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Seidel RW, Goddard R, Lang M, Richter A. Nα-Aroyl-N-Aryl-Phenylalanine Amides: A Promising Class of Antimycobacterial Agents Targeting the RNA Polymerase. Chem Biodivers 2024; 21:e202400267. [PMID: 38588490 DOI: 10.1002/cbdv.202400267] [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: 01/30/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains the leading cause of death from a bacterium in the world. The global prevalence of clinically relevant infections with opportunistically pathogenic non-tuberculous mycobacteria (NTM) has also been on the rise. Pharmacological treatment of both TB and NTM infections usually requires prolonged regimens of drug combinations, and is often challenging because of developed or inherent resistance to common antibiotic drugs. Medicinal chemistry efforts are thus needed to improve treatment options and therapeutic outcomes. Nα-aroyl-N-aryl-phenylalanine amides (AAPs) have been identified as potent antimycobacterial agents that target the RNA polymerase with a low probability of cross resistance to rifamycins, the clinically most important class of antibiotics known to inhibit the bacterial RNA polymerase. In this review, we describe recent developments in the field of AAPs, including synthesis, structural characterization, in vitro microbiological profiling, structure-activity relationships, physicochemical properties, pharmacokinetics and early cytotoxicity assessment.
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Affiliation(s)
- Rüdiger W Seidel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Richard Goddard
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Markus Lang
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
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Pais JP, Antoniuk O, Pires D, Delgado T, Fortuna A, Costa PJ, Anes E, Constantino L. Synthesis, Activity, Toxicity, and In Silico Studies of New Antimycobacterial N-Alkyl Nitrobenzamides. Pharmaceuticals (Basel) 2024; 17:608. [PMID: 38794178 PMCID: PMC11124399 DOI: 10.3390/ph17050608] [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: 03/24/2024] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Tuberculosis (TB) is a disease that plagues the frailest members of society. We have developed a family of N-alkyl nitrobenzamides that exhibit promising antitubercular activities and can be considered a structural simplification of known inhibitors of decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase (DprE1), an essential Mycobacterium tuberculosis (Mtb) enzyme and an emergent antitubercular target. Hereby, we report the development of these compounds via a simple synthetic methodology as well as their stability, cytotoxicity, and antitubercular activity. Studying their in vitro activity revealed that the 3,5-dinitro and the 3-nitro-5-trifluoromethyl derivatives were the most active, and within these, the derivatives with intermediate lipophilicities presented the best activities (MIC of 16 ng/mL). Additionally, in an ex vivo macrophage model of infection, the derivatives with chain lengths of six and twelve carbon atoms presented the best results, exhibiting activity profiles comparable to isoniazid. Although the proof is not definite, the assessment of susceptibility over multiple mycobacterial species, together with the structure similarities with known inhibitors of this enzyme, support DprE1 as a likely target of action for the compounds. This idea is also reinforced by the docking studies, where the fit of our more active compounds to the DprE1 binding pocket is very similar to what was observed for known inhibitors like DNB1.
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Affiliation(s)
- João P. Pais
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
| | - Olha Antoniuk
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
| | - David Pires
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
- Faculdade de Fármácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Centro de Investigação Interdisciplinar em Saúde (CIIS), Faculdade de Medicina, Universidade Católica Portuguesa, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
| | - Tiago Delgado
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
| | - Andreia Fortuna
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
- Instituto de Biosistemas e Ciências Integrativas (BioISI) and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
| | - Paulo J. Costa
- Instituto de Biosistemas e Ciências Integrativas (BioISI) and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
| | - Elsa Anes
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
- Faculdade de Fármácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Luis Constantino
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal (T.D.); (E.A.)
- Faculdade de Fármácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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3
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Delgado T, Pais JP, Pires D, Estrada FGA, Guedes RC, Anes E, Constantino L. Development of New Drugs to Treat Tuberculosis Based on the Dinitrobenzamide Scaffold. Pharmaceuticals (Basel) 2024; 17:559. [PMID: 38794129 PMCID: PMC11124350 DOI: 10.3390/ph17050559] [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: 03/12/2024] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Tuberculosis (TB) continues to be a major global health challenge and a leading cause of death from infectious diseases. Inspired by the results from a previous work by our group on antimycobacterial N-alkylnitrobenzamides, which are structurally related to the nitrobenzamide family of decaprenylphosphoryl-β-d-ribose oxidase (DprE1) inhibitors, the present study explored a broad array of substituted benzamides. We particularly focused on previously unexplored 3,5-dinitrobenzamide derivatives. Starting with 3,5-dinitrobenzoic acid, we synthesized a diverse library of amides, incorporating both linear and cyclic amine moieties and also assessed the impact of terminal aromatic groups connected through ether, ester, or amide bonds on the bioactivity of the compounds. The synthesis primarily utilized nucleophilic addition/elimination, SN2, and Mitsunobu reactions. The activity was impacted mainly by two structural features, the addition of an aromatic moiety as a terminal group and the type of linker. The most interesting compounds (c2, d1, and d2, MIC = 0.031 μg/mL) exhibited activities against Mycobacterium Tuberculosis (Mtb) H37Rv comparable to isoniazid. Complementary computational studies helped elucidate potential interactions with DprE1, enhancing our understanding of the molecular basis of their action. Our findings suggest that the most active compounds provide a promising foundation for the continued development of new antimycobacterial agents.
