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Caradec T, Plé C, Sicoli G, Petrov R, Pradel E, Sobieski C, Antoine R, Orio M, Herledan A, Willand N, Hartkoorn RC. Small molecule MarR modulators potentiate metronidazole antibiotic activity in aerobic E. coli by inducing activation by the nitroreductase NfsA. J Biol Chem 2024; 300:107431. [PMID: 38825006 PMCID: PMC11259696 DOI: 10.1016/j.jbc.2024.107431] [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: 02/24/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
Antibiotic-resistant Enterobacterales pose a major threat to healthcare systems worldwide, necessitating the development of novel strategies to fight such hard-to-kill bacteria. One potential approach is to develop molecules that force bacteria to hyper-activate prodrug antibiotics, thus rendering them more effective. In the present work, we aimed to obtain proof-of-concept data to support that small molecules targeting transcriptional regulators can potentiate the antibiotic activity of the prodrug metronidazole (MTZ) against Escherichia coli under aerobic conditions. By screening a chemical library of small molecules, a series of structurally related molecules were identified that had little inherent antibiotic activity but showed substantial activity in combination with ineffective concentrations of MTZ. Transcriptome analyses, functional genetics, thermal shift assays, and electrophoretic mobility shift assays were then used to demonstrate that these MTZ boosters target the transcriptional repressor MarR, resulting in the upregulation of the marRAB operon and its downstream MarA regulon. The associated upregulation of the flavin-containing nitroreductase, NfsA, was then shown to be critical for the booster-mediated potentiation of MTZ antibiotic activity. Transcriptomic studies, biochemical assays, and electron paramagnetic resonance measurements were then used to show that under aerobic conditions, NfsA catalyzed 1-electron reduction of MTZ to the MTZ radical anion which in turn induced lethal DNA damage in E. coli. This work reports the first example of prodrug boosting in Enterobacterales by transcriptional modulators and highlights that MTZ antibiotic activity can be chemically induced under anaerobic growth conditions.
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Affiliation(s)
- Thibault Caradec
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Coline Plé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Giuseppe Sicoli
- CNRS UMR 8516, Univ. Lille, LASIRE - Laboratory of Advanced Spectroscopy on Interactions, Reactivity and Environment, Villeneuve d'Ascq, France
| | - Ravil Petrov
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Elizabeth Pradel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Cécilia Sobieski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Maylis Orio
- Aix Marseille Univ., CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, Lille, France
| | - Ruben Christiaan Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France.
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Grosse C, Sigoillot M, Megalizzi V, Tanina A, Willand N, Baulard AR, Wintjens R. Crystal structure of the Mycobacterium tuberculosis VirS regulator reveals its interaction with the lead compound SMARt751. J Struct Biol 2024; 216:108090. [PMID: 38548139 DOI: 10.1016/j.jsb.2024.108090] [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: 01/23/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Ethionamide (ETO) is a prodrug that is primarily used as a second-line agent in the treatment of tuberculosis. Among the bacterial ETO activators, the monooxygenase MymA has been recently identified, and its expression is regulated by the mycobacterial regulator VirS. The discovery of VirS ligands that can enhance mymA expression and thereby increase the antimycobacterial efficacy of ETO, has led to the development of a novel therapeutic strategy against tuberculosis. This strategy involves the selection of preclinical candidates, including SMARt751. We report the first crystal structure of the AraC-like regulator VirS, in complex with SMARt751, refined at 1.69 Å resolution. Crystals were obtained via an in situ proteolysis method in the requisite presence of SMARt751. The elucidated structure corresponds to the ligand-binding domain of VirS, adopting an α/β fold with structural similarities to H-NOX domains. Within the VirS structure, SMARt751 is situated in a completely enclosed hydrophobic cavity, where it forms hydrogen bonds with Asn11 and Asn149 as well as van der Waals contacts with various hydrophobic amino acids. Comprehensive structural comparisons within the AraC family of transcriptional regulators are conducted and analyzed to figure out the effects of the SMARt751 binding on the regulatory activity of VirS.
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Affiliation(s)
- Camille Grosse
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Maud Sigoillot
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium
| | - Véronique Megalizzi
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium
| | - Abdalkarim Tanina
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - René Wintjens
- Unit of Microbiology, Bioorganic and Macromolecular Chemistry, Department of Research in Drug Development, Faculty of Pharmacy, Université Libre de Bruxelles, Belgium.
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Le Mouëllic W, Poquet Y, Neyrolles O. Dual-action compounds unleash a one-two punch against tuberculosis. Cell Chem Biol 2024; 31:627-629. [PMID: 38640900 DOI: 10.1016/j.chembiol.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
In this issue of Cell Chemical Biology, Gries et al.1 employ an innovative screening approach to identify anti-tuberculosis compounds with dual modes of action: anti-virulence against the type VII secretion system ESX-1 and enhanced ethionamide efficacy. These compounds hold promise for developing multi-target tuberculosis drugs with potential clinical applications.
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Affiliation(s)
- Wendy Le Mouëllic
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yannick Poquet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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Gries R, Chhen J, van Gumpel E, Theobald SJ, Sonnenkalb L, Utpatel C, Metzen F, Koch M, Dallenga T, Djaout K, Baulard A, Dal Molin M, Rybniker J. Discovery of dual-active ethionamide boosters inhibiting the Mycobacterium tuberculosis ESX-1 secretion system. Cell Chem Biol 2024; 31:699-711.e6. [PMID: 38181799 DOI: 10.1016/j.chembiol.2023.12.007] [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: 01/17/2023] [Revised: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Drug-resistant Mycobacterium tuberculosis (Mtb) remains a major public health concern requiring complementary approaches to standard anti-tuberculous regimens. Anti-virulence molecules or compounds that enhance the activity of antimicrobial prodrugs are promising alternatives to conventional antibiotics. Exploiting host cell-based drug discovery, we identified an oxadiazole compound (S3) that blocks the ESX-1 secretion system, a major virulence factor of Mtb. S3-treated mycobacteria showed impaired intracellular growth and a reduced ability to lyse macrophages. RNA sequencing experiments of drug-exposed bacteria revealed strong upregulation of a distinct set of genes including ethA, encoding a monooxygenase activating the anti-tuberculous prodrug ethionamide. Accordingly, we found a strong ethionamide boosting effect in S3-treated Mtb. Extensive structure-activity relationship experiments revealed that anti-virulence and ethionamide-boosting activity can be uncoupled by chemical modification of the primary hit molecule. To conclude, this series of dual-active oxadiazole compounds targets Mtb via two distinct mechanisms of action.
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Affiliation(s)
- Raphael Gries
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Jason Chhen
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Edeltraud van Gumpel
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Lindsay Sonnenkalb
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Fabian Metzen
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Tobias Dallenga
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Cellular Microbiology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Kamel Djaout
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Alain Baulard
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Michael Dal Molin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany.
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Dixit A, Freschi L, Vargas R, Gröschel MI, Nakhoul M, Tahseen S, Alam SMM, Kamal SMM, Skrahina A, Basilio RP, Lim DR, Ismail N, Farhat MR. Estimation of country-specific tuberculosis resistance antibiograms using pathogen genomics and machine learning. BMJ Glob Health 2024; 9:e013532. [PMID: 38548342 PMCID: PMC10982777 DOI: 10.1136/bmjgh-2023-013532] [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: 07/26/2023] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Global tuberculosis (TB) drug resistance (DR) surveillance focuses on rifampicin. We examined the potential of public and surveillance Mycobacterium tuberculosis (Mtb) whole-genome sequencing (WGS) data, to generate expanded country-level resistance prevalence estimates (antibiograms) using in silico resistance prediction. METHODS We curated and quality-controlled Mtb WGS data. We used a validated random forest model to predict phenotypic resistance to 12 drugs and bias-corrected for model performance, outbreak sampling and rifampicin resistance oversampling. Validation leveraged a national DR survey conducted in South Africa. RESULTS Mtb isolates from 29 countries (n=19 149) met sequence quality criteria. Global marginal genotypic resistance among mono-resistant TB estimates overlapped with the South African DR survey, except for isoniazid, ethionamide and second-line injectables, which were underestimated (n=3134). Among multidrug resistant (MDR) TB (n=268), estimates overlapped for the fluoroquinolones but overestimated other drugs. Globally pooled mono-resistance to isoniazid was 10.9% (95% CI: 10.2-11.7%, n=14 012). Mono-levofloxacin resistance rates were highest in South Asia (Pakistan 3.4% (0.1-11%), n=111 and India 2.8% (0.08-9.4%), n=114). Given the recent interest in drugs enhancing ethionamide activity and their expected activity against isolates with resistance discordance between isoniazid and ethionamide, we measured this rate and found it to be high at 74.4% (IQR: 64.5-79.7%) of isoniazid-resistant isolates predicted to be ethionamide susceptible. The global susceptibility rate to pyrazinamide and levofloxacin among MDR was 15.1% (95% CI: 10.2-19.9%, n=3964). CONCLUSIONS This is the first attempt at global Mtb antibiogram estimation. DR prevalence in Mtb can be reliably estimated using public WGS and phenotypic resistance prediction for key antibiotics, but public WGS data demonstrates oversampling of isolates with higher resistance levels than MDR. Nevertheless, our results raise concerns about the empiric use of short-course fluoroquinolone regimens for drug-susceptible TB in South Asia and indicate underutilisation of ethionamide in MDR treatment.
