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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] [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] [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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3
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Amandy FV, Neri GLL, Manzano JAH, Go AD, Macabeo APG. Polypharmacology-Driven Discovery and Design of Highly Selective, Dual and Multitargeting Inhibitors of Mycobacterium tuberculosis - A Review. Curr Drug Targets 2024; 25:620-634. [PMID: 38859782 DOI: 10.2174/0113894501306302240526160804] [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: 01/24/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024]
Abstract
The increasing demand for novel antitubercular agents has been the main 'force' of many TB research efforts due to the uncontrolled growing number of drug-resistant strains of M. tuberculosis in the clinical setting. Many strategies have been employed to address the drug-resistant issue, including a trend that is gaining attention, which is the design and discovery of Mtb inhibitors that are either dual- or multitargeting. The multiple-target design concept is not new in medicinal chemistry. With a growing number of newly discovered Mtb proteins, numerous targets are now available for developing new biochemical/cell-based assays and computer-aided drug design (CADD) protocols. To describe the achievements and overarching picture of this field in anti- infective drug discovery, we provide in this review small molecules that exhibit profound inhibitory activity against the tubercle bacilli and are identified to trace two or more Mtb targets. This review also presents emerging design methodologies for developing new anti-TB agents, particularly tailored to structure-based CADD.
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Affiliation(s)
- Franklin V Amandy
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
- Department of Chemistry, College of Science, Adamson University, San Marcelino St., Ermita, Manila 1000, Philippines
| | - Gabriel L L Neri
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Joe A H Manzano
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
| | - Adrian D Go
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
- Department of Chemistry, College of Science, Adamson University, San Marcelino St., Ermita, Manila 1000, Philippines
| | - Allan P G Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (Rm. 410), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana Blvd., Manila 1015, Philippines
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4
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Verma A, Naik B, Kumar V, Mishra S, Choudhary M, Khan JM, Gupta AK, Pandey P, Rustagi S, Kakati B, Gupta S. Revolutionizing Tuberculosis Treatment: Uncovering New Drugs and Breakthrough Inhibitors to Combat Drug-Resistant Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:2369-2385. [PMID: 37944023 DOI: 10.1021/acsinfecdis.3c00436] [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] [Indexed: 11/12/2023]
Abstract
Tuberculosis (TB) is a global health threat that causes significant mortality. This review explores chemotherapeutics that target essential processes in Mycobacterium tuberculosis, such as DNA replication, protein synthesis, cell wall formation, energy metabolism, and proteolysis. We emphasize the need for new drugs to treat drug-resistant strains and shorten the treatment duration. Emerging targets and promising inhibitors were identified by examining the intricate biology of TB. This review provides an overview of recent developments in the search for anti-TB drugs with a focus on newly validated targets and inhibitors. We aimed to contribute to efforts to combat TB and improve therapeutic outcomes.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Sadhna Mishra
- Faculty of Agricultural Sciences, GLA University, Mathura 281406, UP, India
| | - Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Arun Kumar Gupta
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchur 788011, Assam, India
| | - Sarvesh Rustagi
- Department of Food Technology, UCALS, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Barnali Kakati
- Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, U.K., India
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
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Yang J, Zhang L, Qiao W, Luo Y. Mycobacterium tuberculosis: Pathogenesis and therapeutic targets. MedComm (Beijing) 2023; 4:e353. [PMID: 37674971 PMCID: PMC10477518 DOI: 10.1002/mco2.353] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health concern in the 21st century, especially due to drug resistance, coinfection with diseases like immunodeficiency syndrome (AIDS) and coronavirus disease 2019, and the lengthy and costly treatment protocols. In this review, we summarize the pathogenesis of TB infection, therapeutic targets, and corresponding modulators, including first-line medications, current clinical trial drugs and molecules in preclinical assessment. Understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection and important biological targets can lead to innovative treatments. While most antitubercular agents target pathogen-related processes, host-directed therapy (HDT) modalities addressing immune defense, survival mechanisms, and immunopathology also hold promise. Mtb's adaptation to the human host involves manipulating host cellular mechanisms, and HDT aims to disrupt this manipulation to enhance treatment effectiveness. Our review provides valuable insights for future anti-TB drug development efforts.
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Affiliation(s)
- Jiaxing Yang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Laiying Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Wenliang Qiao
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduSichuanChina
- Lung Cancer Center, West China HospitalSichuan UniversityChengduSichuanChina
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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Chagaleti BK, Reddy MBR, Saravanan V, B S, D P, Senthil Kumar P, Kathiravan MK. An overview of mechanism and chemical inhibitors of shikimate kinase. J Biomol Struct Dyn 2023; 41:14582-14598. [PMID: 36974959 DOI: 10.1080/07391102.2023.2193985] [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: 09/09/2022] [Accepted: 02/04/2023] [Indexed: 03/29/2023]
Abstract
Tuberculosis is a highly infectious disease other than HIV/AIDS and it is one of the top ten causes of death worldwide. Resistance development in the bacteria occurs because of genetic alterations, and the molecular insights suggest that the accumulation of mutation in the individual drug target genes is the primary mechanism of multi-drug resistant tuberculosis. Chorismate is an essential structural fragment for the synthesis of aromatic amino acids and synthesized biochemically by a number of bacteria, including Mycobacterium tuberculosis, utilizing the shikimate pathway. This shikimate kinase is the newer possible target for the generation of novel antitubercular drug because this pathway is expressed only in mycobacterium and not in Mammals. The discovery and development of shikimate kinase inhibitors provide an opportunity for the development of novel selective medications. Multiple shikimate kinase inhibitors have been identified via insilico virtual screening and related protein-ligand interactions along with their in-vitro studies. These inhibitors bind to the active site in a similar fashion to shikimate. In the current review, we present an overview of the biology and chemistry of the shikimate kinase protein and its inhibitors, with special emphasis on the various active scaffold against the enzyme. A variety of chemically diversified synthetic scaffolds including Benzothiazoles, Oxadiazoles, Thiobarbiturates, Naphthoquinones, Thiazoleacetonitriles, Hybridized Pyrazolone derivatives, Orthologous biological macromolecule derivatives, Manzamine Alkaloids derivatives, Dipeptide inhibitor, and Chalcones are discussed in detail. These derivatives bind to the specific target appropriately proving their potential ability through different binding interactions and effectively explored as an effective and selective Sk inhibitor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - M B Rahul Reddy
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - Shanthakumar B
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - Priya D
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - P Senthil Kumar
- Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - M K Kathiravan
- 209, Dr. APJ Abdul Kalam Research Lab, Dept of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
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7
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Alsayed SSR, Gunosewoyo H. Tuberculosis: Pathogenesis, Current Treatment Regimens and New Drug Targets. Int J Mol Sci 2023; 24:ijms24065202. [PMID: 36982277 PMCID: PMC10049048 DOI: 10.3390/ijms24065202] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