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Affiliation(s)
- Tiago Delgado
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João P. Pais
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - David Pires
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Filipe G. A. Estrada
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Elsa Anes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Luis Constantino
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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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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Tayal S, Singh V, Bhatnagar S. 3D-QSAR and ADMET studies of morpholino-pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-20. [PMID: 38112325 DOI: 10.1080/07391102.2023.2294496] [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: 07/18/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
DprE1 is involved in the synthesis of Mycobacterium tuberculosis cell wall and is a potent drug target for Tuberculosis (TB) treatment. The structure and dynamics of the loops L-I and L-II flanking the inhibitor binding site was studied using molecular dynamics (MD) simulation and MMPBSA in Amber v18. Docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) of 55 Morpholino-pyrimidine (MP) inhibitors was carried out using Autodock v1.2.0 and Forge v10. ADMET analysis was done using SwissADME and pkCSM. All MP inhibitors docked in the DprE1 binding pocket, making contacts with L-II residues. MD studies showed that L-I and L-II unfold in the absence of the inhibitor but fold stably structure with reduced protein motions in the presence of MP-38, the highest affinity inhibitor. This was confirmed by k-means clustering and secondary structure analysis. L-II residues, L317, F320 and R325 contributed most towards the MMPBSA binding free energy of MP-38. A robust field-based 3D-QSAR model showed values of r2train = 0.982, r2test = 0.702 and q2 = 0.516. The MP inhibitor field points were broadly divided into negative electrostatics near the A, B rings and hydrophobic electrostatics near the D, E rings. Addition of negative groups at methanone position and ring B as well as addition of hydrophobic and bulky groups at ring E will improve activity. Highly active compounds 47, 49 and 50 of MP series exhibited highly favourable drug-like properties. SAR and ADMET insights attained from this model will help in the development of active DprE1 inhibitors in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Vasundhara Singh
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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6
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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7
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Yadav S, Soni A, Tanwar O, Bhadane R, Besra GS, Kawathekar N. DprE1 Inhibitors: Enduring Aspirations for Future Antituberculosis Drug Discovery. ChemMedChem 2023; 18:e202300099. [PMID: 37246503 DOI: 10.1002/cmdc.202300099] [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: 02/19/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023]
Abstract
DprE1 is a crucial enzyme involved in the cell wall synthesis of Mycobacterium tuberculosis and a promising target for antituberculosis drug development. However, its unique structural characteristics for ligand binding and association with DprE2 make developing new clinical compounds challenging. This review provides an in-depth analysis of the structural requirements for both covalent and non-covalent inhibitors, their 2D and 3D binding patterns, as well as their biological activity data in vitro and in vivo, including pharmacokinetic information. We also introduce a protein quality score (PQS) and an active-site map of the DprE1 enzyme to help medicinal chemists better understand DprE1 inhibition and develop new and effective anti-TB drugs. Furthermore, we examine the resistance mechanisms associated with DprE1 inhibitors to understand future developments due to resistance emergence. This comprehensive review offers insight into the DprE1 active site, including protein-binding maps, PQS, and graphical representations of known inhibitors, making it a valuable resource for medicinal chemists working on future antitubercular compounds.
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Affiliation(s)
- Saloni Yadav
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Aastha Soni
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Omprakash Tanwar
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Rajendra Bhadane
- Turku Cellular Microbiology Laboratory (TCML), Åbo Akademi University, 20014, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520, Turku, Finland
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Neha Kawathekar
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
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Fan D, Wang B, Stelitano G, Savková K, Riabova O, Shi R, Wu X, Chiarelli LR, Mikušová K, Makarov V, Lu Y, Hong Y, Qiao C. Side Chain-Modified Benzothiazinone Derivatives with Anti-Mycobacterial Activity. Biomedicines 2023; 11:1975. [PMID: 37509615 PMCID: PMC10377601 DOI: 10.3390/biomedicines11071975] [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: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis (TB) is a leading infectious disease with serious antibiotic resistance. The benzothiazinone (BTZ) scaffold PBTZ169 kills Mycobacterium tuberculosis (Mtb) through the inhibition of the essential cell wall enzyme decaprenylphosphoryl-β-D-ribose 2'-oxidase (DprE1). PBTZ169 shows anti-TB potential in animal models and pilot clinical tests. Although highly potent, the BTZ type DprE1 inhibitors in general show extremely low aqueous solubility, which adversely affects the drug-like properties. To improve the compounds physicochemical properties, we generated a series of BTZ analogues. Several optimized compounds had MIC values against Mtb lower than 0.01 µM. The representative compound 37 displays improved solubility and bioavailability compared to the lead compound. Additionally, compound 37 shows Mtb-killing ability in an acute infection mouse model.