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Affiliation(s)
- Avika Dixit
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Center for Computational Biomedicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Nakhoul
- Informatics and Analytics Department, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sabira Tahseen
- National Tuberculosis Control Programme, Islamabad, Pakistan
| | - S M Masud Alam
- Ministry of Health and Family Welfare, Kolkata, West Bengal, India
| | - S M Mostofa Kamal
- National Institute of Diseases of the Chest and Hospital, Dhaka, Bangladesh
| | - Alena Skrahina
- Republican Scientific and Practical Center for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Ramon P Basilio
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Dodge R Lim
- Research Institute for Tropical Medicine, Muntinlupa City, Philippines
| | - Nazir Ismail
- Clinical Microbiology and Infectious Diseases, University of the Witwatersrand Johannesburg Faculty of Health Sciences, Johannesburg, South Africa
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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6
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Chikhale RV, Eldesoky GE, Kolpe MS, Suryawanshi VS, Patil PC, Bhowmick S. Identification of Mycobacterium tuberculosis transcriptional repressor EthR inhibitors: Shape-based search and machine learning studies. Heliyon 2024; 10:e26802. [PMID: 38434349 PMCID: PMC10907797 DOI: 10.1016/j.heliyon.2024.e26802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/16/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024] Open
Abstract
Tuberculosis has been a challenge to the world since prehistoric times, and with the advent of drug-resistant strains, it has become more challenging to treat this infection. Ethionamide (ETH), a second-line drug, acts as a prodrug and targets mycolic acid synthesis by targeting the enoyl-acyl carrier protein reductase (InhA) enzyme. Mycobacterium tuberculosis (Mtb) EthR is an ethA gene repressor required to activate prodrug ETH. Recent studies suggest targeting the EthR could lead to newer drug molecules that would help better activate the ETH or complement this process. In this report, we have attempted and successfully identified three new molecules from the drug repurposing library that can target EthR protein and function as ETH boosters. These molecules were obtained after rigorous filtering of the database for their physicochemical, toxicological properties and safety. The molecular docking, molecular dynamics simulations and binding energy studies yielded three compounds, Ethyl (2-amino-4-((4-fluorobenzyl)amino)phenyl)carbamate) (L1), 2-((2,2-Difluorobenzo [d] [1,3]dioxol-5-yl)amino)-2-oxoethyl (E)-3-(5-bromofuran-2-yl)acrylate (L2), and N-(2,3-Dihydrobenzo [b] [1,4]dioxin-6-yl)-4-(2-((4-fluorophenyl)amino)-2-oxoethoxy)-3-methoxy benzamide (L3) are potential EthR inhibitors. We applied machine learning methods to evaluate these molecules for toxicity and synthesisability, suggesting safety and ease of synthesis for these molecules. These molecules are known for other pharmacological activities and can be repurposed faster as adjuvant therapy for tuberculosis.
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Affiliation(s)
- Rupesh V. Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK
| | - Gaber E. Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mahima Sudhir Kolpe
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Vikramsinh Sardarsinh Suryawanshi
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
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Maitre T, Baulard A, Aubry A, Veziris N. Optimizing the use of current antituberculosis drugs to overcome drug resistance in Mycobacterium tuberculosis. Infect Dis Now 2024; 54:104807. [PMID: 37839674 DOI: 10.1016/j.idnow.2023.104807] [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: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Antibiotic-resistant tuberculosis continues to be one of the major threats to global tuberculosis control. After a hiatus of over 40 years in antituberculosis drug development, the last decade has seen a resurgence of research, yielding a number of promising compounds in the tuberculosis drug pipeline, with some that are now game changers in the treatment of MDRTB. Despite this progress, there are still obstacles restricting the use of these molecules as first-line drugs. The quick appearance of bacteria resistant to these new treatments highlights a continuing need to fuel the discovery and development of new molecules. With this in mind, alternative strategies aimed at optimizing the utilization of existing antituberculosis agents are currently under evaluation. They are focused on enhancing the efficacy of antibiotics against their bacterial targets, primarily by augmenting the quantity of antibiotic that engages with these targets. This objective can be achieved through two primary approaches: (1) Provided that toxicity concerns are not a limiting factor, increased dosing is a viable avenue, as demonstrated by rifampicin, isoniazid, and fluoroquinolones, for which escalated dosing has been effective; and (2) Employing enhancers such as drug activator boosters (ethionamide), efflux pump inhibitors, or hydrolytic enzyme inhibitors (kanamycin) can elevate the concentration of antibiotics in bacterial cells. These strategies offer the potential to mitigate antibiotic obsolescence and complement the discovery of new antibiotics.
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Affiliation(s)
- Thomas Maitre
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; Service de Pneumologie et d'Oncologie Thoracique, Centre constitutif maladies rares, Hôpital Tenon, AP-HP, Sorbonne-Université, Paris, France.
| | - Alain Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Alexandra Aubry
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Universite, Hôpital Pitié Salpêtrière, Laboratoire de Bactériologie-Hygiene, Centre National de Référence des Mycobactéries, Paris France
| | - Nicolas Veziris
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), UMR 1135, Paris, France; AP-HP, Sorbonne-Université, Hôpital Saint-Antoine, Département de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Hôpital Pitié-Salpêtrière, Paris, France
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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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Villemagne B, Faion L, Tangara S, Willand N. Recent advances in Fragment-based strategies against tuberculosis. Eur J Med Chem 2023; 258:115569. [PMID: 37423127 DOI: 10.1016/j.ejmech.2023.115569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Tuberculosis remains one of the world's leading infectious disease killers, causing more than 1.5 million of deaths each year. It is therefore a priority to discover and develop new classes of anti-tuberculosis drugs to design new treatments in order to fight the increasing burden of resistant-tuberculosis. Fragment-based drug discovery (FBDD) relies on the identification of small molecule hits, further improved to high-affinity ligands through three main approaches: fragment growing, merging and linking. The aim of this review is to highlight the recent progresses made in fragment-based approaches for the discovery and development of Mycobacterium tuberculosis inhibitors in a wide range of pathways. Hit discovery, hit-to-lead optimization, SAR and binding mode when available are discussed.
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Affiliation(s)
- Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
| | - Léo Faion
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Salia Tangara
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
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10
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Chopra H, Mohanta YK, Rauta PR, Ahmed R, Mahanta S, Mishra PK, Panda P, Rabaan AA, Alshehri AA, Othman B, Alshahrani MA, Alqahtani AS, AL Basha BA, Dhama K. An Insight into Advances in Developing Nanotechnology Based Therapeutics, Drug Delivery, Diagnostics and Vaccines: Multidimensional Applications in Tuberculosis Disease Management. Pharmaceuticals (Basel) 2023; 16:581. [PMID: 37111338 PMCID: PMC10145450 DOI: 10.3390/ph16040581] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/29/2023] Open
Abstract
Tuberculosis (TB), one of the deadliest contagious diseases, is a major concern worldwide. Long-term treatment, a high pill burden, limited compliance, and strict administration schedules are all variables that contribute to the development of MDR and XDR tuberculosis patients. The rise of multidrug-resistant strains and a scarcity of anti-TB medications pose a threat to TB control in the future. As a result, a strong and effective system is required to overcome technological limitations and improve the efficacy of therapeutic medications, which is still a huge problem for pharmacological technology. Nanotechnology offers an interesting opportunity for accurate identification of mycobacterial strains and improved medication treatment possibilities for tuberculosis. Nano medicine in tuberculosis is an emerging research field that provides the possibility of efficient medication delivery using nanoparticles and a decrease in drug dosages and adverse effects to boost patient compliance with therapy and recovery. Due to their fascinating characteristics, this strategy is useful in overcoming the abnormalities associated with traditional therapy and leads to some optimization of the therapeutic impact. It also decreases the dosing frequency and eliminates the problem of low compliance. To develop modern diagnosis techniques, upgraded treatment, and possible prevention of tuberculosis, the nanoparticle-based tests have demonstrated considerable advances. The literature search was conducted using Scopus, PubMed, Google Scholar, and Elsevier databases only. This article examines the possibility of employing nanotechnology for TB diagnosis, nanotechnology-based medicine delivery systems, and prevention for the successful elimination of TB illnesses.