Mycobacterium tuberculosis (M. tb), the causative agent of TB, is a recalcitrant pathogen that is rife around the world, latently infecting approximately a quarter of the worldwide population. The asymptomatic status of the dormant bacteria escalates to the transmissible, active form when the host's immune system becomes debilitated. The current front-line treatment regimen for drug-sensitive (DS) M. tb strains is a 6-month protocol involving four different drugs that requires stringent adherence to avoid relapse and resistance. Poverty, difficulty to access proper treatment, and lack of patient compliance contributed to the emergence of more sinister drug-resistant (DR) strains, which demand a longer duration of treatment with more toxic and more expensive drugs compared to the first-line regimen. Only three new drugs, bedaquiline (BDQ) and the two nitroimidazole derivatives delamanid (DLM) and pretomanid (PMD) were approved in the last decade for treatment of TB-the first anti-TB drugs with novel mode of actions to be introduced to the market in more than 50 years-reflecting the attrition rates in the development and approval of new anti-TB drugs. Herein, we will discuss the M. tb pathogenesis, current treatment protocols and challenges to the TB control efforts. This review also aims to highlight several small molecules that have recently been identified as promising preclinical and clinical anti-TB drug candidates that inhibit new protein targets in M. tb.
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Affiliation(s)
- Shahinda S R Alsayed
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Hendra Gunosewoyo
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia
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8
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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: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [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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Williams JT, Abramovitch RB. Molecular Mechanisms of MmpL3 Function and Inhibition. Microb Drug Resist 2023; 29:190-212. [PMID: 36809064 PMCID: PMC10171966 DOI: 10.1089/mdr.2021.0424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
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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10
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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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11
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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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12
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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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13
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Stevens CM, Babii SO, Pandya AN, Li W, Li Y, Mehla J, Scott R, Hegde P, Prathipati PK, Acharya A, Liu J, Gumbart JC, North J, Jackson M, Zgurskaya HI. Proton transfer activity of the reconstituted Mycobacterium tuberculosis MmpL3 is modulated by substrate mimics and inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2113963119. [PMID: 35858440 PMCID: PMC9335285 DOI: 10.1073/pnas.2113963119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/03/2022] [Indexed: 01/21/2023] Open
Abstract
Transporters belonging to the Resistance-Nodulation-cell Division (RND) superfamily of proteins such as Mycobacterium tuberculosis MmpL3 and its analogs are the focus of intense investigations due to their importance in the physiology of Corynebacterium-Mycobacterium-Nocardia species and antimycobacterial drug discovery. These transporters deliver trehalose monomycolates, the precursors of major lipids of the outer membrane, to the periplasm by a proton motive force-dependent mechanism. In this study, we successfully purified, from native membranes, the full-length and the C-terminal truncated M. tuberculosis MmpL3 and Corynebacterium glutamicum CmpL1 proteins and reconstituted them into proteoliposomes. We also generated a series of substrate mimics and inhibitors specific to these transporters, analyzed their activities in the reconstituted proteoliposomes, and carried out molecular dynamics simulations of the model MmpL3 transporter at different pH. We found that all reconstituted proteins facilitate proton translocation across a phospholipid bilayer, but MmpL3 and CmpL1 differ dramatically in their responses to pH and interactions with substrate mimics and indole-2-carboxamide inhibitors. Our results further suggest that some inhibitors abolish the transport activity of MmpL3 and CmpL1 by inhibition of proton translocation.
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Affiliation(s)
- Casey M. Stevens
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Svitlana O. Babii
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Amitkumar N. Pandya
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Yupeng Li
- College of Chemistry, Jilin University, 130012 Changchun, China
- Tang Aoqing Honors Program in Science, Jilin University, 130012 Changchun, China
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Robyn Scott
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178
| | - Pooja Hegde
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178
| | - Pavan K. Prathipati
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178
| | - Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jinchan Liu
- College of Chemistry, Jilin University, 130012 Changchun, China
- Tang Aoqing Honors Program in Science, Jilin University, 130012 Changchun, China
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - Jeffrey North
- School of Pharmacy & Health Professions, Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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14
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Fernandes GFS, Thompson AM, Castagnolo D, Denny WA, Dos Santos JL. Tuberculosis Drug Discovery: Challenges and New Horizons. J Med Chem 2022; 65:7489-7531. [PMID: 35612311 DOI: 10.1021/acs.jmedchem.2c00227] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the past 2000 years, tuberculosis (TB) has claimed more lives than any other infectious disease. In 2020 alone, TB was responsible for 1.5 million deaths worldwide, comparable to the 1.8 million deaths caused by COVID-19. The World Health Organization has stated that new TB drugs must be developed to end this pandemic. After decades of neglect in this field, a renaissance era of TB drug discovery has arrived, in which many novel candidates have entered clinical trials. However, while hundreds of molecules are reported annually as promising anti-TB agents, very few successfully progress to clinical development. In this Perspective, we critically review those anti-TB compounds published in the last 6 years that demonstrate good in vivo efficacy against Mycobacterium tuberculosis. Additionally, we highlight the main challenges and strategies for developing new TB drugs and the current global pipeline of drug candidates in clinical studies to foment fresh research perspectives.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800903, Brazil
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15
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Li M, Patel HV, Cognetta AB, Smith TC, Mallick I, Cavalier JF, Previti ML, Canaan S, Aldridge BB, Cravatt BF, Seeliger JC. Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling. Cell Chem Biol 2022; 29:883-896.e5. [PMID: 34599873 PMCID: PMC8964833 DOI: 10.1016/j.chembiol.2021.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/08/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022]
Abstract
The identification and validation of a small molecule's targets is a major bottleneck in the discovery process for tuberculosis antibiotics. Activity-based protein profiling (ABPP) is an efficient tool for determining a small molecule's targets within complex proteomes. However, how target inhibition relates to biological activity is often left unexplored. Here, we study the effects of 1,2,3-triazole ureas on Mycobacterium tuberculosis (Mtb). After screening ∼200 compounds, we focus on 4 compounds that form a structure-activity series. The compound with negligible activity reveals targets, the inhibition of which is functionally less relevant for Mtb growth and viability, an aspect not addressed in other ABPP studies. Biochemistry, computational docking, and morphological analysis confirms that active compounds preferentially inhibit serine hydrolases with cell wall and lipid metabolism functions and that disruption of the cell wall underlies biological activity. Our findings show that ABPP identifies the targets most likely relevant to a compound's antibacterial activity.