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Affiliation(s)
- Dongguang Fan
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research, Beijing Chest Hospital, Beijing 101149, China
| | - Giovanni Stelitano
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Olga Riabova
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Rui Shi
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaomei Wu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Laurent R Chiarelli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Vadim Makarov
- Research Center of Biotechnology of 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, Beijing Chest Hospital, Beijing 101149, China
| | - Yuzhi Hong
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou Medical College, Soochow University, Suzhou 215123, China
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9
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Pais JP, Antoniuk O, Freire R, Pires D, Valente E, Anes E, Constantino L. Nitrobenzoates and Nitrothiobenzoates with Activity against M. tuberculosis. Microorganisms 2023; 11:microorganisms11040969. [PMID: 37110393 PMCID: PMC10142844 DOI: 10.3390/microorganisms11040969] [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: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Esters of weak acids have shown improved antimycobacterial activity over the corresponding free acids and nitro benzoates in particular have previously shown to have a very intriguing activity. To expand the potential of nitro-derivatives of benzoic acid as antimycobacterial drugs and explore the effects of various structural features on the activity of these compounds, we have obtained a library of 64 derivatives containing esters and thioesters of benzoates and studied their activity against M. tuberculosis, the stability of the compounds, their activation by mycobacterial enzymes and the potential cytotoxicity against human monocytic THP-1 cell line. Our results showed that the most active compounds are those with an aromatic nitro substitution, with the 3,5-dinitro esters series being the most active. Also, the greater antitubercular activity for the nitro derivatives was shown to be unrelated to their pKa values or hydrolysis rates. Given the conventional relationship between nitro-containing substances and toxicity, one might anticipate that the great antimicrobial activity of nitro compounds would be associated with high toxicity; yet, we have not found such a relationship. The nitrobenzoate scaffold, particularly the 3,5-dinitrobenzoate scaffold, merits further investigation, because it has the potential to generate future antimycobacterial agents with improved activity.
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Affiliation(s)
- João P Pais
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Olha Antoniuk
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Raquel Freire
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - David Pires
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Center for Interdisciplinary Research in Health, Católica Medical School, Universidade Católica Portuguesa, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
| | - Emília Valente
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Elsa Anes
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Luis Constantino
- Research Institute for Medicines (iMed.UL), Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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10
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Batt SM, Toth S, Rodriguez B, Abrahams KA, Veerapen N, Chiodarelli G, Cox LR, Moynihan PJ, Lelievre J, Fütterer K, Besra GS. Assay development and inhibition of the Mt-DprE2 essential reductase from Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001288. [PMID: 36748627 PMCID: PMC9993113 DOI: 10.1099/mic.0.001288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DprE2 is an essential enzyme in the synthesis of decaprenylphosphoryl-β-d-arabinofuranose (DPA) and subsequently arabinogalactan, and is a significant new drug target for M. tuberculosis. Two compounds from the GSK-177 box set, GSK301A and GSK032A, were identified through Mt-DprE2-target overexpression studies. The Mt-DprE1-DprE2 complex was co-purified and a new in vitro DprE2 assay developed, based on the oxidation of the reduced nicotinamide adenine dinucleotide cofactor of DprE2 (NADH/NADPH). The Mt-DprE1-DprE2 complex showed interesting kinetics in both the DprE1 resazurin-based assay, where Mt-DprE2 was found to enhance Mt-DprE1 activity and reduce substrate inhibition; and also in the DprE2 assay, which similarly exhibited substrate inhibition and a difference in kinetics of the two potential cofactors, NADH and NADPH. Although, no inhibition was observed in the DprE2 assay by the two GSK set compounds, spontaneous mutant generation indicated a possible explanation in the form of a pro-drug activation pathway, involving fgd1 and fbiC.
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Affiliation(s)
- Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Szilvi Toth
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Beatriz Rodriguez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Liam R Cox
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Klaus Fütterer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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11
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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [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: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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12
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Imran M. Ethionamide and Prothionamide Based Coumarinyl-Thiazole Derivatives: Synthesis, Antitubercular Activity, Toxicity Investigations and Molecular Docking Studies. Pharm Chem J 2022; 56:1215-1225. [PMCID: PMC9734486 DOI: 10.1007/s11094-022-02782-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Mohd Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha, Saudi Arabia
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13
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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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14
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Richter A, Seidel R, Goddard R, Eckhardt T, Lehmann C, Dörner J, Siersleben F, Sondermann T, Mann L, Patzer M, Jäger C, Reiling N, Imming P. BTZ-Derived Benzisothiazolinones with In Vitro Activity against Mycobacterium tuberculosis. ACS Med Chem Lett 2022; 13:1302-1310. [PMID: 35982823 PMCID: PMC9380706 DOI: 10.1021/acsmedchemlett.2c00215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022] Open
Abstract
8-Nitro-1,3-benzothiazin-4-ones (BTZs) are known as potent antitubercular agents. BTZ043 as one of the most advanced compounds has reached clinical trials. The putative oxidation products of BTZ043, namely, the corresponding BTZ sulfoxide and sulfone, were reported in this journal (Tiwari et al. ACS Med. Chem Lett. 2015, 6, 128-133). The molecular structures were later revised to the constitutionally isomeric benzisothiazolone and its 1-oxide, respectively. Here, we report two BTZ043-derived benzisothiazolinones (BITs) with in vitro activity against mycobacteria. The constitutionally isomeric O-acyl benzisothiazol-3-ols, in contrast, show little or no antimycobacterial activity in vitro. The structures of the four compounds were investigated by X-ray crystallography and NMR spectroscopy. Molecular covalent docking of the new compounds to Mycobacerium tuberculosis decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) suggests that the active BITs exert antimycobacterial activity through inhibition of DprE1 like BTZs.
