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Keiff F, Bernal FA, Joch M, Jacques Dit Lapierre TJW, Li Y, Liebing P, Dahse HM, Vilotijevic I, Kloss F. Modulation of the Meisenheimer complex metabolism of nitro-benzothiazinones by targeted C-6 substitution. Commun Chem 2024; 7:153. [PMID: 38971912 PMCID: PMC11227536 DOI: 10.1038/s42004-024-01235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, remains a major public health concern, demanding new antibiotics with innovative therapeutic principles due to the emergence of resistant strains. Benzothiazinones (BTZs) have been developed to address this problem. However, an unprecedented in vivo biotransformation of BTZs to hydride-Meisenheimer complexes has recently been discovered. Herein, we present a study of the influence of electron-withdrawing groups on the propensity of HMC formation in whole cells for a series of C-6-substituted BTZs obtained through reductive fluorocarbonylation as a late-stage functionalization key step. Gibbs free energy of reaction and Mulliken charges and Fukui indices on C-5 at quantum mechanics level were found as good indicators of in vitro HMC formation propensity. These results provide a first blueprint for the evaluation of HMC formation in drug development and set the stage for rational pharmacokinetic optimization of BTZs and similar drug candidates.
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Affiliation(s)
- François Keiff
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Freddy A Bernal
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Melanie Joch
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Thibault J W Jacques Dit Lapierre
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Yan Li
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Phil Liebing
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Humboldtstr. 8, 07743, Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, Jena, 07743, Germany
| | - Florian Kloss
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany.
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2
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Chen K, Xu R, Hu X, Li D, Hou T, Kang Y. Recent advances in the development of DprE1 inhibitors using AI/CADD approaches. Drug Discov Today 2024; 29:103987. [PMID: 38670256 DOI: 10.1016/j.drudis.2024.103987] [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: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Tuberculosis (TB) is a global lethal disease caused by Mycobacterium tuberculosis (Mtb). The flavoenzyme decaprenylphosphoryl-β-d-ribose 2'-oxidase (DprE1) plays a crucial part in the biosynthesis of lipoarabinomannan and arabinogalactan for the cell wall of Mtb and represents a promising target for anti-TB drug development. Therefore, there is an urgent need to discover DprE1 inhibitors with novel scaffolds, improved bioactivity and high drug-likeness. Recent studies have shown that artificial intelligence/computer-aided drug design (AI/CADD) techniques are powerful tools in the discovery of novel DprE1 inhibitors. This review provides an overview of the discovery of DprE1 inhibitors and their underlying mechanism of action and highlights recent advances in the discovery and optimization of DprE1 inhibitors using AI/CADD approaches.
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Affiliation(s)
- Kepeng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ruolan Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueping Hu
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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3
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Joch M, Wojtas KP, Torres-Gómez H, Li Y, Meyer F, Straßburger M, Kerndl V, Dahse HM, Hertweck C, Hoffmann H, Görls H, Walter K, Hölscher C, Kloss F. Whole cell hydride Meisenheimer complex biotransformation guided optimization of antimycobacterial benzothiazinones. Eur J Med Chem 2024; 264:116023. [PMID: 38071794 DOI: 10.1016/j.ejmech.2023.116023] [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: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023]
Abstract
Nitrobenzothiazinones (BTZs) are potent active substances against Mycobacterium tuberculosis with currently two investigational drugs in clinical development for the treatment of tuberculosis. BTZs are the first examples for which a metabolic pathway towards transient hydride Meisenheimer complexes (HMC) has been shown in mammals, including humans. In this study, lead optimization efforts on BTZs are guided by the systematic evaluation of the HMC formation propensity combined with multiparameter assessment. For this purpose, a novel cell-based assay was specifically developed and fully implemented, and a library of 5- and 7-substituted BTZs was prepared to study substituent effects on the HMC formation. The multiparameter optimization revealed 5-methylated BTZs as the most preferred scaffolds, demonstrating a reduced HMC formation propensity combined with potent activity and good microsomal stability in vitro. In vivo experiments showed good systemic exposure upon oral administration and efficacy in a murine M. tuberculosis infection model. This study reports a qualified in vitro HMC assay, which not only enabled the selection of next-generation BTZs with improved pharmacokinetic properties but also allowed forecasting their in vivo metabolism.