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Affiliation(s)
- Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - Yugal Kishore Mohanta
- Nanobiotechnology and Translational Knowledge Laboratory, Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), Techno City, 9th Mile, Ri-Bhoi, Baridua 793101, Meghalaya, India
| | | | - Ramzan Ahmed
- Nanobiotechnology and Translational Knowledge Laboratory, Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya (USTM), Techno City, 9th Mile, Ri-Bhoi, Baridua 793101, Meghalaya, India
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology (NIELIT), Guwahati Centre, Guwahati 781008, Assam, India
| | | | - Paramjot Panda
- School of Biological Sciences, AIPH University, Bhubaneswar 754001, Odisha, India
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Basim Othman
- Department of Public Health, Faculty of Applied Medical Sciences, Albaha University, Albaha 65779, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ali S. Alqahtani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha 61481, Saudi Arabia
| | - Baneen Ali AL Basha
- Laboratory Department, King Fahad Specialist Hospital, Dammam 32253, Saudi Arabia
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India
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11
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Singh V, Dziwornu GA, Chibale K. The implication of Mycobacterium tuberculosis-mediated metabolism of targeted xenobiotics. Nat Rev Chem 2023; 7:340-354. [PMID: 37117810 PMCID: PMC10026799 DOI: 10.1038/s41570-023-00472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2023] [Indexed: 03/29/2023]
Abstract
Drug metabolism is generally associated with liver enzymes. However, in the case of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), Mtb-mediated drug metabolism plays a significant role in treatment outcomes. Mtb is equipped with enzymes that catalyse biotransformation reactions on xenobiotics with consequences either in its favour or as a hindrance by deactivating or activating chemical entities, respectively. Considering the range of chemical reactions involved in the biosynthetic pathways of Mtb, information related to the biotransformation of antitubercular compounds would provide opportunities for the development of new chemical tools to study successful TB infections while also highlighting potential areas for drug discovery, host-directed therapy, dose optimization and elucidation of mechanisms of action. In this Review, we discuss Mtb-mediated biotransformations and propose a holistic approach to address drug metabolism in TB drug discovery and related areas. ![]()
Mycobacterium tuberculosis-mediated metabolism of xenobiotics poses an important research question for antitubercular drug discovery. Identification of the metabolic fate of compounds can inform requisite structure–activity relationship strategies early on in a drug discovery programme towards improving the properties of the compound.
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Affiliation(s)
- Vinayak Singh
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Godwin Akpeko Dziwornu
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- grid.7836.a0000 0004 1937 1151Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
- grid.7836.a0000 0004 1937 1151Department of Chemistry, University of Cape Town, Rondebosch, South Africa
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12
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Implications of Fragment-Based Drug Discovery in Tuberculosis and HIV. Pharmaceuticals (Basel) 2022; 15:ph15111415. [PMID: 36422545 PMCID: PMC9692459 DOI: 10.3390/ph15111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) remains a global health problem and the emergence of HIV has further worsened it. Long chemotherapy and the emergence of drug-resistance strains of Mycobacterium tuberculosis as well as HIV has aggravated the problem. This demands urgent the need to develop new anti-tuberculosis and antiretrovirals to treat TB and HIV. The lack of diversity in drugs designed using traditional approaches is a major disadvantage and limits the treatment options. Therefore, new technologies and approaches are required to solve the current issues and enhance the production of drugs. Interestingly, fragment-based drug discovery (FBDD) has gained an advantage over high-throughput screenings as FBDD has enabled rapid and efficient progress to develop potent small molecule compounds that specifically bind to the target. Several potent inhibitor compounds of various targets have been developed using FBDD approach and some of them are under progression to clinical trials. In this review, we emphasize some of the important targets of mycobacteria and HIV. We also discussed about the target-based druggable molecules that are identified using the FBDD approach, use of these druggable molecules to identify novel binding sites on the target and assays used to evaluate inhibitory activities of these identified druggable molecules on the biological activity of the targets.
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13
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Roubert C, Fontaine E, Upton AM. “Upcycling” known molecules and targets for drug-resistant TB. Front Cell Infect Microbiol 2022; 12:1029044. [PMID: 36275029 PMCID: PMC9582839 DOI: 10.3389/fcimb.2022.1029044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Despite reinvigorated efforts in Tuberculosis (TB) drug discovery over the past 20 years, relatively few new drugs and candidates have emerged with clear utility against drug resistant TB. Over the same period, significant technological advances and learnings around target value have taken place. This has offered opportunities to re-assess the potential for optimization of previously discovered chemical matter against Mycobacterium tuberculosis (M.tb) and for reconsideration of clinically validated targets encumbered by drug resistance. A re-assessment of discarded compounds and programs from the “golden age of antibiotics” has yielded new scaffolds and targets against TB and uncovered classes, for example beta-lactams, with previously unappreciated utility for TB. Leveraging validated classes and targets has also met with success: booster technologies and efforts to thwart efflux have improved the potential of ethionamide and spectinomycin classes. Multiple programs to rescue high value targets while avoiding cross-resistance are making progress. These attempts to make the most of known classes, drugs and targets complement efforts to discover new chemical matter against novel targets, enhancing the chances of success of discovering effective novel regimens against drug-resistant TB.
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14
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Bhagwat A, Deshpande A, Parish T. How Mycobacterium tuberculosis drug resistance has shaped anti-tubercular drug discovery. Front Cell Infect Microbiol 2022; 12:974101. [PMID: 36159638 PMCID: PMC9500310 DOI: 10.3389/fcimb.2022.974101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Drug resistance is an increasing problem for the treatment of tuberculosis. The prevalence of clinical isolates with pre-existing resistance needs to be considered in any drug discovery program. Non-specific mechanisms of resistance such as increased efflux or decreased permeability need to be considered both in developing individual drug candidates and when designing novel regimens. We review a number of different approaches to develop new analogs and drug combinations or improve efficacy of existing drugs that may overcome or delay the appearance of clinical resistance. We also discuss the need to fully characterize mechanisms of resistance and cross- resistance to existing drugs to ensure that novel drugs will be clinically effective.
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15
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
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16
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Antitubercular, Cytotoxicity, and Computational Target Validation of Dihydroquinazolinone Derivatives. Antibiotics (Basel) 2022; 11:antibiotics11070831. [PMID: 35884084 PMCID: PMC9311641 DOI: 10.3390/antibiotics11070831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023] Open
Abstract
A series of 2,3-dihydroquinazolin-4(1H)-one derivatives (3a–3m) was screened for in vitro whole-cell antitubercular activity against the tubercular strain H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 3l and 3m with di-substituted aryl moiety (halogens) attached to the 2-position of the scaffold showed a minimum inhibitory concentration (MIC) of 2 µg/mL against the MTB strain H37Rv. Compound 3k with an imidazole ring at the 2-position of the dihydroquinazolin-4(1H)-one also showed significant inhibitory action against both the susceptible strain H37Rv and MDR strains with MIC values of 4 and 16 µg/mL, respectively. The computational results revealed the mycobacterial pyridoxal-5′-phosphate (PLP)-dependent aminotransferase (BioA) enzyme as the potential target for the tested compounds. In vitro, ADMET calculations and cytotoxicity studies against the normal human dermal fibroblast cells indicated the safety and tolerability of the test compounds 3k–3m. Thus, compounds 3k–3m warrant further optimization to develop novel BioA inhibitors for the treatment of drug-sensitive H37Rv and drug-resistant MTB.
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17
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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18
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Flipo M, Frita R, Bourotte M, Martínez-Martínez MS, Boesche M, Boyle GW, Derimanov G, Drewes G, Gamallo P, Ghidelli-Disse S, Gresham S, Jiménez E, de Mercado J, Pérez-Herrán E, Porras-De Francisco E, Rullas J, Casado P, Leroux F, Piveteau C, Kiass M, Mathys V, Soetaert K, Megalizzi V, Tanina A, Wintjens R, Antoine R, Brodin P, Delorme V, Moune M, Djaout K, Slupek S, Kemmer C, Gitzinger M, Ballell L, Mendoza-Losana A, Lociuro S, Deprez B, Barros-Aguirre D, Remuiñán MJ, Willand N, Baulard AR. The small-molecule SMARt751 reverses Mycobacterium tuberculosis resistance to ethionamide in acute and chronic mouse models of tuberculosis. Sci Transl Med 2022; 14:eaaz6280. [PMID: 35507672 DOI: 10.1126/scitranslmed.aaz6280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The sensitivity of Mycobacterium tuberculosis, the pathogen that causes tuberculosis (TB), to antibiotic prodrugs is dependent on the efficacy of the activation process that transforms the prodrugs into their active antibacterial moieties. Various oxidases of M. tuberculosis have the potential to activate the prodrug ethionamide. Here, we used medicinal chemistry coupled with a phenotypic assay to select the N-acylated 4-phenylpiperidine compound series. The lead compound, SMARt751, interacted with the transcriptional regulator VirS of M. tuberculosis, which regulates the mymA operon encoding a monooxygenase that activates ethionamide. SMARt751 boosted the efficacy of ethionamide in vitro and in mouse models of acute and chronic TB. SMARt751 also restored full efficacy of ethionamide in mice infected with M. tuberculosis strains carrying mutations in the ethA gene, which cause ethionamide resistance in the clinic. SMARt751 was shown to be safe in tests conducted in vitro and in vivo. A model extrapolating animal pharmacokinetic and pharmacodynamic parameters to humans predicted that as little as 25 mg of SMARt751 daily would allow a fourfold reduction in the dose of ethionamide administered while retaining the same efficacy and reducing side effects.