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Affiliation(s)
- Adrian Richter
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Rüdiger
W. Seidel
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Richard Goddard
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Tamira Eckhardt
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Christoph Lehmann
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Julia Dörner
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Fabienne Siersleben
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Theresia Sondermann
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Lea Mann
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Michael Patzer
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christian Jäger
- Fraunhofer-Institut
für Zelltherapie und Immunologie, Außenstelle Molekulare Wirkstoffbiochemie und Therapieentwicklung, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Norbert Reiling
- Microbial
Interface Biology, Research Center Borstel,
Leibniz Lung Center, 23845 Borstel, Germany
- German
Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - Peter Imming
- Martin-Luther-Universität
Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
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15
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Singh R, Kumar S, Bhardwaj VK, Purohit R. Screening and reckoning of potential therapeutic agents against DprE1 protein of Mycobacterium tuberculosis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Schieferdecker S, Bernal FA, Wojtas KP, Keiff F, Li Y, Dahse HM, Kloss F. Development of Predictive Classification Models for Whole Cell Antimycobacterial Activity of Benzothiazinones. J Med Chem 2022; 65:6748-6763. [PMID: 35502994 DOI: 10.1021/acs.jmedchem.2c00098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nitrobenzothiazinones (BTZs) are a very potent class of antibiotics against Mycobacterium tuberculosis. However, relationships between their structural properties and whole cell activity remain poorly predictable. Herein, we present the synthesis and antimycobacterial evaluation of a diverse set of BTZs. High potency was predominantly achieved by piperidine and piperazine substitutions, whereupon three compounds were identified as promising candidates, showing preferable metabolic stability. Lack of correlation between potency and calculated binding energies suggested that target inhibition is not the only requirement to obtain suitable antimycobacterial agents. In contrast, prediction of whole cell activity class was successfully accomplished by extensively validated machine learning models. The performance of the superior model was further verified by >70% correct class predictions for a large set of reported BTZs. Our generated model is thus a key prerequisite to streamline lead optimization endeavors, particularly regarding the improvement of overall hit rates in whole cell antimycobacterial assays.
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Affiliation(s)
- Sebastian Schieferdecker
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Freddy A Bernal
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - K Philip Wojtas
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - François Keiff
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Yan Li
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Florian Kloss
- Transfer Group Anti-infectives, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
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17
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dos Santos Macêdo DC, Cavalcanti IDL, de Fátima Ramos dos Santos Medeiros SM, de Souza JB, de Britto Lira Nogueira MC, Cavalcanti IMF. Nanotechnology and tuberculosis: An old disease with new treatment strategies. Tuberculosis (Edinb) 2022; 135:102208. [DOI: 10.1016/j.tube.2022.102208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/22/2022] [Accepted: 04/17/2022] [Indexed: 11/16/2022]
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18
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Richter A, Seidel RW, Graf J, Goddard R, Lehmann C, Schlegel T, Khater N, Imming P. New Insight into Dearomatization and Decarbonylation of Antitubercular 4H-Benzo[e][1,3]thiazinones: Stable 5H- and 7H-Benzo[e][1,3]thiazines. ChemMedChem 2022; 17:e202200021. [PMID: 35170242 PMCID: PMC9306624 DOI: 10.1002/cmdc.202200021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 11/20/2022]
Abstract
8‐Nitro‐4H‐benzo[e][1,3]thiazinones (BTZs) are potent in vitro antimycobacterial agents. New chemical transformations, viz. dearomatization and decarbonylation, of two BTZs and their influence on the compounds’ antimycobacterial properties are described. Reactions of 8‐nitro‐2‐(piperidin‐1‐yl)‐6‐(trifluoromethyl)‐4H‐benzo[e][1,3]thiazin‐4‐one and the clinical drug candidate BTZ043 with the Grignard reagent CH3MgBr afford the corresponding dearomatized stable 4,5‐dimethyl‐5H‐ and 4,7‐dimethyl‐7H‐benzo[e][1,3]thiazines. These methine compounds are structurally characterized by X‐ray crystallography for the first time. Reduction of the BTZ carbonyl group, leading to the corresponding markedly non‐planar 4H‐benzo[e][1,3]thiazine systems, is achieved using the reducing agent (CH3)2S ⋅ BH3. Double methylation with dearomatization and decarbonylation renders the two BTZs studied inactive against Mycobacterium tuberculosis and Mycobacterium smegmatis, as proven by in vitro growth inhibition assays.