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Affiliation(s)
- Michael Li
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Hiren V Patel
- Department of Microbiology and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Armand B Cognetta
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Ivy Mallick
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | | | - Mary L Previti
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, IMM FR3479, 13402 Marseille, France
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences and Immunology Stony Brook University, Stony Brook, NY 11790, USA.
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16
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Challenges in targeting mycobacterial ATP synthase: The known and beyond. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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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] [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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18
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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: 25] [Impact Index Per Article: 8.3] [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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19
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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: 25] [Impact Index Per Article: 8.3] [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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20
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Targeting MmpL3 for anti-tuberculosis drug development. Biochem Soc Trans 2021; 48:1463-1472. [PMID: 32662825 PMCID: PMC7458404 DOI: 10.1042/bst20190950] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 02/07/2023]
Abstract
The unique architecture of the mycobacterial cell envelope plays an important role in Mycobacterium tuberculosis (Mtb) pathogenesis. A critical protein in cell envelope biogenesis in mycobacteria, required for transport of precursors, trehalose monomycolates (TMMs), is the Mycobacterial membrane protein large 3 (MmpL3). Due to its central role in TMM transport, MmpL3 has been an attractive therapeutic target and a key target for several preclinical agents. In 2019, the first crystal structures of the MmpL3 transporter and its complexes with lipids and inhibitors were reported. These structures revealed several unique structural features of MmpL3 and provided invaluable information on the mechanism of TMM transport. This review aims to highlight the recent advances made in the function of MmpL3 and summarises structural findings. The overall goal is to provide a mechanistic perspective of MmpL3-mediated lipid transport and inhibition, and to highlight the prospects for potential antituberculosis therapies.
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21
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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: 42] [Impact Index Per Article: 14.0] [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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22
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Jackson M, Stevens CM, Zhang L, Zgurskaya HI, Niederweis M. Transporters Involved in the Biogenesis and Functionalization of the Mycobacterial Cell Envelope. Chem Rev 2021; 121:5124-5157. [PMID: 33170669 PMCID: PMC8107195 DOI: 10.1021/acs.chemrev.0c00869] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The biology of mycobacteria is dominated by a complex cell envelope of unique composition and structure and of exceptionally low permeability. This cell envelope is the basis of many of the pathogenic features of mycobacteria and the site of susceptibility and resistance to many antibiotics and host defense mechanisms. This review is focused on the transporters that assemble and functionalize this complex structure. It highlights both the progress and the limits of our understanding of how (lipo)polysaccharides, (glyco)lipids, and other bacterial secretion products are translocated across the different layers of the cell envelope to their final extra-cytoplasmic location. It further describes some of the unique strategies evolved by mycobacteria to import nutrients and other products through this highly impermeable barrier.
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Affiliation(s)
- Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Casey M. Stevens
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
| | - Helen I. Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
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23
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Yuan T, Werman JM, Sampson NS. The pursuit of mechanism of action: uncovering drug complexity in TB drug discovery. RSC Chem Biol 2021; 2:423-440. [PMID: 33928253 PMCID: PMC8081351 DOI: 10.1039/d0cb00226g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Whole cell-based phenotypic screens have become the primary mode of hit generation in tuberculosis (TB) drug discovery during the last two decades. Different drug screening models have been developed to mirror the complexity of TB disease in the laboratory. As these culture conditions are becoming more and more sophisticated, unraveling the drug target and the identification of the mechanism of action (MOA) of compounds of interest have additionally become more challenging. A good understanding of MOA is essential for the successful delivery of drug candidates for TB treatment due to the high level of complexity in the interactions between Mycobacterium tuberculosis (Mtb) and the TB drug used to treat the disease. There is no single "standard" protocol to follow and no single approach that is sufficient to fully investigate how a drug restrains Mtb. However, with the recent advancements in -omics technologies, there are multiple strategies that have been developed generally in the field of drug discovery that have been adapted to comprehensively characterize the MOAs of TB drugs in the laboratory. These approaches have led to the successful development of preclinical TB drug candidates, and to a better understanding of the pathogenesis of Mtb infection. In this review, we describe a plethora of efforts based upon genetic, metabolomic, biochemical, and computational approaches to investigate TB drug MOAs. We assess these different platforms for their strengths and limitations in TB drug MOA elucidation in the context of Mtb pathogenesis. With an emphasis on the essentiality of MOA identification, we outline the unmet needs in delivering TB drug candidates and provide direction for further TB drug discovery.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
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24
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Oh S, Trifonov L, Yadav VD, Barry CE, Boshoff HI. Tuberculosis Drug Discovery: A Decade of Hit Assessment for Defined Targets. Front Cell Infect Microbiol 2021; 11:611304. [PMID: 33791235 PMCID: PMC8005628 DOI: 10.3389/fcimb.2021.611304] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/20/2022] Open
Abstract
More than two decades have elapsed since the publication of the first genome sequence of Mycobacterium tuberculosis (Mtb) which, shortly thereafter, enabled methods to determine gene essentiality in the pathogen. Despite this, target-based approaches have not yielded drugs that have progressed to clinical testing. Whole-cell screening followed by elucidation of mechanism of action has to date been the most fruitful approach to progressing inhibitors into the tuberculosis drug discovery pipeline although target-based approaches are gaining momentum. This review discusses scaffolds that have been identified over the last decade from screens of small molecule libraries against Mtb or defined targets where mechanism of action investigation has defined target-hit couples and structure-activity relationship studies have described the pharmacophore.