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Affiliation(s)
- Melanie Joch
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - K Philip Wojtas
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - Héctor Torres-Gómez
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - Yan Li
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - Florian Meyer
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - Maria Straßburger
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - Valerie Kerndl
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany
| | - Hans-Martin Dahse
- Infection Biology, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a, 07745, Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, IMLred GmbH, Robert-Koch-Allee 2, 82131, Gauting, Germany; SYNLAB Gauting, SYNLAB MVZ Dachau GmbH, Robert-Koch-Allee 2, 82131, Gauting, Germany
| | - Helmar Görls
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Humboldtstrasse 8, 07743, Jena, Germany
| | - Kerstin Walter
- Infection Immunology, Leibniz Lung Center, Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany; German Center for Infection Research (DZIF), Innenhofstrasse 7, 38124, Braunschweig, Germany
| | - Christoph Hölscher
- Infection Immunology, Leibniz Lung Center, Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany; German Center for Infection Research (DZIF), Innenhofstrasse 7, 38124, Braunschweig, Germany
| | - Florian Kloss
- Transfer Group Anti-infectives, Leibniz Institute for Natural Products Research and Infection Biology, Leibniz-HKI, Beutenbergstr. 11a., 07745, Jena, Germany.
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4
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Wu X, Wang W, Stelitano G, Riabova O, Wang B, Niu W, Cocorullo M, Shi R, Chiarelli LR, Makarov V, Lu Y, Li C, Qiao C. Benzothiozinone derivatives with anti-tubercular Activity-Further side chain investigation. Eur J Med Chem 2024; 264:115976. [PMID: 38039794 DOI: 10.1016/j.ejmech.2023.115976] [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: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
A series of novel benzothiozinone (BTZ) derivatives were designed, prepared and evaluated for antituberculosis activity. Specifically, the BTZ pharmacophore is retained and the previous heterocyclic ring linker is replaced by alkynyl or vinyl linker, the resulting compounds displayed about 5-fold improved antimycobacterial activity. We further revealed that the linker attached tail group affects the compound metabolic stability, potency and other drug like properties. This work led to the discovery of two compounds (A1 and A11) with acceptable low MICs and improved metabolic stability. The representative compound A11 demonstrated bactericidal efficacy in an acute TB infection mouse model.
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Affiliation(s)
- Xiaomei Wu
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Wenxin Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu Province, China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Olga Riabova
- Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, 119071, Russia
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Wei Niu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mario Cocorullo
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Rui Shi
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, 27100, Italy
| | - Vadim Makarov
- Research Center of Biotechnology, The Russian Academy of Sciences, Moscow, 119071, Russia
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
| | - Chuan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Zhongshan Institute for Drug Discovery, Zhongshan, 528400, Guangdong Province, China.
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
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5
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Keiff F, Jacques Dit Lapierre TJW, Bernal FA, Kloss F. Design and synthesis of benzofuran- and naphthalene-fused thiazinones as antimycobacterial agents. Arch Pharm (Weinheim) 2023; 356:e2300356. [PMID: 37667452 DOI: 10.1002/ardp.202300356] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
Benzothiazinones (BTZs) have widely inspired medicinal chemistry and translational research due to their remarkable antitubercular potency and clinical potential. While most structure-activity relationship campaigns have largely focused on lateral chain modifications and substituents on the BTZ core, scaffold hopping strategies have been rarely investigated previously. In this work, we report the first example of ring expansion of the BTZ core toward benzofuran- and naphthalene-fused thiazinones. In vitro testing showed micromolar activity for both compounds, and molecular docking simulations provided insights into their reduced inhibitory capacity toward the enzymatic target (DprE1). Calculated electrochemical potentials revealed a lower susceptibility to reduction as opposed to BTZ drug candidates, in line with the mechanistic requirement for covalent binding.