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Affiliation(s)
- Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Rüdiger W Seidel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Jürgen Graf
- Incoatec GmbH, Max-Planck-Str. 2, 21502, Geesthacht, Germany
| | - Richard Goddard
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Christoph Lehmann
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Tom Schlegel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Nour Khater
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
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19
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Scarim CB, Pavan FR. Recent advancement in drug development of nitro(NO 2 )-heterocyclic compounds as lead scaffolds for the treatment of Mycobacterium tuberculosis. Drug Dev Res 2022; 83:842-858. [PMID: 35106801 DOI: 10.1002/ddr.21921] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/26/2021] [Accepted: 01/13/2022] [Indexed: 11/11/2022]
Abstract
Tuberculosis (TB) is an infectious disease caused predominantly by Mycobacterium tuberculosis (Mtb). It was responsible for approximately 1.4 million deaths worldwide in 2019. The lack of new drugs to treat drug-resistant strains is a principal factor for the slow rise in TB infections. Our aim is to aid the development of new TB treatments by describing improvements (last decade, 2011-2021) to nitro(NO2 )-based compounds that have shown activity or pharmacological properties (e.g., anti-proliferative, anti-kinetoplastid) against Mtb. For all compounds, we have included final correlations of minimum inhibitory concentrations against Mtb (H37 Rv).
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Affiliation(s)
- Cauê Benito Scarim
- Department of Cell and Molecular Biology, University of Mississippi Medical Center (UMMC), Jackson, Mississippi, USA
| | - Fernando Rogério Pavan
- School of Pharmaceutical Sciences, Sao Paulo State University (UNESP), Araraquara, Sao Paulo, Brazil
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20
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Structural elucidation of the antitubercular benzothiazinone BTZ043: A combined X-ray, variable temperature NMR and DFT study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis. Molecules 2021; 26:molecules26237082. [PMID: 34885662 PMCID: PMC8659263 DOI: 10.3390/molecules26237082] [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: 10/15/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/04/2022] Open
Abstract
The elucidation of the structure of enzymes and their complexes with ligands continues to provide invaluable insights for the development of drugs against many diseases, including bacterial infections. After nearly three decades since the World Health Organization’s (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. The structural elucidation of enzyme-ligand complexes is fundamental to identify hot-spots, define possible interaction sites, and elaborate strategies to develop optimized molecules with high affinity. This review offers a critical and comprehensive overview of the most recent structural information on traditional and emerging mycobacterial enzymatic targets. A selection of more than twenty enzymes is here discussed, with a special emphasis on the analysis of their binding sites, the definition of the structure–activity relationships (SARs) of their inhibitors, and the study of their main intermolecular interactions. This work corroborates the potential of structural studies, substantiating their relevance in future anti-mycobacterial drug discovery and development efforts.
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22
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Synthesis, structural characterization and antimycobacterial evaluation of several halogenated non-nitro benzothiazinones. Med Chem Res 2021; 30:1523-1533. [PMID: 34131377 PMCID: PMC8192043 DOI: 10.1007/s00044-021-02735-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 10/25/2022]
Abstract
8-Nitro-1,3-benzothiazin-4-ones (BTZs), with BTZ043 and PBTZ169 as the most advanced compounds, represent a new class of potent antitubercular agents, which irreversibly inhibit decaprenylphosphoryl-β-d-ribose-2'-epimerase (DprE1), an enzyme crucial for cell wall synthesis in the pathogen Mycobacterium tuberculosis. Synthesis, structural characterization and in vitro testing against Mycobacterium aurum DSM 43999 and M. tuberculosis H37Rv of halogenated 2-(4-ethoxycarbonylpiperazin-1-yl)-1,3-benzothiazin-4-ones lacking a nitro group are reported. X-ray crystallography reveals that the structure of the BTZ scaffold can significantly deviate from planarity. In contrast to recent reports, the results of the present study indicate that further investigation of halogenated non-nitro BTZs for antitubercular activity is less than a promising approach.
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23
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Richter A, Goddard R, Schlegel T, Imming P, Seidel RW. 2-Chloro-3-nitro-5-(tri-fluoro-meth-yl)benzoic acid and -benzamide: structural characterization of two precursors for anti-tubercular benzo-thia-zinones. Acta Crystallogr E Crystallogr Commun 2021; 77:142-147. [PMID: 33614143 PMCID: PMC7869535 DOI: 10.1107/s2056989021000517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 01/13/2021] [Indexed: 11/10/2022]
Abstract
8-Nitro-1,3-benzo-thia-zin-4-ones are a promising class of new anti-tubercular agents, two candidates of which, namely BTZ043 and PBTZ169 (INN: macozinone), have reached clinical trials. The crystal and mol-ecular structures of two synthetic precursors, 2-chloro-3-nitro-5-(tri-fluoro-meth-yl)benzoic acid, C8H3ClF3NO4 (1), and 2-chloro-3-nitro-5-(tri-fluoro-meth-yl)benzamide, C8H4ClF3N2O3 (2), are reported. In 1 and 2, the respective carb-oxy, carboxamide and the nitro groups are significantly twisted out of the plane of the benzene ring. In 1, the nitro group is oriented almost perpendicular to the benzene ring plane. In the crystal, 1 and 2 form O-H⋯O and N-H⋯O hydrogen-bonded dimers, respectively, which in 2 extend into primary amide tapes along the [101] direction. The tri-fluoro-methyl group in 2 exhibits rotational disorder with an occupancy ratio of 0.876 (3):0.124 (3).