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Affiliation(s)
- Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Lena Trifonov
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Veena D Yadav
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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25
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Ray P, Huggett M, Turner PA, Taylor M, Cleghorn LAT, Early J, Kumar A, Bonnett SA, Flint L, Joerss D, Johnson J, Korkegian A, Mullen S, Moure AL, Davis SH, Murugesan D, Mathieson M, Caldwell N, Engelhart CA, Schnappinger D, Epemolu O, Zuccotto F, Riley J, Scullion P, Stojanovski L, Massoudi L, Robertson GT, Lenaerts AJ, Freiberg G, Kempf DJ, Masquelin T, Hipskind PA, Odingo J, Read KD, Green SR, Wyatt PG, Parish T. Spirocycle MmpL3 Inhibitors with Improved hERG and Cytotoxicity Profiles as Inhibitors of Mycobacterium tuberculosis Growth. ACS OMEGA 2021; 6:2284-2311. [PMID: 33521468 PMCID: PMC7841955 DOI: 10.1021/acsomega.0c05589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Abstract
With the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, there is a pressing need for new oral drugs with novel mechanisms of action. A number of scaffolds with potent anti-tubercular in vitro activity have been identified from phenotypic screening that appear to target MmpL3. However, the scaffolds are typically lipophilic, which facilitates partitioning into hydrophobic membranes, and several contain basic amine groups. Highly lipophilic basic amines are typically cytotoxic against mammalian cell lines and have associated off-target risks, such as inhibition of human ether-à-go-go related gene (hERG) and IKr potassium current modulation. The spirocycle compound 3 was reported to target MmpL3 and displayed promising efficacy in a murine model of acute tuberculosis (TB) infection. However, this highly lipophilic monobasic amine was cytotoxic and inhibited the hERG ion channel. Herein, the related spirocycles (1-2) are described, which were identified following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis. The novel N-alkylated pyrazole portion offered improved physicochemical properties, and optimization led to identification of a zwitterion series, exemplified by lead 29, with decreased HepG2 cytotoxicity as well as limited hERG ion channel inhibition. Strains with mutations in MmpL3 were resistant to 29, and under replicating conditions, 29 demonstrated bactericidal activity against M. tuberculosis. Unfortunately, compound 29 had no efficacy in an acute model of TB infection; this was most likely due to the in vivo exposure remaining above the minimal inhibitory concentration for only a limited time.
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Affiliation(s)
- Peter
C. Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Penelope A. Turner
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Julie Early
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Anuradha Kumar
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Shilah A. Bonnett
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Douglas Joerss
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - James Johnson
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Steven Mullen
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Abraham L. Moure
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan H. Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lisa Massoudi
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne J. Lenaerts
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gail Freiberg
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thierry Masquelin
- Discovery
Chemistry Research, Eli Lilly and Company, Lilly Corporate Centre, MC/87/02/203, G17, Indianapolis, Indiana 46285, United States
| | | | - Joshua Odingo
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
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26
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Grover S, Engelhart CA, Pérez-Herrán E, Li W, Abrahams KA, Papavinasasundaram K, Bean JM, Sassetti CM, Mendoza-Losana A, Besra GS, Jackson M, Schnappinger D. Two-Way Regulation of MmpL3 Expression Identifies and Validates Inhibitors of MmpL3 Function in Mycobacterium tuberculosis. ACS Infect Dis 2021; 7:141-152. [PMID: 33319550 PMCID: PMC7802072 DOI: 10.1021/acsinfecdis.0c00675] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
MmpL3,
an essential mycolate transporter in the inner membrane
of Mycobacterium tuberculosis (Mtb), has been identified as a target of multiple, chemically diverse
antitubercular drugs. However, several of these molecules seem to
have secondary targets and inhibit bacterial growth by more than one
mechanism. Here, we describe a cell-based assay that utilizes two-way
regulation of MmpL3 expression to readily identify MmpL3-specific
inhibitors. We successfully used this assay to identify a novel guanidine-based
MmpL3 inhibitor from a library of 220 compounds that inhibit growth
of Mtb by largely unknown mechanisms. We furthermore
identified inhibitors of cytochrome bc1-aa3 oxidase as one class of off-target hits in whole-cell screens for
MmpL3 inhibitors and report a novel sulfanylacetamide as a potential
QcrB inhibitor.