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Affiliation(s)
- François Keiff
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Jena, Germany
| | | | - Freddy A Bernal
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Jena, Germany
| | - Florian Kloss
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Leibniz-HKI, Jena, Germany
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6
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Amado PM, Woodley C, Cristiano MLS, O’Neill PM. Recent Advances of DprE1 Inhibitors against Mycobacterium tuberculosis: Computational Analysis of Physicochemical and ADMET Properties. ACS OMEGA 2022; 7:40659-40681. [PMID: 36406587 PMCID: PMC9670723 DOI: 10.1021/acsomega.2c05307] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/21/2022] [Indexed: 05/14/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) is a critical flavoenzyme in Mycobacterium tuberculosis, catalyzing a vital step in the production of lipoarabinomannan and arabinogalactan, both of which are essential for cell wall biosynthesis. Due to its periplasmic localization, DprE1 is a susceptible target, and several compounds with diverse scaffolds have been discovered that inhibit this enzyme, covalently or noncovalently. We evaluated a total of ∼1519 DprE1 inhibitors disclosed in the literature from 2009 to April 2022 by performing an in-depth analysis of physicochemical descriptors and absorption, distribution, metabolism, excretion, and toxicity (ADMET), to gain new insights into these properties in DprE1 inhibitors. Several molecular properties that should facilitate the design and optimization of future DprE1 inhibitors are described, allowing for the development of improved analogues targeting M. tuberculosis.
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Affiliation(s)
- Patrícia
S. M. Amado
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Christopher Woodley
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Maria L. S. Cristiano
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Email
for M.L.S.C.:
| | - Paul M. O’Neill
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Email for P.M.O.:
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7
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Sahoo SK, Gajula SNR, Ahmad MN, Kaul G, Nanduri S, Sonti R, Dasgupta A, Chopra S, Yaddanapudi VM. Bioevaluation of quinoline-4-carbonyl derivatives of piperazinyl-benzothiazinones as promising antimycobacterial agents. Arch Pharm (Weinheim) 2022; 355:e2200168. [PMID: 35876343 DOI: 10.1002/ardp.202200168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/12/2022]
Abstract
The quinoline moiety remains a privileged antitubercular (anti-TB) pharmacophore, whereas 8-nitrobenzothiazinones are emerging potent antimycobacterial agents with two investigational candidates in the clinical pipeline. Herein, we report the synthesis and bioevaluation of 30 piperazinyl-benzothiazinone-based quinoline hybrids as prospective anti-TB agents. Preliminary evaluation revealed 24/30 compounds exhibiting substantial activity (minimum inhibitory concentration [MIC] = 0.06-1 µg/ml) against Mycobacterium tuberculosis (Mtb) H37Rv. Cytotoxicity analysis against Vero cells found these to be devoid of any significant toxicity, with the majority displaying a selectivity index of >80. Furthermore, potent nontoxic compounds, when screened against clinical isolates of drug-resistant Mtb strains, demonstrated equipotent inhibition with MIC values of 0.03-0.25 µg/ml. A time-kill study identified a lead compound exhibiting concentration-dependent bactericidal activity, with 10× MIC completely eliminating Mtb bacilli within 7 days. Along with acceptable aqueous solubility and microsomal stability, the optimum active compounds of the series manifested all desirable traits of a promising antimycobacterial candidate.
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Affiliation(s)
- Santosh K Sahoo
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Siva N R Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Mohammad N Ahmad
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.,Biological Sciences Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Grace Kaul
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.,Biological Sciences Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Srinivas Nanduri
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Arunava Dasgupta
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.,Biological Sciences Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.,Biological Sciences Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Venkata M Yaddanapudi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
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