis bacilli to resist the current drugs increases multidrug-resistant tuberculosis that exacerbates the situation. Identification of novel drug targets is important for the advancement of drug development against Mycobacterium tuberculosis. The development of an effective treatment course that could help us eradicates TB. Hence, we require drugs that could eliminate the bacteria and shorten the treatment duration. This review briefly describes the available data on the peptidoglycan component structural characterization, identification of the metabolic pathway, and the key enzymes involved in the peptidoglycan synthesis, like N-Acetylglucosamine-1-phosphate uridyltransferase, mur enzyme, alanine racemase as well as their inhibition. Besides, this paper also provides studies on mycolic acid and arabinogalactan synthesis and the transport mechanisms that show considerable promise as new targets to develop a new product with their inhibiter.
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Affiliation(s)
- Tafere Mulaw Belete
- Department of Pharmacology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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22
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Mandelic acid-based spirothiazolidinones targeting M. tuberculosis: Synthesis, in vitro and in silico investigations. Bioorg Chem 2022; 121:105688. [DOI: 10.1016/j.bioorg.2022.105688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/09/2022] [Accepted: 02/13/2022] [Indexed: 01/01/2023]
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23
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Kuang W, Zhang H, Wang X, Yang P. Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis. Acta Pharm Sin B 2022; 12:3201-3214. [PMID: 35967276 PMCID: PMC9366312 DOI: 10.1016/j.apsb.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) utilizes multiple mechanisms to obtain antibiotic resistance during the treatment of infections. In addition, the biofilms, secreted by MTB, can further protect the latter from the contact with drug molecules and immune cells. These self-defending mechanisms lay a formidable challenge to develop effective therapeutic agents against chronic and recurring antibiotic-tolerant MTB infections. Although several inexpensive and effective drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) have been discovered for the treatment regimen, MTB continues to cause considerable morbidity and mortality worldwide. Antibiotic resistance and tolerance remain major global issues, and innovative therapeutic strategies are urgently needed to address the challenges associated with pathogenic bacteria. Gratifyingly, the cell wall synthesis of tubercle bacilli requires the participation of many enzymes which exclusively exist in prokaryotic organisms. These enzymes, absent in human hepatocytes, are recognized as promising targets to develop anti-tuberculosis drug. In this paper, we discussed the critical roles of potential drug targets in regulating cell wall synthesis of MTB. And also, we systematically reviewed the advanced development of novel bioactive compounds or drug leads for inhibition of cell wall synthesis, including their discovery, chemical modification, in vitro and in vivo evaluation.
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Affiliation(s)
- Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haolin Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding author.
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24
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Identification of anti-mycobacterial agents against mmpL3: Virtual screening, ADMET analysis and MD simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130941] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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25
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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] [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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26
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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] [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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27
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Klenotic PA, Moseng MA, Morgan CE, Yu EW. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters. Chem Rev 2021; 121:5378-5416. [PMID: 33211490 PMCID: PMC8119314 DOI: 10.1021/acs.chemrev.0c00621] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug resistant (MDR) bacteria are a global threat with many common infections becoming increasingly difficult to eliminate. While significant effort has gone into the development of potent biocides, the effectiveness of many first-line antibiotics has been diminished due to adaptive resistance mechanisms. Bacterial membrane proteins belonging to the resistance-nodulation-cell division (RND) superfamily play significant roles in mediating bacterial resistance to antimicrobials. They participate in multidrug efflux and cell wall biogenesis to transform bacterial pathogens into "superbugs" that are resistant even to last resort antibiotics. In this review, we summarize the RND superfamily of efflux transporters with a primary focus on the assembly and function of the inner membrane pumps. These pumps are critical for extrusion of antibiotics from the cell as well as the transport of lipid moieties to the outer membrane to establish membrane rigidity and stability. We analyze recently solved structures of bacterial inner membrane efflux pumps as to how they bind and transport their substrates. Our cumulative data indicate that these RND membrane proteins are able to utilize different oligomerization states to achieve particular activities, including forming MDR pumps and cell wall remodeling machineries, to ensure bacterial survival. This mechanistic insight, combined with simulated docking techniques, allows for the design and optimization of new efflux pump inhibitors to more effectively treat infections that today are difficult or impossible to cure.
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Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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28
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Fullam E, Young RJ. Physicochemical properties and Mycobacterium tuberculosis transporters: keys to efficacious antitubercular drugs? RSC Med Chem 2020; 12:43-56. [PMID: 34041481 PMCID: PMC8130550 DOI: 10.1039/d0md00265h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
Securing novel, safe, and effective medicines to treat Mycobacterium tuberculosis remains an elusive goal, particularly influenced by the largely impervious Mtb envelope that limits exposure and thus efficacy of inhibitors at their cellular and periplasmic targets. The impact of physicochemical properties on pharmacokinetic parameters that govern oral absorption and exposure at sites of infection is considered alongside how these properties influence penetration of the Mtb envelope, with the likely influence of transporter proteins. The findings are discussed to benchmark current drugs and the emerging pipeline, whilst considering tactics for future rational and targeted design strategies, based around emerging data on Mtb transporters and their structures and functions.
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Affiliation(s)
- Elizabeth Fullam
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK
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29
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Appetecchia F, Consalvi S, Scarpecci C, Biava M, Poce G. SAR Analysis of Small Molecules Interfering with Energy-Metabolism in Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:E227. [PMID: 32878317 PMCID: PMC7557483 DOI: 10.3390/ph13090227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis remains the world's top infectious killer: it caused a total of 1.5 million deaths and 10 million people fell ill with TB in 2018. Thanks to TB diagnosis and treatment, mortality has been falling in recent years, with an estimated 58 million saved lives between 2000 and 2018. However, the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains is a major concern that might reverse this progress. Therefore, the development of new drugs acting upon novel mechanisms of action is a high priority in the global health agenda. With the approval of bedaquiline, which targets mycobacterial energy production, and delamanid, which targets cell wall synthesis and energy production, the energy-metabolism in Mtb has received much attention in the last decade as a potential target to investigate and develop new antimycobacterial drugs. In this review, we describe potent anti-mycobacterial agents targeting the energy-metabolism at different steps with a special focus on structure-activity relationship (SAR) studies of the most advanced compound classes.
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Affiliation(s)
| | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy; (F.A.); (S.C.); (C.S.); (M.B.)
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