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Affiliation(s)
- Adrian Richter
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Richard Goddard
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Tom Schlegel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Rüdiger W. Seidel
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
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Baptista R, Bhowmick S, Shen J, Mur LAJ. Molecular Docking Suggests the Targets of Anti-Mycobacterial Natural Products. Molecules 2021; 26:475. [PMID: 33477495 PMCID: PMC7831053 DOI: 10.3390/molecules26020475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is a major global threat, mostly due to the development of antibiotic-resistant forms of Mycobacterium tuberculosis, the causal agent of the disease. Driven by the pressing need for new anti-mycobacterial agents several natural products (NPs) have been shown to have in vitro activities against M. tuberculosis. The utility of any NP as a drug lead is augmented when the anti-mycobacterial target(s) is unknown. To suggest these, we used a molecular reverse docking approach to predict the interactions of 53 selected anti-mycobacterial NPs against known "druggable" mycobacterial targets ClpP1P2, DprE1, InhA, KasA, PanK, PknB and Pks13. The docking scores/binding free energies were predicted and calculated using AutoDock Vina along with physicochemical and structural properties of the NPs, using PaDEL descriptors. These were compared to the established inhibitor (control) drugs for each mycobacterial target. The specific interactions of the bisbenzylisoquinoline alkaloids 2-nortiliacorinine, tiliacorine and 13'-bromotiliacorinine against the targets PknB and DprE1 (-11.4, -10.9 and -9.8 kcal·mol-1; -12.7, -10.9 and -10.3 kcal·mol-1, respectively) and the lignan α-cubebin and Pks13 (-11.0 kcal·mol-1) had significantly superior docking scores compared to controls. Our approach can be used to suggest predicted targets for the NP to be validated experimentally, but these in silico steps are likely to facilitate drug optimization.
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Affiliation(s)
- Rafael Baptista
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, Wales SY23 2DA, UK; (R.B.); (S.B.)
| | - Sumana Bhowmick
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, Wales SY23 2DA, UK; (R.B.); (S.B.)
| | - Jianying Shen
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, Wales SY23 2DA, UK; (R.B.); (S.B.)
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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25
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Zhang G, Sheng L, Hegde P, Li Y, Aldrich CC. 8-cyanobenzothiazinone analogs with potent antitubercular activity. Med Chem Res 2021; 30:449-458. [PMID: 33462533 PMCID: PMC7805566 DOI: 10.1007/s00044-020-02676-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 01/27/2023]
Abstract
8-Nitrobenzothiazinones (BTZs) exemplified by macozinone are a new class of antitubercular agents with exceptionally potent activity. The aryl nitro group has been considered indispensable for activity since this is bioactivated within mycobacteria by the flavoenzyme DprE1 to a reactive nitroso metabolite that covalently labels Cys387. However, the aryl nitro group is a potential liability with regards to safety, stability, and resistance. In this paper, we introduced a nitrile as a bioisosteric replacement of the nitro group, which we hypothesize can maintain a similar covalent mechanism of inhibition, but mitigate against the aforementioned concerns. 8-cyanobenzothiazinone 1d displayed potent antitubercular activity with an MIC of 130 nM and had an improved volume of distribution in mice that increased the intrinsic half-life by twofold compared to macozinone. Analysis of the C-2 substituent of 1d revealed similar structure-activity relationships as observed for macozinone. Overall, the results confirm the 8-nitro group of benzothiazinones can be successfully replaced with a nitrile to retain useful activity and favorable pharmacokinetic properties.
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Affiliation(s)
- Gang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050 China
| | - Li Sheng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050 China
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Yan Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050 China
| | - Courtney C. Aldrich
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050 China
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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Liu R, Markley L, Miller PA, Franzblau S, Shetye G, Ma R, Savková K, Mikušová K, Lee BS, Pethe K, Moraski GC, Miller MJ. Hydride-induced Meisenheimer complex formation reflects activity of nitro aromatic anti-tuberculosis compounds. RSC Med Chem 2021; 12:62-72. [PMID: 34046598 PMCID: PMC8130608 DOI: 10.1039/d0md00390e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/13/2020] [Indexed: 11/21/2022] Open
Abstract
The formation efficiency of hydride-induced Meisenheimer complexes of nitroaromatic compounds is consistent with their anti-TB activities exemplied by MDL860 and benzothiazol N-oxide (BTO) analogs. Herein we report that nitro cyano phenoxybenzenes (MDL860 and analogs) reacted slowly and incompletely which reflected their moderate anti-TB activity, in contrast to the instantaneous reaction of BTO derivatives to quantitatively generate Meisenheimer complexes which corresponded to their enhanced anti-TB activity. These results were corroborated by mycobacterial and radiolabelling studies that confirmed inhibition of the DprE1 enzyme by BTO derivatives but not MDL860 analogs.