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Affiliation(s)
- Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Marilyne Bourotte
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.,BioVersys SAS, Lille, France
| | | | - Markus Boesche
- Cellzome GmbH . A GSK Company, 69117 Heidelberg, Germany
| | - Gary W Boyle
- GSK, David Jack Centre for R&D, Park Road, Ware, Hertfordshire SG12 ODP, UK
| | - Geo Derimanov
- GSK, Clinical Pharmacology and Experimental Medicine, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Gerard Drewes
- Cellzome GmbH . A GSK Company, 69117 Heidelberg, Germany
| | - Pablo Gamallo
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | - Stephanie Gresham
- GSK, David Jack Centre for R&D, Park Road, Ware, Hertfordshire SG12 ODP, UK
| | - Elena Jiménez
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | | | | | - Joaquín Rullas
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Mehdi Kiass
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Vanessa Mathys
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Karine Soetaert
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Véronique Megalizzi
- Microbiology, Bioorganic and Macromolecular Chemistry, Facult. de Pharmacie, Universit. Libre de Bruxelles, Brussels, Belgium
| | - Abdalkarim Tanina
- Microbiology, Bioorganic and Macromolecular Chemistry, Facult. de Pharmacie, Universit. Libre de Bruxelles, Brussels, Belgium
| | - René Wintjens
- Microbiology, Bioorganic and Macromolecular Chemistry, Facult. de Pharmacie, Universit. Libre de Bruxelles, Brussels, Belgium
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Vincent Delorme
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Stéphanie Slupek
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | | | | | - Lluis Ballell
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | | | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | | | | | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
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19
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Heo J, Koh D, Woo M, Kwon D, de Almeida Falcão VC, Wood C, Lee H, Kim K, Choi I, Jang J, Brodin P, Shum D, Delorme V. A combination screening to identify enhancers of para-aminosalicylic acid against Mycobacterium tuberculosis. Sci Rep 2022; 12:5635. [PMID: 35379873 PMCID: PMC8980009 DOI: 10.1038/s41598-022-08209-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/04/2022] [Indexed: 11/26/2022] Open
Abstract
Para-aminosalicylic acid (PAS) is an antibiotic that was largely used for the multi-therapy of tuberculosis in the twentieth century. To try to overcome the inconvenience of its low efficacy and poor tolerance, we searched for novel chemical entities able to synergize with PAS using a combination screening against growing axenic Mycobacterium tuberculosis. The screening was performed at a sub-inhibitory concentration of PAS on a library of about 100,000 small molecules. Selected hit compounds were analyzed by dose–response and further probed with an intracellular macrophage assay. Scaffolds with potential additive effect with PAS are reported, opening interesting prospects for mechanism of action studies. We also report here evidence of a yet unknown bio-activation mechanism, involving activation of pyrido[1,2-a]pyrimidin-4-one (PP) derivatives through the Rv3087 protein.
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Affiliation(s)
- Jinyeong Heo
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Dahae Koh
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Minjeong Woo
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Doyoon Kwon
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | | | - Connor Wood
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Honggun Lee
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Kideok Kim
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Inhee Choi
- Medicinal Chemistry Platform, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Jichan Jang
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Priscille Brodin
- University of Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea
| | - Vincent Delorme
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam, Gyeonggi, 13488, Republic of Korea.
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20
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Deb PK, Al-Shar’i NA, Venugopala KN, Pillay M, Borah P. In vitro anti-TB properties, in silico target validation, molecular docking and dynamics studies of substituted 1,2,4-oxadiazole analogues against Mycobacterium tuberculosis. J Enzyme Inhib Med Chem 2021; 36:869-884. [PMID: 34060396 PMCID: PMC8172222 DOI: 10.1080/14756366.2021.1900162] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
The alarming increase in multi- and extensively drug-resistant (MDR and XDR) strains of Mycobacterium tuberculosis (MTB) has triggered the scientific community to search for novel, effective, and safer therapeutics. To this end, a series of 3,5-disubstituted-1,2,4-oxadiazole derivatives (3a-3i) were tested against H37Rv, MDR and XDR strains of MTB. Of which, compound 3a with para-trifluorophenyl substituted oxadiazole showed excellent activity against the susceptible H37Rv and MDR-MTB strain with a MIC values of 8 and 16 µg/ml, respectively.To understand the mechanism of action of these compounds (3a-3i) and identify their putative drug target, molecular docking and dynamics studies were employed against a panel of 20 mycobacterial enzymes reported to be essential for mycobacterial growth and survival. These computational studies revealed polyketide synthase (Pks13) enzyme as the putative target. Moreover, in silico ADMET predictions showed satisfactory properties for these compounds, collectively, making them, particularly compound 3a, promising leads worthy of further optimisation.
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Affiliation(s)
- Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman, Jordan
| | - Nizar A. Al-Shar’i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, India
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21
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Vianna JF, Bezerra KS, Lima Costa AH, Barbosa ED, Lima Neto JX, Oliveira JIN, Freire VN, Fulco UL. New ethionamide boosters and EthR2: structural and energetic analysis. Phys Chem Chem Phys 2021; 23:23233-23241. [PMID: 34623361 DOI: 10.1039/d1cp02853g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethionamide (ETH) is a high-profile drug for the treatment of patients with multidrug-resistant Mycobacterium tuberculosis and, in order to produce its inhibitory effects, it needs to be bioactivated by monooxygenase EthA. This process is under the control of the transcriptional repressors EthR and EthR2, so that their inhibition results in the boosting of ethionamide activation. Herein, through crystallographic data and computer simulations, we calculated the interaction binding energies of four inhibitors with improved in vitro potency, namely BDM76060 (PDB ID: 6HS1), BDM72201 (PDB ID: 6HRX), BDM76150 (PDB ID: 6HS2) and BDM72719 (PDB ID: 6HRY), in complexes with the transcriptional repressor EthR2, using density functional theory (DFT) within the molecular fractionation with conjugated caps (MFCC) approach. It was observed that these ligands share the same binding site within a 10.0 Å radius of the EthR2 protein; however, their structural particularities have a significant impact on the global energies of systems. The BDM72201 and BDM72719 components are weakly attached to the binding site, while BDM76060 and BDM76150 components produce stronger bonds, corroborating with experimental studies demonstrating that BDM76060 and BDM76150 are more successful in producing inhibitory effects. BDM76060 and BDM76150 have many functional groups that increase the contact surface with the protein and attract a more significant number of amino acid residues, being able to produce polarities that generate stronger interactions. In the current scenario of a growing number of cases of bacterial resistance, the obtained data can be used to guide clinical trials of these inhibitors and other inhibitors that act on the alternative EthR2 pathway, focusing on improving the activity of ethionamide, its effectiveness, a reduction in the treatment time and exposure to cytotoxic effects.
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Affiliation(s)
- J F Vianna
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - A H Lima Costa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - E D Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, 60455-760, Fortaleza, CE, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
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22
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Deprez B, Bosc D, Charton J, Couturier C, Deprez-Poulain R, Flipo M, Leroux F, Villemagne B, Willand N. Molecular Design in Practice: A Review of Selected Projects in a French Research Institute That Illustrates the Link between Chemical Biology and Medicinal Chemistry. Molecules 2021; 26:6083. [PMID: 34641626 PMCID: PMC8512331 DOI: 10.3390/molecules26196083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/19/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical biology and drug discovery are two scientific activities that pursue different goals but complement each other. The former is an interventional science that aims at understanding living systems through the modulation of its molecular components with compounds designed for this purpose. The latter is the art of designing drug candidates, i.e., molecules that act on selected molecular components of human beings and display, as a candidate treatment, the best reachable risk benefit ratio. In chemical biology, the compound is the means to understand biology, whereas in drug discovery, the compound is the goal. The toolbox they share includes biological and chemical analytic technologies, cell and whole-body imaging, and exploring the chemical space through state-of-the-art design and synthesis tools. In this article, we examine several tools shared by drug discovery and chemical biology through selected examples taken from research projects conducted in our institute in the last decade. These examples illustrate the design of chemical probes and tools to identify and validate new targets, to quantify target engagement in vitro and in vivo, to discover hits and to optimize pharmacokinetic properties with the control of compound concentration both spatially and temporally in the various biophases of a biological system.
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Affiliation(s)
- Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, F-59000 Lille, France
| | - Damien Bosc
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Cyril Couturier
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41-UMS 2014-PLBS, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France; (D.B.); (J.C.); (C.C.); (R.D.-P.); (M.F.); (F.L.); (B.V.)
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23
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Halder SK, Elma F. In silico identification of novel chemical compounds with antituberculosis activity for the inhibition of InhA and EthR proteins from Mycobacterium tuberculosis. J Clin Tuberc Other Mycobact Dis 2021; 24:100246. [PMID: 34124395 PMCID: PMC8173314 DOI: 10.1016/j.jctube.2021.100246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) continuously poses a major public health concern around the globe, with a mounting death toll of approximately 1.4 million in 2019. Reduced bioavailability, elevated toxicity, increased side effects, and resistance of multiple first-line and second-line TB medications, including isoniazid, ethionamide necessitate studies of new drugs. The method of computational biology and bioinformatics approach allows virtual screening of a large number of drugs, reduces growing side effects of medications, and predicts potential drug resistance over time. In this study, we have analyzed fifty small molecules with antituberculosis properties using in silico approach including molecular docking, drug-likeness assessment, ADMET (absorption, distribution, metabolism, excretion, toxicity) profile evaluation, P450 site of metabolism prediction, and molecular dynamics simulation. Among those fifty compounds, 3-[3-(4-Fluorophenyl)-1,2,4-oxadiazol-5-yl]-N-(2-methylphenyl) piperidine-1-carboxamide (C22) and 5-(4-Ethyl-phenyl)-2-(1H-tetrazol-5-ylmethyl)-2H-tetrazole (C29) were found to pass the two-step molecular docking, P450 site of metabolism prediction and pharmacokinetics analysis successfully. Their binding stability for target proteins has been evaluated through root mean square deviation and root mean square fluctuation, Radius of gyration analysis from 10 ns Molecular Dynamics Simulation (MDS). Our identified drugs (C22 and C29) performed better than the control drugs (Isoniazid, Ethionamide) regarding binding affinity and molecular stability with the regulatory proteins (InhA, EthR) of Mycobacterium tuberculosis. The study proposed these compounds as effective therapeutic agents for Tuberculosis drug discovery, but further in vitro and in vivo testing are needed to substantiate their potential as novel drugs and modes of action.