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Affiliation(s)
- Shipra Grover
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Curtis A. Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Esther Pérez-Herrán
- TB Research Unit, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Katherine A. Abrahams
- Institute of Microbiology and Infection, School of Biological Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - James M. Bean
- Sloan Kettering Institute, New York, New York 10065, United States
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Alfonso Mendoza-Losana
- TB Research Unit, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biological Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
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27
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Abstract
Mycobacterium tuberculosis is a major global human pathogen, and new drugs and new drug targets are urgently required. Cell wall biosynthesis is a major target of current tuberculosis drugs and of new agents under development. Several new classes of molecules appear to have the same target, MmpL3, which is involved in the export and synthesis of the mycobacterial cell wall. However, there is still debate over whether MmpL3 is the primary or only target for these classes. We wanted to confirm the mechanism of resistance for one series. We identified mutations in MmpL3 which led to resistance to the spiral amine series. High-level resistance to these compounds and two other series was conferred by multiple mutations in the same protein (MmpL3). These mutations did not reduce growth rate in culture. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores. The Mycobacterium tuberculosis protein MmpL3 performs an essential role in cell wall synthesis, since it effects the transport of trehalose monomycolates across the inner membrane. Numerous structurally diverse pharmacophores have been identified as inhibitors of MmpL3 largely based on the identification of resistant isolates with mutations in MmpL3. For some compounds, it is possible there are different primary or secondary targets. Here, we have investigated resistance to the spiral amine class of compounds. Isolation and sequencing of resistant mutants demonstrated that all had mutations in MmpL3. We hypothesized that if additional targets of this pharmacophore existed, then successive rounds to generate resistant isolates might reveal mutations in other loci. Since compounds were still active against resistant isolates, albeit with reduced potency, we isolated resistant mutants in this background at higher concentrations. After a second round of isolation with the spiral amine, we found additional mutations in MmpL3. To increase our chance of finding alternative targets, we ran a third round of isolation using a different molecule scaffold (AU1235, an adamantyl urea). Surprisingly, we obtained further mutations in MmpL3. Multiple mutations in MmpL3 increased the level and spectrum of resistance to different pharmacophores but did not incur a fitness cost in vitro. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores. IMPORTANCEMycobacterium tuberculosis is a major global human pathogen, and new drugs and new drug targets are urgently required. Cell wall biosynthesis is a major target of current tuberculosis drugs and of new agents under development. Several new classes of molecules appear to have the same target, MmpL3, which is involved in the export and synthesis of the mycobacterial cell wall. However, there is still debate over whether MmpL3 is the primary or only target for these classes. We wanted to confirm the mechanism of resistance for one series. We identified mutations in MmpL3 which led to resistance to the spiral amine series. High-level resistance to these compounds and two other series was conferred by multiple mutations in the same protein (MmpL3). These mutations did not reduce growth rate in culture. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores.
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28
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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: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [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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29
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Shao M, McNeil M, Cook GM, Lu X. MmpL3 inhibitors as antituberculosis drugs. Eur J Med Chem 2020; 200:112390. [DOI: 10.1016/j.ejmech.2020.112390] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
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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] [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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31
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Yang X, Hu T, Yang X, Xu W, Yang H, Guddat LW, Zhang B, Rao Z. Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO. J Mol Biol 2020; 432:4426-4434. [DOI: 10.1016/j.jmb.2020.05.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/13/2020] [Accepted: 05/25/2020] [Indexed: 10/24/2022]
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32
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Shetye GS, Franzblau SG, Cho S. New tuberculosis drug targets, their inhibitors, and potential therapeutic impact. Transl Res 2020; 220:68-97. [PMID: 32275897 DOI: 10.1016/j.trsl.2020.03.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 11/18/2022]
Abstract
The current tuberculosis (TB) predicament poses numerous challenges and therefore every incremental scientific work and all positive socio-political engagements, are steps taken in the right direction to eradicate TB. Progression of the late stage TB-drug pipeline into the clinics is an immediate deliverable of this global effort. At the same time, fueling basic research and pursuing early discovery work must be sustained to maintain a healthy TB-drug pipeline. This review encompasses a broad analysis of chemotherapeutic strategies that target the DNA replication, protein synthesis, cell wall biosynthesis, energy metabolism and proteolysis of Mycobacterium tuberculosis (Mtb). It includes a status check of the current TB-drug pipeline with a focus on the associated biology, emerging targets, and their promising chemical inhibitors. Potential synergies and/or gaps within or across different chemotherapeutic strategies are systematically reviewed as well.
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Affiliation(s)
- Gauri S Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois.
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33
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Balabon O, Pitta E, Rogacki MK, Meiler E, Casanueva R, Guijarro L, Huss S, Lopez-Roman EM, Santos-Villarejo Á, Augustyns K, Ballell L, Aguirre DB, Bates RH, Cunningham F, Cacho M, Van der Veken P. Optimization of Hydantoins as Potent Antimycobacterial Decaprenylphosphoryl-β-d-Ribose Oxidase (DprE1) Inhibitors. J Med Chem 2020; 63:5367-5386. [DOI: 10.1021/acs.jmedchem.0c00107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olga Balabon
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universitieitsplein 1, 2610 Wilrijk, Belgium
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Eleni Pitta
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universitieitsplein 1, 2610 Wilrijk, Belgium
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Maciej K. Rogacki
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universitieitsplein 1, 2610 Wilrijk, Belgium
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Eugenia Meiler
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Ruth Casanueva
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Laura Guijarro
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Sophie Huss
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Eva Maria Lopez-Roman
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | | | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universitieitsplein 1, 2610 Wilrijk, Belgium
| | - Lluis Ballell
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - David Barros Aguirre
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Robert H. Bates
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Fraser Cunningham
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Monica Cacho
- Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universitieitsplein 1, 2610 Wilrijk, Belgium
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Ma S, Huang Y, Xie F, Gong Z, Zhang Y, Stojkoska A, Xie J. Transport mechanism of Mycobacterium tuberculosis MmpL/S family proteins and implications in pharmaceutical targeting. Biol Chem 2020; 401:331-348. [DOI: 10.1515/hsz-2019-0326] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022]
Abstract
AbstractTuberculosis caused by Mycobacterium tuberculosis remains a serious threat to public health. The M. tuberculosis cell envelope is closely related to its virulence and drug resistance. Mycobacterial membrane large proteins (MmpL) are lipid-transporting proteins of the efflux pump resistance nodulation cell division (RND) superfamily with lipid substrate specificity and non-transport lipid function. Mycobacterial membrane small proteins (MmpS) are small regulatory proteins, and they are also responsible for some virulence-related effects as accessory proteins of MmpL. The MmpL transporters are the candidate targets for the development of anti-tuberculosis drugs. This article summarizes the structure, function, phylogenetics of M. tuberculosis MmpL/S proteins and their roles in host immune response, inhibitors and regulatory system.