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Affiliation(s)
- Rui Liu
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Lowell Markley
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Patricia A Miller
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
| | - Scott Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago Il 60612 USA
| | - Gauri Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago Il 60612 USA
| | - Rui Ma
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago 833 South Wood Street Chicago Il 60612 USA
| | - Karin Savková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava Ilkovičova 6 84215 Bratislava Slovakia
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava Ilkovičova 6 84215 Bratislava Slovakia
| | - Bei Shi Lee
- School of Biological Sciences, Nanyang Technological University Singapore 637551
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University Singapore 637551
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore 636921
| | - Garrett C Moraski
- Department of Chemistry and Biochemistry, Montana State University Bozeman MT 59717 USA
| | - Marvin J Miller
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame IN 46556 USA
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Patel A, Redinger N, Richter A, Woods A, Neumann PR, Keegan G, Childerhouse N, Imming P, Schaible UE, Forbes B, Dailey LA. In vitro and in vivo antitubercular activity of benzothiazinone-loaded human serum albumin nanocarriers designed for inhalation. J Control Release 2020; 328:339-349. [PMID: 32827612 DOI: 10.1016/j.jconrel.2020.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 08/10/2020] [Accepted: 08/16/2020] [Indexed: 01/03/2023]
Abstract
The aim of this study was to investigate the potential of human serum albumin (HSA) as a solubilising agent/drug delivery vehicle for pulmonary administration of antimycobacterial benzothiazinone (BTZ) compounds. The solubility of four novel BTZ compounds (IR 20, IF 274, FG 2, AR 112) was enhanced 2 to 140-fold by incubation with albumin (0.38-134 μg/mL). Tryptophan 213 residue quenching studies indicated moderate binding strength to Sudlow's site I. Nanoparticle manufacture achieved 37-60% encapsulation efficiency in HSA particles (169 nm, zeta potential -31 mV). Drug release was triggered by proteases with >50% released in 4 h. The antimycobacterial activity of IR 20 and FG 2 loaded in HSA nanoparticles was enhanced compared to DMSO/phosphate buffered saline (PBS) or albumin/PBS solutions in an in vitro M. tuberculosis-infected macrophage model. Intranasal instillation was used to achieve pulmonary delivery daily over 10 days to M. tuberculosis infected mice for FG2 HSA nanoparticles (0.4 mg/kg), FG 2 DMSO/saline (0.4 and 8 mg/kg) and a reference compound, BTZ043, DMSO/saline (0.4 and 8 mg/kg). A lower lung M. tuberculosis burden was apparent for all BTZ cohorts, but only significant for BTZ043 at both doses. In conclusion, mechanisms of HSA nanoparticle loading and release of BTZ compounds were demonstrated, enhanced antimycobacterial activity of the nanoparticle formulations was demonstrated in a biorelevant in vitro bioassay and the effectiveness of BTZ by pulmonary delivery in vivo was established with pilot evidence for effectiveness when delivered by HSA nanoparticles. Finally, the feasibility of developing an inhaled nanoparticle-in-microparticle powder formulation was ascertained.
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Affiliation(s)
- Ayasha Patel
- Drug Delivery Research Group, Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Natalja Redinger
- Forschungszentrum Borstel - Leibniz Lung Center, PA Infections, Div. Cellular Microbiology, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Germany
| | - Adrian Richter
- Martin Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Str.4, 06120 Halle, Germany
| | - Arcadia Woods
- Drug Delivery Research Group, Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Paul Robert Neumann
- Martin Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Str.4, 06120 Halle, Germany
| | - Gemma Keegan
- Vectura Group plc, One Prospect West, Chippenham SN14 6FH, United Kingdom
| | - Nick Childerhouse
- Vectura Group plc, One Prospect West, Chippenham SN14 6FH, United Kingdom
| | - Peter Imming
- Martin Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Str.4, 06120 Halle, Germany
| | - Ulrich E Schaible
- Forschungszentrum Borstel - Leibniz Lung Center, PA Infections, Div. Cellular Microbiology, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Germany
| | - Ben Forbes
- Drug Delivery Research Group, Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom.
| | - Lea Ann Dailey
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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Eckhardt T, Goddard R, Rudolph I, Richter A, Lehmann C, Imming P, Seidel RW. [2-Chloro-3-nitro-5-(tri-fluoro-meth-yl)phen-yl](piperidin-1-yl)methanone: structural characterization of a side product in benzo-thia-zinone synthesis. Acta Crystallogr E Crystallogr Commun 2020; 76:1442-1446. [PMID: 32939297 PMCID: PMC7472761 DOI: 10.1107/s2056989020010658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/03/2020] [Indexed: 11/23/2022]
Abstract
1,3-Benzo-thia-zin-4-ones (BTZs) are a promising new class of anti-tuberculosis drug candidates, some of which have reached clinical trials. The title compound, the benzamide derivative [2-chloro-3-nitro-5-(tri-fluoro-meth-yl)phen-yl](piper-id-in-1-yl)methanone, C13H12ClF3N2O3, occurs as a side product as a result of competitive reaction pathways in the nucleophilic attack during the synthesis of the BTZ 8-nitro-2-(piperidin-1-yl)-6-(tri-fluoro-meth-yl)-1,3-benzo-thia-zin-4-one, following the original synthetic route, whereby the corresponding benzoyl iso-thio-cyanate is reacted with piperidine as secondary amine. In the title compound, the nitro group and the nearly planar amide group are significantly twisted out of the plane of the benzene ring. The piperidine ring adopts a chair conformation. The tri-fluoro-methyl group exhibits slight rotational disorder with a refined ratio of occupancies of 0.972 (2):0.028 (2). There is structural evidence for inter-molecular weak C-H⋯O hydrogen bonds.