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Affiliation(s)
- Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
- Research assistant at Padma Bioresearch, Dhaka, Bangladesh
| | - Fatiha Elma
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
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24
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Moureu S, Caradec T, Trivelli X, Drobecq H, Beury D, Bouquet P, Caboche S, Desmecht E, Maurier F, Muharram G, Villemagne B, Herledan A, Hot D, Willand N, Hartkoorn RC. Rubrolone production by Dactylosporangium vinaceum: biosynthesis, modulation and possible biological function. Appl Microbiol Biotechnol 2021; 105:5541-5551. [PMID: 34189614 DOI: 10.1007/s00253-021-11404-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Rare actinomycetes are likely treasure troves for bioactive natural products, and it is therefore important that we enrich our understanding of biosynthetic potential of these relatively understudied bacteria. Dactylosporangium are a genus of such rare Actinobacteria that are known to produce a number of important antibacterial compounds, but for which there are still no fully assembled reference genomes, and where the extent of encoded biosynthetic capacity is not defined. Dactylosporangium vinaceum (NRRL B-16297) is known to readily produce a deep wine red-coloured diffusible pigment of unknown origin, and it was decided to define the chemical identity of this natural product pigment, and in parallel use whole genome sequencing and transcriptional analysis to lay a foundation for understanding the biosynthetic capacity of these bacteria. Results show that the produced pigment is made of various rubrolone conjugates, the spontaneous product of the reactive pre-rubrolone, produced by the bacterium. Genome and transcriptome analysis identified the highly expressed biosynthetic gene cluster (BGC) for pre-rubrolone. Further analysis of the fully assembled genome found it to carry 24 additional BGCs, of which the majority were poorly transcribed, confirming the encoded capacity of this bacterium to produce natural products but also illustrating the main bottleneck to exploiting this capacity. Finally, analysis of the potential environmental role of pre-rubrolone found it to react with a number of amine containing antibiotics, antimicrobial peptides and siderophores pointing to its potential role as a "minesweeper" of xenobiotic molecules in the bacterial environment. KEY POINTS: • D. vinaceum encodes many BGC, but the majority are transcriptionally silent. • Chemical screening identifies molecules that modulate rubrolone production. • Pre-rubrolone is efficient at binding and inactivating many natural antibiotics.
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Affiliation(s)
- Sophie Moureu
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Thibault Caradec
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Xavier Trivelli
- Univ. Lille, CNRS, INRA, Centrale Lille, Univ. Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, 59000, Lille, France
| | - Hervé Drobecq
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Delphine Beury
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, F-59000, Lille, France
| | - Peggy Bouquet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Segolene Caboche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, F-59000, Lille, France
| | - Eva Desmecht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florence Maurier
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, F-59000, Lille, France
| | - Ghaffar Muharram
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR2014 - US41 - PLBS-Plateformes Lilloises de Biologie & Santé, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Ruben Christiaan Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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25
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Sharma A, De Rosa M, Singla N, Singh G, Barnwal RP, Pandey A. Tuberculosis: An Overview of the Immunogenic Response, Disease Progression, and Medicinal Chemistry Efforts in the Last Decade toward the Development of Potential Drugs for Extensively Drug-Resistant Tuberculosis Strains. J Med Chem 2021; 64:4359-4395. [PMID: 33826327 DOI: 10.1021/acs.jmedchem.0c01833] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis (TB) is a slow growing, potentially debilitating disease that has plagued humanity for centuries and has claimed numerous lives across the globe. Concerted efforts by researchers have culminated in the development of various strategies to combat this malady. This review aims to raise awareness of the rapidly increasing incidences of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, highlighting the significant modifications that were introduced in the TB treatment regimen over the past decade. A description of the role of pathogen-host immune mechanisms together with strategies for prevention of the disease is discussed. The struggle to develop novel drug therapies has continued in an effort to reduce the treatment duration, improve patient compliance and outcomes, and circumvent TB resistance mechanisms. Herein, we give an overview of the extensive medicinal chemistry efforts made during the past decade toward the discovery of new chemotypes, which are potentially active against TB-resistant strains.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India.,UIPS, Panjab University, Chandigarh 160014, India
| | - Maria De Rosa
- Drug Discovery Unit, Ri.MED Foundation, Palermo 90133, Italy
| | - Neha Singla
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- UIPS, Panjab University, Chandigarh 160014, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
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26
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Heterologous Expression of ethA and katG in Mycobacterium marinum Enables the Rapid Identification of New Prodrugs Active against Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:AAC.01445-20. [PMID: 33495223 DOI: 10.1128/aac.01445-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/12/2021] [Indexed: 01/05/2023] Open
Abstract
Screening strategies for antituberculosis compounds using Mycobacterium tuberculosis are time consuming and require biosafety level 3 (BSL3) facilities, which makes the development of high-throughput assays difficult and expensive. Mycobacterium marinum, a close genetic relative of M. tuberculosis, possesses several advantages as a suitable model for tuberculosis drug screening. However, despite the high genetic similarity, there are some obvious differences in susceptibility to some tuberculosis drugs between these two species, especially for the prodrugs ethionamide and isoniazid. In this study, we aimed to improve M. marinum as a model for antituberculosis drug identification by heterologous expression of two common drug activators, EthA and KatG. These two activators were overexpressed in M. marinum, and the strains were tested against ethionamide, isoniazid, and a library of established antimycobacterial compounds from TB Alliance to compare drug susceptibility. Both in vitro and in vivo using zebrafish larvae, these genetically modified M. marinum strains showed significantly higher susceptibility against ethionamide and isoniazid, which require activation by EthA and KatG. More importantly, a strain overexpressing both ethA and katG was potentially more susceptible to approximately 20% of the antituberculosis hit compounds from the TB Alliance library. Most of these compounds were activated by EthA in M. marinum Four of these compounds were selected for further analysis, and three of them showed obvious EthA-dependent activity against M. tuberculosis Overall, our developed M. marinum strains are valuable tools for high-throughput discovery of potential novel antituberculosis prodrugs.
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27
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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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28
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Chauhan A, Kumar M, Kumar A, Kanchan K. Comprehensive review on mechanism of action, resistance and evolution of antimycobacterial drugs. Life Sci 2021; 274:119301. [PMID: 33675895 DOI: 10.1016/j.lfs.2021.119301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
Tuberculosis is one of the deadliest infectious diseases existing in the world since ancient times and still possesses serious threat across the globe. Each year the number of cases increases due to high drug resistance shown by Mycobacterium tuberculosis (Mtb). Available antimycobacterial drugs have been classified as First line, Second line and Third line antibiotics depending on the time of their discoveries and their effectiveness in the treatment. These antibiotics have a broad range of targets ranging from cell wall to metabolic processes and their non-judicious and uncontrolled usage in the treatment for years has created a significant problem called multi-drug resistant (MDR) tuberculosis. In this review, we have summarized the mechanism of action of all the classified antibiotics currently in use along with the resistance mechanisms acquired by Mtb. We have focused on the new drug candidates/repurposed drugs, and drug in combinations, which are in clinical trials for either treating the MDR tuberculosis more effectively or involved in reducing the time required for the chemotherapy of drug sensitive TB. This information is not discussed very adequately on a single platform. Additionally, we have discussed the recent technologies that are being used to discover novel resistance mechanisms acquired by Mtb and for exploring novel drugs. The story of intrinsic resistance mechanisms and evolution in Mtb is far from complete. Therefore, we have also discussed intrinsic resistance mechanisms of Mtb and their evolution with time, emphasizing the hope for the development of novel antimycobacterial drugs for effective therapy of tuberculosis.
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Affiliation(s)
- Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
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29
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Verma H, Nagar S, Vohra S, Pandey S, Lal D, Negi RK, Lal R, Rawat CD. Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. Microb Genom 2021; 7:mgen000542. [PMID: 33750515 PMCID: PMC8190606 DOI: 10.1099/mgen.0.000542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis is a known human pathogen that causes the airborne infectious disease tuberculosis (TB). Every year TB infects millions of people worldwide. The emergence of multi-drug resistant (MDR), extensively drug resistant (XDR) and totally drug resistant (TDR) M. tuberculosis strains against the first- and second-line anti-TB drugs has created an urgent need for the development and implementation of new drug strategies. In this study, the complete genomes of 174 strains of M. tuberculosis are analysed to understand the evolution of molecular drug target (MDT) genes. Phylogenomic placements of M. tuberculosis strains depicted close association and temporal clustering. Selection pressure analysis by deducing the ratio of non-synonymous to synonymous substitution rates (dN/dS) in 51 MDT genes of the 174 M. tuberculosis strains led to categorizing these genes into diversifying (D, dN/dS>0.70), moderately diversifying (MD, dN/dS=0.35-0.70) and stabilized (S, dN/dS<0.35) genes. The genes rpsL, gidB, pncA and ahpC were identified as diversifying, and Rv0488, kasA, ndh, ethR, ethA, embR and ddn were identified as stabilized genes. Furthermore, sequence similarity networks were drawn that supported these divisions. In the multiple sequence alignments of diversifying and stabilized proteins, previously reported resistance mutations were checked to predict sensitive and resistant strains of M. tuberculosis. Finally, to delineate the potential of stabilized or least diversified genes/proteins as anti-TB drug targets, protein-protein interactions of MDT proteins with human proteins were analysed. We predict that kasA (dN/dS=0.29), a stabilized gene that encodes the most host-interacting protein, KasA, should serve as a potential drug target for the treatment of TB.