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Affiliation(s)
- Shuang Ma
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Yu Huang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Fuling Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Zhen Gong
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Yuan Zhang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Andrea Stojkoska
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400700, China
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Alsayed SSR, Lun S, Luna G, Beh CC, Payne AD, Foster N, Bishai WR, Gunosewoyo H. Design, synthesis, and biological evaluation of novel arylcarboxamide derivatives as anti-tubercular agents. RSC Adv 2020; 10:7523-7540. [PMID: 33014349 PMCID: PMC7497412 DOI: 10.1039/c9ra10663d] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/10/2020] [Indexed: 12/19/2022] Open
Abstract
Our group has previously reported several indolecarboxamides exhibiting potent antitubercular activity. Herein, we rationally designed several arylcarboxamides based on our previously reported homology model and the recently published crystal structure of the mycobacterial membrane protein large 3 (MmpL3). Many analogues showed considerable anti-TB activity against drug-sensitive (DS) Mycobacterium tuberculosis (M. tb) strain. Naphthamide derivatives 13c and 13d were the most active compounds in our study (MIC: 6.55, 7.11 μM, respectively), showing comparable potency to the first line anti-tuberculosis (anti-TB) drug ethambutol (MIC: 4.89 μM). In addition to the naphthamide derivatives, we also identified the quinolone-2-carboxamides and 4-arylthiazole-2-carboxamides as potential MmpL3 inhibitors in which compounds 8i and 18b had MIC values of 9.97 and 9.82 μM, respectively. All four compounds retained their high activity against multidrug-resistant (MDR) and extensively drug-resistant (XDR) M. tb strains. It is worth noting that the two most active compounds 13c and 13d also exhibited the highest selective activity towards DS, MDR and XDR M. tb strains over mammalian cells [IC50 (Vero cells) ≥ 227 μM], indicating their potential lack of cytotoxicity. The four compounds were docked into the MmpL3 active site and were studied for their drug-likeness using Lipinski's rule of five. Synthesis and pharmacological evaluation of arylcarboxamide derivatives based on an antimycobacterial indole-2-carboxamide scaffold. The most active compounds demonstrated activities against MDR and XDR M. tb strains.![]()
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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, Maryland 21231-1044, USA.
| | - Giuseppe Luna
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Chau Chun Beh
- Western Australia School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Bentley 6102, WA, Australia
| | - Alan D Payne
- School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Neil Foster
- Western Australia School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Bentley 6102, WA, Australia
| | - William R Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, 1550, Orleans Street, Baltimore, Maryland 21231-1044, USA. .,Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815-6789, USA
| | - Hendra Gunosewoyo
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
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Promiscuous Targets for Antitubercular Drug Discovery: The Paradigm of DprE1 and MmpL3. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10020623] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The development and spread of Mycobacterium tuberculosis multi-drug resistant strains still represent a great global health threat, leading to an urgent need for novel anti-tuberculosis drugs. Indeed, in the last years, several efforts have been made in this direction, through a number of high-throughput screenings campaigns, which allowed for the identification of numerous hit compounds and novel targets. Interestingly, several independent screening assays identified the same proteins as the target of different compounds, and for this reason, they were named “promiscuous” targets. These proteins include DprE1, MmpL3, QcrB and Psk13, and are involved in the key pathway for M. tuberculosis survival, thus they should represent an Achilles’ heel which could be exploited for the development of novel effective drugs. Indeed, among the last molecules which entered clinical trials, four inhibit a promiscuous target. Within this review, the two most promising promiscuous targets, the oxidoreductase DprE1 involved in arabinogalactan synthesis and the mycolic acid transporter MmpL3 are discussed, along with the latest advancements in the development of novel inhibitors with anti-tubercular activity.
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Khaligh NG, Abbo H, Titinchi SJ, Johan MR. An Overview of Recent Advances in Biological and Pharmaceutical Developments of Fluoro-containing Drugs. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824666191213123930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
:
This review article provides a brief assessment of the biological and pharmaceutical
developments of fluorinated drugs. It also discusses possible impacts on the further
development of new fluoro-containing pharmaceuticals. Structural aspects of new
drug-candidates currently under development and their biological properties, therapeutic
potential and syntheses are critically evaluated
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Affiliation(s)
- Nader G. Khaligh
- Nanotechnology and Catalysis Research Center, Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hanna Abbo
- Department of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Salam J.J. Titinchi
- Department of Chemistry, University of the Western Cape, Cape Town, South Africa
| | - Mohd R. Johan
- Nanotechnology and Catalysis Research Center, Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
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38
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Zhang B, Li J, Yang X, Wu L, Zhang J, Yang Y, Zhao Y, Zhang L, Yang X, Yang X, Cheng X, Liu Z, Jiang B, Jiang H, Guddat LW, Yang H, Rao Z. Crystal Structures of Membrane Transporter MmpL3, an Anti-TB Drug Target. Cell 2019; 176:636-648.e13. [PMID: 30682372 DOI: 10.1016/j.cell.2019.01.003] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/22/2018] [Accepted: 12/31/2018] [Indexed: 01/01/2023]
Abstract
Despite intensive efforts to discover highly effective treatments to eradicate tuberculosis (TB), it remains as a major threat to global human health. For this reason, new TB drugs directed toward new targets are highly coveted. MmpLs (Mycobacterial membrane proteins Large), which play crucial roles in transporting lipids, polymers and immunomodulators and which also extrude therapeutic drugs, are among the most important therapeutic drug targets to emerge in recent times. Here, crystal structures of mycobacterial MmpL3 alone and in complex with four TB drug candidates, including SQ109 (in Phase 2b-3 clinical trials), are reported. MmpL3 consists of a periplasmic pore domain and a twelve-helix transmembrane domain. Two Asp-Tyr pairs centrally located in this domain appear to be key facilitators of proton-translocation. SQ109, AU1235, ICA38, and rimonabant bind inside the transmembrane region and disrupt these Asp-Tyr pairs. This structural data will greatly advance the development of MmpL3 inhibitors as new TB drugs.
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Affiliation(s)
- Bing Zhang
- 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
| | - Jun Li
- 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.
| | - Xiaolin Yang
- 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
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Jia Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yang Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yao Zhao
- 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
| | - Lu Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300353, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaobao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xi Cheng
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhijie Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, 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.
| | - Zihe Rao
- 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; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300353, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Laboratory of Structural Biology, Tsinghua University, Beijing, 100084, China.