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Affiliation(s)
- Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Shivani Vohra
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi 110021, India
| | - Shubhanshu Pandey
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Biotechnology, Jamia Millia Islamia, Okhla, New Delhi 110025, India
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | | | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
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30
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Miller CA, Ho JM, Parks SE, Bennett MR. Macrolide Biosensor Optimization through Cellular Substrate Sequestration. ACS Synth Biol 2021; 10:258-264. [PMID: 33555859 PMCID: PMC7901672 DOI: 10.1021/acssynbio.0c00572] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Developing and optimizing small-molecule biosensors is a central goal of synthetic
biology. Here we incorporate additional cellular components to improve biosensor
sensitivity by preventing target molecules from diffusing out of cells. We demonstrate
that trapping erythromycin within Escherichia coli through
phosphorylation increases the sensitivity of its biosensor (MphR) by approximately
10-fold. When combined with prior engineering efforts, our optimized biosensor can
detect erythromycin concentrations as low as 13 nM. We show that this strategy works
with a range of macrolide substrates, enabling the potential usage of our optimized
system for drug development and metabolic engineering. This strategy can be extended in
future studies to improve the sensitivity of other biosensors. Our findings further
suggest that many naturally evolved genes involved in resistance to multiple classes of
antibiotics may increase intracellular drug concentrations to modulate their own
expression, acting as a form of regulatory feedback.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Joanne M. Ho
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Sydney E. Parks
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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31
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Guieu B, Jourdan JP, Dreneau A, Willand N, Rochais C, Dallemagne P. Desirable drug-drug interactions or when a matter of concern becomes a renewed therapeutic strategy. Drug Discov Today 2020; 26:315-328. [PMID: 33253919 DOI: 10.1016/j.drudis.2020.11.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/14/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
Drug-drug interactions are sometimes considered to be detrimental and responsible for adverse effects. In some cases, however, some are stakeholders of the efficiency of the treatment and this combinatorial strategy is exploited by some drug associations, including levodopa (L-Dopa) and dopadecarboxylase inhibitors, β-lactam antibiotics and clavulanic acid, 5-fluorouracil (5-FU) and folinic acid, and penicillin and probenecid. More recently, some drug-drug combinations have been integrated in modern drug design strategies, aiming to enhance the efficiency of already marketed drugs with new compounds acting not only as synergistic associations, but also as real boosters of activity. In this review, we provide an update of examples of such strategies, with a special focus on microbiology and oncology.
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Affiliation(s)
- Benjamin Guieu
- Normandie University, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France
| | - Jean-Pierre Jourdan
- Normandie University, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France; Department of Pharmacy, Caen University Hospital, Caen, F-14000, France
| | - Aurore Dreneau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Christophe Rochais
- Normandie University, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France
| | - Patrick Dallemagne
- Normandie University, UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie), F-14032 Caen, France.
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32
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Velappan AB, Datta D, Ma R, Rana S, Ghosh KS, Hari N, Franzblau SG, Debnath J. 2-Aryl benzazole derived new class of anti-tubercular compounds: Endowed to eradicate mycobacterium tuberculosis in replicating and non-replicating forms. Bioorg Chem 2020; 103:104170. [PMID: 32890990 DOI: 10.1016/j.bioorg.2020.104170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/30/2020] [Accepted: 08/02/2020] [Indexed: 11/30/2022]
Abstract
The high mortality rate and the increasing prevalence of Mtb resistance are the major concerns for the Tuberculosis (TB) treatment in this century. To counteract the prevalence of Mtb resistance, we have synthesized 2-aryl benzazole based dual targeted molecules. Compound 9m and 9n were found to be equally active against replicating and non-replicating form of Mtb (MIC(MABA) 1.98 and 1.66 μg/ml; MIC(LORA) 2.06 and 1.59 μg/ml respectively). They arrested the cell division (replicating Mtb) by inhibiting the GTPase activity of FtsZ with IC50 values 45 and 64 μM respectively. They were also capable of kill Mtb in non-replicating form by inhibiting the biosynthesis of menaquinone which was substantiated by the MenG inhibition (IC50 = 11.62 and 7.49 μM respectively) followed by the Vit-K2 rescue study and ATP production assay.
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Affiliation(s)
- Anand Babu Velappan
- Department of Chemistry, SCBT, SASTRA Deemed to be University, Tamilnadu 613401, India
| | - Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Rui Ma
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA
| | - Shiwani Rana
- Department of Chemistry, National Institute of Technology Hamirpur, Himachal Pradesh 177005, India
| | - Kalyan Sundar Ghosh
- Department of Chemistry, National Institute of Technology Hamirpur, Himachal Pradesh 177005, India
| | - Natarajan Hari
- NMR Laboratory, SCBT, SASTRA Deemed to be University, Tamilnadu 613401, India
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA
| | - Joy Debnath
- Department of Chemistry, SCBT, SASTRA Deemed to be University, Tamilnadu 613401, India.
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33
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Lara J, Diacovich L, Trajtenberg F, Larrieux N, Malchiodi EL, Fernández MM, Gago G, Gramajo H, Buschiazzo A. Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine. Nat Commun 2020; 11:3703. [PMID: 32710080 PMCID: PMC7382501 DOI: 10.1038/s41467-020-17504-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 06/30/2020] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis is a pathogen with a unique cell envelope including very long fatty acids, implicated in bacterial resistance and host immune modulation. FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis. Here we disclose crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms. A long tunnel traverses the entire effector-binding domain, enabling long fatty acyl effectors to bind. Only when the tunnel is entirely occupied, the protein dimer adopts a rigid configuration with its DNA-binding domains in an open state, leading to DNA dissociation. The protein-folding hydrophobic core connects the two domains, and is completed into a continuous spine when the effector binds. Such a transmission spine is conserved in a large number of TetR-like regulators, offering insight into effector-triggered allosteric functional control. FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis in Mycobacterium tuberculosis. Here authors present crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms.
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Affiliation(s)
- Julia Lara
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Lautaro Diacovich
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Rosario, 2000, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Nicole Larrieux
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Emilio L Malchiodi
- Instituto de Estudios de la Inmunidad Humoral (IDEHU/CONICET-UBA), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, 1113, Argentina
| | - Marisa M Fernández
- Instituto de Estudios de la Inmunidad Humoral (IDEHU/CONICET-UBA), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, 1113, Argentina
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina.
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay. .,Integrative Microbiology of Zoonotic Agents, International Joint Research Unit, Department of Microbiology, Institut Pasteur, Paris, 75724, Cedex 15, France.
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34
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Makarov V, Salina E, Reynolds RC, Kyaw Zin PP, Ekins S. Molecule Property Analyses of Active Compounds for Mycobacterium tuberculosis. J Med Chem 2020; 63:8917-8955. [PMID: 32259446 DOI: 10.1021/acs.jmedchem.9b02075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) continues to claim the lives of around 1.7 million people per year. Most concerning are the reports of multidrug drug resistance. Paradoxically, this global health pandemic is demanding new therapies when resources and interest are waning. However, continued tuberculosis drug discovery is critical to address the global health need and burgeoning multidrug resistance. Many diverse classes of antitubercular compounds have been identified with activity in vitro and in vivo. Our analyses of over 100 active leads are representative of thousands of active compounds generated over the past decade, suggests that they come from few chemical classes or natural product sources. We are therefore repeatedly identifying compounds that are similar to those that preceded them. Our molecule-centered cheminformatics analyses point to the need to dramatically increase the diversity of chemical libraries tested and get outside of the historic Mtb property space if we are to generate novel improved antitubercular leads.
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Affiliation(s)
- Vadim Makarov
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Elena Salina
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Robert C Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Phyo Phyo Kyaw Zin
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, North Carolina 27606, United States
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35
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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36
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Villemagne B, Machelart A, Tran NC, Flipo M, Moune M, Leroux F, Piveteau C, Wohlkönig A, Wintjens R, Li X, Gref R, Brodin P, Deprez B, Baulard AR, Willand N. Fragment-Based Optimized EthR Inhibitors with in Vivo Ethionamide Boosting Activity. ACS Infect Dis 2020; 6:366-378. [PMID: 32011115 DOI: 10.1021/acsinfecdis.9b00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Killing more than one million people each year, tuberculosis remains the leading cause of death from a single infectious agent. The growing threat of multidrug-resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. EthR, a mycobacterial transcriptional regulator, is involved in the control of the bioactivation of the second-line drug ethionamide. We have previously reported the discovery of in vitro nanomolar boosters of ethionamide through fragment-based approaches. In this study, we have further explored the structure-activity and structure-property relationships in this chemical family. By combining structure-based drug design and in vitro evaluation of the compounds, we identified a new oxadiazole compound as the first fragment-based ethionamide booster which proved to be active in vivo, in an acute model of tuberculosis infection.
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Affiliation(s)
- Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Arnaud Machelart
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ngoc Chau Tran
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alexandre Wohlkönig
- Structural Biology Brussels and Molecular and Cellular Interactions, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie bioorganique et Macromoléculaire (CP206/04), Institut de Pharmacie, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Xue Li
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Ruxandra Gref
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
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37
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Multitargeting Compounds: A Promising Strategy to Overcome Multi-Drug Resistant Tuberculosis. Molecules 2020; 25:molecules25051239. [PMID: 32182964 PMCID: PMC7179463 DOI: 10.3390/molecules25051239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis is still an urgent global health problem, mainly due to the spread of multi-drug resistant M. tuberculosis strains, which lead to the need of new more efficient drugs. A strategy to overcome the problem of the resistance insurgence could be the polypharmacology approach, to develop single molecules that act on different targets. Polypharmacology could have features that make it an approach more effective than the classical polypharmacy, in which different drugs with high affinity for one target are taken together. Firstly, for a compound that has multiple targets, the probability of development of resistance should be considerably reduced. Moreover, such compounds should have higher efficacy, and could show synergic effects. Lastly, the use of a single molecule should be conceivably associated with a lower risk of side effects, and problems of drug–drug interaction. Indeed, the multitargeting approach for the development of novel antitubercular drugs have gained great interest in recent years. This review article aims to provide an overview of the most recent and promising multitargeting antitubercular drug candidates.
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38
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Huszár S, Chibale K, Singh V. The quest for the holy grail: new antitubercular chemical entities, targets and strategies. Drug Discov Today 2020; 25:772-780. [PMID: 32062007 PMCID: PMC7215093 DOI: 10.1016/j.drudis.2020.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/23/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022]
Abstract
In 2018 1.2 million people died of tuberculosis. The ideal drug candidate should be active against replicating and nonreplicating Mycobacterium tuberculosis. New drug targets such as EfpA, PptT, ClpP, Pks13, DnaN and QcrB have been identified. Tuberculosis drug discovery is advancing with innovative screens.
Tuberculosis (TB) remains the leading cause of death from an infectious disease worldwide. TB therapy is complicated by the protracted treatment regimens, development of resistance coupled with toxicity and insufficient sterilizing capacity of current drugs. Although considerable progress has been made on establishing a TB drug pipeline, the high attrition rate reinforces the need to continually replenish the pipeline with high-quality leads that act through inhibition of novel targets. In this review, we highlight some of the key advances that have assisted TB drug discovery with novel chemical matter, targets and strategies – to fuel the TB drug pipeline.
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Affiliation(s)
- Stanislav Huszár
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa.
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39
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Kang SM, Kim DH, Jin C, Ahn HC, Lee BJ. The crystal structure of AcrR from Mycobacterium tuberculosis reveals a one-component transcriptional regulation mechanism. FEBS Open Bio 2019; 9:1713-1725. [PMID: 31369208 PMCID: PMC6768106 DOI: 10.1002/2211-5463.12710] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/23/2019] [Accepted: 07/31/2019] [Indexed: 12/15/2022] Open
Abstract
Transcriptional regulator proteins are closely involved in essential survival strategies in bacteria. AcrR is a one-component allosteric repressor of the genes associated with lipid transport and antibiotic resistance. When fatty acid ligands bind to the C-terminal ligand-binding cavity of AcrR, a conformational change in the N-terminal operator-binding region of AcrR is triggered, which releases the repressed DNA and initiates transcription. This paper focuses on the structural transition mechanism of AcrR of Mycobacterium tuberculosis upon DNA and ligand binding. AcrR loses its structural integrity upon ligand-mediated structural alteration and bends toward the promoter DNA in a more compact form, initiating a rotational motion. Our functional characterization of AcrR and description of the ligand- and DNA-recognition mechanism may facilitate the discovery of new therapies for tuberculosis.
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Affiliation(s)
- Sung-Min Kang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Do-Hee Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hee-Chul Ahn
- Department of Pharmacy, Dongguk University-Seoul, Ilsandong-gu, Goyang, Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
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40
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Mycobacterium tuberculosis topoisomerases and EthR as the targets for new anti-TB drugs development. Future Med Chem 2019; 11:2193-2203. [DOI: 10.4155/fmc-2018-0232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The significant increase in the detection of drug-resistant strains of Mycobacterium tuberculosis caused an urgent need for the discovery new antituberculosis drugs. Development of bioinformatics and computational sciences enabled the progress of new strategies leading to design, discovery and identification of a series of interesting drug candidates. In this short review, we would like to present recently discovered compounds targeting important mycobacterial proteins: DNA topoisomerases and the transcriptional repressor of EthA monooxygenase – EthR.
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41
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Pastor A, Machelart A, Li X, Willand N, Baulard A, Brodin P, Gref R, Desmaële D. A novel codrug made of the combination of ethionamide and its potentiating booster: synthesis, self-assembly into nanoparticles and antimycobacterial evaluation. Org Biomol Chem 2019; 17:5129-5137. [PMID: 31073555 DOI: 10.1039/c9ob00680j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethionamide (ETH) is one of the most widely used second-line chemotherapeutic drugs for the treatment of multi-drug-resistant tuberculosis. The bioactivation and activity of ETH is dramatically potentiated by a family of molecules called "boosters" among which BDM43266 is one of the most potent. However, the co-administration of these active molecules is hampered by their low solubility in biological media and by the strong tendency of ETH to crystallize. A novel strategy that involves synthesizing a codrug able to self-associate into nanoparticles prone to be taken up by infected macrophages is proposed here. This codrug is designed by tethering N-hydroxymethyl derivatives of both ETH and its booster through a glutaric linker. This codrug self-assembles into nanoparticles of around 200 nm, stable upon extreme dilution without disaggregating as well as upon concentration. The nanoparticles of the codrug can be intranasally administered overcoming the unfavorable physico-chemical profiles of the parent drugs. Intrapulmonary delivery of the codrug nanoparticles to Mtb infected mice via the intranasal route at days 7, 9, 11, 14, 16 and 18 post-infection reduces the bacterial load in the lungs by a factor of 6.
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Affiliation(s)
- Alexandra Pastor
- Institut Galien Paris-Sud, UMR 8612, CNRS, Université Paris-Sud, Faculté de Pharmacie, 5 rue JB Clément, 92296 Châtenay-Malabry, France.
| | - Arnaud Machelart
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Xue Li
- Institute of Molecular Sciences, UMR CNRS 8214, Université Paris-Sud, 91400 Orsay, France
| | - Nicolas Willand
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain Baulard
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Priscille Brodin
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ruxandra Gref
- Institute of Molecular Sciences, UMR CNRS 8214, Université Paris-Sud, 91400 Orsay, France
| | - Didier Desmaële
- Institut Galien Paris-Sud, UMR 8612, CNRS, Université Paris-Sud, Faculté de Pharmacie, 5 rue JB Clément, 92296 Châtenay-Malabry, France.
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42
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Tatum N, Duarte F, Kamerlin SCL, Pohl E. Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds. J Phys Chem Lett 2019; 10:2244-2249. [PMID: 30965004 PMCID: PMC6503467 DOI: 10.1021/acs.jpclett.9b00741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.
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Affiliation(s)
- Natalie
J. Tatum
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K.
| | - Fernanda Duarte
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Shina C. L. Kamerlin
- Department
of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Ehmke Pohl
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K.
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Biophysical
Sciences Institute, Durham University, Durham DH1 3LE, U.K.
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43
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Machelart A, Salzano G, Li X, Demars A, Debrie AS, Menendez-Miranda M, Pancani E, Jouny S, Hoffmann E, Deboosere N, Belhaouane I, Rouanet C, Simar S, Talahari S, Giannini V, Villemagne B, Flipo M, Brosch R, Nesslany F, Deprez B, Muraille E, Locht C, Baulard AR, Willand N, Majlessi L, Gref R, Brodin P. Intrinsic Antibacterial Activity of Nanoparticles Made of β-Cyclodextrins Potentiates Their Effect as Drug Nanocarriers against Tuberculosis. ACS NANO 2019; 13:3992-4007. [PMID: 30822386 PMCID: PMC6718168 DOI: 10.1021/acsnano.8b07902] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/01/2019] [Indexed: 05/23/2023]
Abstract
Multi-drug-resistant tuberculosis (TB) is a major public health problem, concerning about half a million cases each year. Patients hardly adhere to the current strict treatment consisting of more than 10 000 tablets over a 2-year period. There is a clear need for efficient and better formulated medications. We have previously shown that nanoparticles made of cross-linked poly-β-cyclodextrins (pβCD) are efficient vehicles for pulmonary delivery of powerful combinations of anti-TB drugs. Here, we report that in addition to being efficient drug carriers, pβCD nanoparticles are endowed with intrinsic antibacterial properties. Empty pβCD nanoparticles are able to impair Mycobacterium tuberculosis (Mtb) establishment after pulmonary administration in mice. pβCD hamper colonization of macrophages by Mtb by interfering with lipid rafts, without inducing toxicity. Moreover, pβCD provoke macrophage apoptosis, leading to depletion of infected cells, thus creating a lung microenvironment detrimental to Mtb persistence. Taken together, our results suggest that pβCD nanoparticles loaded or not with antibiotics have an antibacterial action on their own and could be used as a carrier in drug regimen formulations effective against TB.