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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] [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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40
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Identification of New MmpL3 Inhibitors by Untargeted and Targeted Mutant Screens Defines MmpL3 Domains with Differential Resistance. Antimicrob Agents Chemother 2019; 63:AAC.00547-19. [PMID: 31405862 DOI: 10.1128/aac.00547-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/26/2019] [Indexed: 12/13/2022] Open
Abstract
The Mycobacterium tuberculosis mycolate flippase MmpL3 has been the proposed target for multiple inhibitors with diverse chemical scaffolds. This diversity in chemical scaffolds has made it difficult to predict compounds that inhibit MmpL3 without whole-genome sequencing of isolated resistant mutants. Here, we describe the identification of four new inhibitors that select for resistance mutations in mmpL3. Using these resistant mutants, we conducted a targeted whole-cell phenotypic screen of 163 novel M. tuberculosis growth inhibitors for differential growth inhibition of wild-type M. tuberculosis compared to the growth of a pool of 24 unique mmpL3 mutants. The screen successfully identified six additional putative MmpL3 inhibitors. The compounds were bactericidal both in vitro and against intracellular M. tuberculosis M. tuberculosis cells treated with these compounds were shown to accumulate trehalose monomycolates, have reduced levels of trehalose dimycolate, and displace an MmpL3-specific probe, supporting MmpL3 as the target. The inhibitors were mycobacterium specific, with several also showing activity against the nontuberculous mycobacterial species M. abscessus Cluster analysis of cross-resistance profiles generated by dose-response experiments for each combination of 13 MmpL3 inhibitors against each of the 24 mmpL3 mutants defined two clades of inhibitors and two clades of mmpL3 mutants. Pairwise combination studies of the inhibitors revealed interactions that were specific to the clades identified in the cross-resistance profiling. Additionally, modeling of resistance-conferring substitutions to the MmpL3 crystal structure revealed clade-specific localization of the residues to specific domains of MmpL3, with the clades showing differential resistance. Several compounds exhibited high solubility and stability in microsomes and low cytotoxicity in macrophages, supporting their further development. The combined study of multiple mutants and novel compounds provides new insights into structure-function interactions of MmpL3 and small-molecule inhibitors.
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41
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Advancing the Therapeutic Potential of Indoleamides for Tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.00343-19. [PMID: 31010860 PMCID: PMC6591635 DOI: 10.1128/aac.00343-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/12/2019] [Indexed: 12/18/2022] Open
Abstract
Indole-2-carboxamide derivatives are inhibitors of MmpL3, the cell wall-associated mycolic acid transporter of Mycobacterium tuberculosis. In the present study, we characterized indoleamide effects on bacterial cell morphology and reevaluated pharmacokinetics and in vivo efficacy using an optimized oral formulation. Indole-2-carboxamide derivatives are inhibitors of MmpL3, the cell wall-associated mycolic acid transporter of Mycobacterium tuberculosis. In the present study, we characterized indoleamide effects on bacterial cell morphology and reevaluated pharmacokinetics and in vivo efficacy using an optimized oral formulation. Morphologically, indoleamide-treated M. tuberculosis cells demonstrated significantly higher numbers of dimples near the poles or septum, which may serve as the mechanism of cell death for this bactericidal scaffold. Using the optimized formulation, an expanded-spectrum indoleamide, compound 2, showed significantly improved pharmacokinetic (PK) parameters and in vivo efficacy in mouse infection models. In a comparative study, compound 2 showed superior efficacy over compound 3 (NITD-304) in a high-dose aerosol mouse infection model. Since indoleamides are equally active on drug-resistant M. tuberculosis, these findings demonstrate the therapeutic potential of this novel scaffold for the treatment of both drug-susceptible and drug-resistant tuberculosis.
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42
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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: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [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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43
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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44
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Rogacki MK, Pitta E, Balabon O, Huss S, Lopez-Roman EM, Argyrou A, Blanco-Ruano D, Cacho M, Vande Velde CML, Augustyns K, Ballell L, Barros D, Bates RH, Cunningham F, Van der Veken P. Identification and Profiling of Hydantoins-A Novel Class of Potent Antimycobacterial DprE1 Inhibitors. J Med Chem 2018; 61:11221-11249. [PMID: 30500189 DOI: 10.1021/acs.jmedchem.8b01356] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tuberculosis is the leading cause of death worldwide from infectious diseases. With the development of drug-resistant strains of Mycobacterium tuberculosis, there is an acute need for new medicines with novel modes of action. Herein, we report the discovery and profiling of a novel hydantoin-based family of antimycobacterial inhibitors of the decaprenylphospho-β-d-ribofuranose 2-oxidase (DprE1). In this study, we have prepared a library of more than a 100 compounds and evaluated them for their biological and physicochemical properties. The series is characterized by high enzymatic and whole-cell activity, low cytotoxicity, and a good overall physicochemical profile. In addition, we show that the series acts via reversible inhibition of the DprE1 enzyme. Overall, the novel compound family forms an attractive base for progression to further stages of optimization and may provide a promising drug candidate in the future.
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Affiliation(s)
- Maciej K Rogacki
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium.,Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Eleni Pitta
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium.,Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Olga Balabon
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium.,Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Sophie Huss
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Eva Maria Lopez-Roman
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Argyrides Argyrou
- Platform Technology and Science , GlaxoSmithKline , Stevenage SG1 2NY , U.K
| | - Delia Blanco-Ruano
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Monica Cacho
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Christophe M L Vande Velde
- Faculty of Applied Engineering, Advanced Reactor Technology , University of Antwerp , Groenenborgerlaan 171 , 2020 Antwerpen , Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
| | - Lluis Ballell
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - David Barros
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Robert H Bates
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Fraser Cunningham
- Diseases of the Developing World (DDW), Tres Cantos Medicines Development Campus (TCMDC) , GlaxoSmithKline , Severo Ochoa 2 , Tres Cantos, 28760 Madrid , Spain
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
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45
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Guardia A, Baiget J, Cacho M, Pérez A, Ortega-Guerra M, Nxumalo W, Khanye SD, Rullas J, Ortega F, Jiménez E, Pérez-Herrán E, Fraile-Gabaldón MT, Esquivias J, Fernández R, Porras-De Francisco E, Encinas L, Alonso M, Giordano I, Rivero C, Miguel-Siles J, Osende JG, Badiola KA, Rutledge PJ, Todd MH, Remuiñán M, Alemparte C. Easy-To-Synthesize Spirocyclic Compounds Possess Remarkable in Vivo Activity against Mycobacterium tuberculosis. J Med Chem 2018; 61:11327-11340. [PMID: 30457865 DOI: 10.1021/acs.jmedchem.8b01533] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Society urgently needs new, effective medicines for the treatment of tuberculosis. To kick-start the required hit-to-lead campaigns, the libraries of pharmaceutical companies have recently been evaluated for starting points. The GlaxoSmithKline (GSK) library yielded many high-quality hits, and the associated data were placed in the public domain to stimulate engagement by the wider community. One such series, the spiro compounds, are described here. The compounds were explored by a combination of traditional in-house research and open source methods. The series benefits from a particularly simple structure and a short associated synthetic chemistry route. Many members of the series displayed striking potency and low toxicity, and highly promising in vivo activity in a mouse model was confirmed with one of the analogues. Ultimately the series was discontinued due to concerns over safety, but the associated data remain public domain, empowering others to resume the series if the perceived deficiencies can be overcome.