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Affiliation(s)
- Arnaud Machelart
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Giuseppina Salzano
- Université
Paris Sud, Université Paris-Saclay, CNRS, UMR 8214 - Institute for Molecular Sciences of Orsay (ISMO), F-91405 Orsay, France
| | - Xue Li
- Université
Paris Sud, Université Paris-Saclay, CNRS, UMR 8214 - Institute for Molecular Sciences of Orsay (ISMO), F-91405 Orsay, France
| | - Aurore Demars
- Research
Unit in Microorganisms Biology (URBM), Laboratory of Immunology and
Microbiology, Université de Namur, Narilis, B-5000 Namur, Belgium
| | - Anne-Sophie Debrie
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Mario Menendez-Miranda
- Université
Paris Sud, Université Paris-Saclay, CNRS, UMR 8214 - Institute for Molecular Sciences of Orsay (ISMO), F-91405 Orsay, France
| | - Elisabetta Pancani
- Université
Paris Sud, Université Paris-Saclay, CNRS, UMR 8214 - Institute for Molecular Sciences of Orsay (ISMO), F-91405 Orsay, France
| | - Samuel Jouny
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Eik Hoffmann
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nathalie Deboosere
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Imène Belhaouane
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Carine Rouanet
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Sophie Simar
- Université
de Lille, Institut Pasteur de Lille, EA 4483, F-59000 Lille, France
| | - Smaïl Talahari
- Université
de Lille, Institut Pasteur de Lille, EA 4483, F-59000 Lille, France
| | - Valerie Giannini
- Institut
Pasteur, Unit for Integrated
Mycobacterial Pathogenomics, Paris, CNRS
UMR 3525, 25 Rue du Dr. Roux, F-75015 Paris, France
| | - Baptiste Villemagne
- Université
de Lille, INSERM, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Marion Flipo
- Université
de Lille, INSERM, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Roland Brosch
- Institut
Pasteur, Unit for Integrated
Mycobacterial Pathogenomics, Paris, CNRS
UMR 3525, 25 Rue du Dr. Roux, F-75015 Paris, France
| | - Fabrice Nesslany
- Université
de Lille, Institut Pasteur de Lille, EA 4483, F-59000 Lille, France
| | - Benoit Deprez
- Université
de Lille, INSERM, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Eric Muraille
- Research
Unit in Microorganisms Biology (URBM), Laboratory of Immunology and
Microbiology, Université de Namur, Narilis, B-5000 Namur, Belgium
- Laboratory
of Parasitology, Faculty of Medicine, Université
Libre de Bruxelles, B-1070 Brussels, Belgium
| | - Camille Locht
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Alain R. Baulard
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Université
de Lille, INSERM, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Laleh Majlessi
- Institut
Pasteur, Unit for Integrated
Mycobacterial Pathogenomics, Paris, CNRS
UMR 3525, 25 Rue du Dr. Roux, F-75015 Paris, France
| | - Ruxandra Gref
- Université
Paris Sud, Université Paris-Saclay, CNRS, UMR 8214 - Institute for Molecular Sciences of Orsay (ISMO), F-91405 Orsay, France
| | - Priscille Brodin
- Université
de Lille, CNRS, INSERM, CHU Lille, Institut
Pasteur de Lille, U1019 - UMR 8204 - CIIL
- Center for Infection and Immunity of Lille, F-59000 Lille, France
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44
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Prevet H, Moune M, Tanina A, Kemmer C, Herledan A, Frita R, Wohlkönig A, Bourotte M, Villemagne B, Leroux F, Gitzinger M, Baulard AR, Déprez B, Wintjens R, Willand N, Flipo M. A fragment-based approach towards the discovery of N-substituted tropinones as inhibitors of Mycobacterium tuberculosis transcriptional regulator EthR2. Eur J Med Chem 2019; 167:426-438. [PMID: 30784877 DOI: 10.1016/j.ejmech.2019.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/04/2019] [Accepted: 02/07/2019] [Indexed: 01/27/2023]
Abstract
Tuberculosis (TB) caused by the pathogen Mycobacterium tuberculosis, represents one of the most challenging threat to public health worldwide, and with the increasing resistance to approved TB drugs, it is needed to develop new strategies to address this issue. Ethionamide is one of the most widely used drugs for the treatment of multidrug-resistant TB. It is a prodrug that requires activation by mycobacterial monooxygenases to inhibit the enoyl-ACP reductase InhA, which is involved in mycolic acid biosynthesis. Very recently, we identified that inhibition of a transcriptional repressor, termed EthR2, derepresses a new bioactivation pathway that results in the boosting of ethionamide activation. Herein, we describe the identification of potent EthR2 inhibitors using fragment-based screening and structure-based optimization. A target-based screening of a fragment library using thermal shift assay followed by X-ray crystallography identified 5 hits. Rapid optimization of the tropinone chemical series led to compounds with improved in vitro potency.
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Affiliation(s)
- Hugues Prevet
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Martin Moune
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, U1019-UMR8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Abdalkarim Tanina
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | | | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Rosangela Frita
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, U1019-UMR8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Alexandre Wohlkönig
- Structural Biology Brussels, Vlaams Instituut voor Biotechnology (VIB), B-1050, Brussels, Belgium
| | | | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Marc Gitzinger
- Bioversys AG, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Alain R Baulard
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, U1019-UMR8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - René Wintjens
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
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45
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. A Structural View on Medicinal Chemistry Strategies against Drug Resistance. Angew Chem Int Ed Engl 2019; 58:3300-3345. [PMID: 29846032 DOI: 10.1002/anie.201802416] [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: 02/27/2018] [Revised: 04/24/2018] [Indexed: 12/31/2022]
Abstract
The natural phenomenon of drug resistance is a widespread issue that hampers the performance of drugs in many major clinical indications. Antibacterial and antifungal drugs are affected, as well as compounds for the treatment of cancer, viral infections, or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, the underlying molecular mechanisms have been identified to understand the emergence of resistance and to overcome this detrimental process. Detailed structural information on the root causes for drug resistance is nowadays frequently available, so next-generation drugs can be designed that are anticipated to suffer less from resistance. This knowledge-based approach is essential for fighting the inevitable occurrence of drug resistance.
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Affiliation(s)
- Stefano Agnello
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Silvia Gazzola
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
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46
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201802416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stefano Agnello
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Michael Brand
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Mathieu F. Chellat
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Silvia Gazzola
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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47
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Tanina A, Wohlkönig A, Soror SH, Flipo M, Villemagne B, Prevet H, Déprez B, Moune M, Perée H, Meyer F, Baulard AR, Willand N, Wintjens R. A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:248-258. [PMID: 30553830 DOI: 10.1016/j.bbapap.2018.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/05/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn179 and the high occurrence of π-π interactions involving Phe110. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed.
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Affiliation(s)
- Abdalkarim Tanina
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Alexandre Wohlkönig
- Center for Structural Biology, Vlaams Instituut voor Biotechnology (VIB), B-1050 Brussels, Belgium
| | - Sameh H Soror
- Center of scientific excellence, Helwan Structural Biology Research, Faculty of Pharmacy, Helwan University, Ain helwan, 11792 Helwan, Cairo, Egypt
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Hugues Prevet
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Hélène Perée
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Franck Meyer
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.
| | - René Wintjens
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium.
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48
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Integrated analysis of ethionamide resistance loci in Mycobacterium tuberculosis clinical isolates. Tuberculosis (Edinb) 2018; 113:163-174. [DOI: 10.1016/j.tube.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/15/2018] [Accepted: 08/22/2018] [Indexed: 01/31/2023]
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49
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Prieri M, Frita R, Probst N, Sournia-Saquet A, Bourotte M, Déprez B, Baulard AR, Willand N. Efficient analoging around ethionamide to explore thioamides bioactivation pathways triggered by boosters in Mycobacterium tuberculosis. Eur J Med Chem 2018; 159:35-46. [DOI: 10.1016/j.ejmech.2018.09.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/27/2018] [Accepted: 09/14/2018] [Indexed: 11/17/2022]
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50
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Lee BS, Pethe K. Therapeutic potential of promiscuous targets in Mycobacterium tuberculosis. Curr Opin Pharmacol 2018; 42:22-26. [PMID: 30015177 DOI: 10.1016/j.coph.2018.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 11/16/2022]
Abstract
In the field of tuberculosis drug development, the term 'promiscuous' was coined to collectively describe targets that repeatedly show up in whole-cell screenings. With the current climate leaning towards the exclusion of these targets in future drug screens, this review discusses and clarifies misconceptions surrounding this classification, the prospects of developing compounds targeting promiscuous targets, and their potential impact on tuberculosis drug development. The dominance of these targets in cell-based screens reflect not only bias introduced by experimental setup, but also some of the pathogen's greatest vulnerabilities. Coupled with favourable predictions of their in vivo efficacies and synergism with other TB drugs, these targets open opportunities to be explored for the development of rational drug combination for tuberculosis.
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Affiliation(s)
- Bei Shi Lee
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore.
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