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Affiliation(s)
- Ana Guardia
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Jessica Baiget
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Mónica Cacho
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Arancha Pérez
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Montserrat Ortega-Guerra
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Winston Nxumalo
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Setshaba D Khanye
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Joaquín Rullas
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Fátima Ortega
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Elena Jiménez
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Esther Pérez-Herrán
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | | | - Jorge Esquivias
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Raquel Fernández
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Esther Porras-De Francisco
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Lourdes Encinas
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Marta Alonso
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Ilaria Giordano
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Cristina Rivero
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Juan Miguel-Siles
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Javier G Osende
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Katrina A Badiola
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Peter J Rutledge
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia
| | - Matthew H Todd
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia.,School of Pharmacy , University College London , 29-39 Brunswick Square , London WC1N 1AX , U.K
| | - Modesto Remuiñán
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
| | - Carlos Alemparte
- GlaxoSmithKline , Tres Cantos Medicines Development Campus, Severo Ochoa 2 , 28760 Tres Cantos , Madrid , Spain
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46
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Shetty A, Xu Z, Lakshmanan U, Hill J, Choong ML, Chng SS, Yamada Y, Poulsen A, Dick T, Gengenbacher M. Novel Acetamide Indirectly Targets Mycobacterial Transporter MmpL3 by Proton Motive Force Disruption. Front Microbiol 2018; 9:2960. [PMID: 30564212 PMCID: PMC6289072 DOI: 10.3389/fmicb.2018.02960] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/16/2018] [Indexed: 02/05/2023] Open
Abstract
To identify novel inhibitors of Mycobacterium tuberculosis cell envelope biosynthesis, we employed a two-step approach. First, we screened the diverse synthetic small molecule 71,544-compound Enamine library for growth inhibitors using the non-pathogenic surrogate Mycobacterium bovis BCG as screening strain and turbidity as readout. Second, 16 confirmed hits were tested for their ability to induce the cell envelope stress responsive promoter piniBAC controlling expression of red fluorescent protein in an M. bovis BCG reporter strain. Using a fluorescence readout, the acetamide E11 was identified. Resistant mutant selection and whole genome sequencing revealed the mycolic acid transporter Mmpl3 as a candidate target of E11. Biochemical analysis using mycobacterial spheroplasts and various membrane assays suggest that E11 indirectly inhibits MmpL3-facilitated translocation of trehalose monomycolates by proton motive force disruption. E11 showed potent bactericidal activity against growing and non-growing M. tuberculosis, low cytotoxic, and hemolytic activity and a dynamic structure activity relationship. In addition to activity against M. tuberculosis, E11 was active against the non-tuberculous mycobacterium M. abscessus, an emerging opportunistic pathogen. In conclusion, we identified a novel bactericidal anti-mycobacterial lead compound targeting MmpL3 providing an attractive starting point for optimization.
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Affiliation(s)
- Annanya Shetty
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Antimicrobial Drug Discovery Laboratory, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhujun Xu
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | | | - Jeffrey Hill
- Experimental Therapeutics Center, ASTAR, Singapore, Singapore
| | | | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, Singapore.,Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yoshiyuki Yamada
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anders Poulsen
- Experimental Therapeutics Center, ASTAR, Singapore, Singapore
| | - Thomas Dick
- Antimicrobial Drug Discovery Laboratory, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Martin Gengenbacher
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
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47
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Richter A, Strauch A, Chao J, Ko M, Av-Gay Y. Screening of Preselected Libraries Targeting Mycobacterium abscessus for Drug Discovery. Antimicrob Agents Chemother 2018; 62:e00828-18. [PMID: 30012760 PMCID: PMC6125491 DOI: 10.1128/aac.00828-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/08/2018] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium abscessus is intrinsically resistant to many antimycobacterial antibiotics, which presents serious problems in therapy. Here, we describe the development of a novel phenotype-based microscopic and computerized imaging drug screening approach. A pilot screen of 568 compounds from two libraries identified 17 hits. Eleven of these compounds are described for the first time as active against M. abscessus The impact of growth media on the activity of these compounds was tested, revealing that cation-adjusted Mueller-Hinton broth (MHII) supports better growth of actively replicating M. abscessus and improves the activity of associated compounds.
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Affiliation(s)
- Adrian Richter
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angelika Strauch
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joseph Chao
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mary Ko
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yossef Av-Gay
- Division of Infectious Diseases, Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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48
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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] [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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49
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HC2091 Kills Mycobacterium tuberculosis by Targeting the MmpL3 Mycolic Acid Transporter. Antimicrob Agents Chemother 2018; 62:AAC.02459-17. [PMID: 29661875 DOI: 10.1128/aac.02459-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [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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50
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AlMatar M, Makky EA, Var I, Kayar B, Köksal F. Novel compounds targeting InhA for TB therapy. Pharmacol Rep 2018; 70:217-226. [DOI: 10.1016/j.pharep.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/26/2017] [Accepted: 09/12/2017] [Indexed: 02/07/2023]
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