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Affiliation(s)
- Tamira Eckhardt
- Institut für Pharmazie, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Richard Goddard
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ines Rudolph
- Institut für Pharmazie, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Adrian Richter
- Institut für Pharmazie, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Christoph Lehmann
- Institut für Pharmazie, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Peter Imming
- Institut für Pharmazie, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Rüdiger W. Seidel
- Institut für Pharmazie, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
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29
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Promiscuous Targets for Antitubercular Drug Discovery: The Paradigm of DprE1 and MmpL3. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10020623] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The development and spread of Mycobacterium tuberculosis multi-drug resistant strains still represent a great global health threat, leading to an urgent need for novel anti-tuberculosis drugs. Indeed, in the last years, several efforts have been made in this direction, through a number of high-throughput screenings campaigns, which allowed for the identification of numerous hit compounds and novel targets. Interestingly, several independent screening assays identified the same proteins as the target of different compounds, and for this reason, they were named “promiscuous” targets. These proteins include DprE1, MmpL3, QcrB and Psk13, and are involved in the key pathway for M. tuberculosis survival, thus they should represent an Achilles’ heel which could be exploited for the development of novel effective drugs. Indeed, among the last molecules which entered clinical trials, four inhibit a promiscuous target. Within this review, the two most promising promiscuous targets, the oxidoreductase DprE1 involved in arabinogalactan synthesis and the mycolic acid transporter MmpL3 are discussed, along with the latest advancements in the development of novel inhibitors with anti-tubercular activity.
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Karabanovich G, Dušek J, Savková K, Pavliš O, Pávková I, Korábečný J, Kučera T, Kočová Vlčková H, Huszár S, Konyariková Z, Konečná K, Jand'ourek O, Stolaříková J, Korduláková J, Vávrová K, Pávek P, Klimešová V, Hrabálek A, Mikušová K, Roh J. Development of 3,5-Dinitrophenyl-Containing 1,2,4-Triazoles and Their Trifluoromethyl Analogues as Highly Efficient Antitubercular Agents Inhibiting Decaprenylphosphoryl-β-d-ribofuranose 2'-Oxidase. J Med Chem 2019; 62:8115-8139. [PMID: 31393122 DOI: 10.1021/acs.jmedchem.9b00912] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report herein the discovery of 3,5-dinitrophenyl 1,2,4-triazoles with excellent and selective antimycobacterial activities against Mycobacterium tuberculosis strains, including clinically isolated multidrug-resistant strains. Thorough structure-activity relationship studies of 3,5-dinitrophenyl-containing 1,2,4-triazoles and their trifluoromethyl analogues revealed the key role of the position of the 3,5-dinitrophenyl fragment in the antitubercular efficiency. Among the prepared compounds, the highest in vitro antimycobacterial activities against M. tuberculosis H37Rv and against seven clinically isolated multidrug-resistant strains of M. tuberculosis were found with S-substituted 4-alkyl-5-(3,5-dinitrophenyl)-4H-1,2,4-triazole-3-thiols and their 3-nitro-5-(trifluoromethyl)phenyl analogues. The minimum inhibitory concentrations of these compounds reached 0.03 μM, which is superior to all the current first-line anti-tuberculosis drugs. Furthermore, almost all compounds with excellent antimycobacterial activities exhibited very low in vitro cytotoxicities against two proliferating mammalian cell lines. The docking study indicated that these compounds acted as the inhibitors of decaprenylphosphoryl-β-d-ribofuranose 2'-oxidase enzyme, which was experimentally confirmed by two independent radiolabeling experiments.
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Affiliation(s)
- Galina Karabanovich
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Jan Dušek
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Karin Savková
- Faculty of Natural Sciences, Department of Biochemistry , Comenius University in Bratislava , Mlynská Dolina, Ilkovičova 6 , 842 15 Bratislava , Slovakia
| | - Oto Pavliš
- Biological Defense Department , Military Health Institute , 561 64 Techonin , Czech Republic
| | - Ivona Pávková
- Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 50005 Hradec Králové , Czech Republic
| | - Jan Korábečný
- Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 50005 Hradec Králové , Czech Republic.,Biomedical Research Center , University Hospital Hradec Králové , Sokolska 581 , 500 05 Hradec Králové , Czech Republic
| | - Tomáš Kučera
- Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 50005 Hradec Králové , Czech Republic
| | - Hana Kočová Vlčková
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Stanislav Huszár
- Faculty of Natural Sciences, Department of Biochemistry , Comenius University in Bratislava , Mlynská Dolina, Ilkovičova 6 , 842 15 Bratislava , Slovakia
| | - Zuzana Konyariková
- Faculty of Natural Sciences, Department of Biochemistry , Comenius University in Bratislava , Mlynská Dolina, Ilkovičova 6 , 842 15 Bratislava , Slovakia
| | - Klára Konečná
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Ondřej Jand'ourek
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Jiřina Stolaříková
- Department of Bacteriology and Mycology , Regional Institute of Public Health , Partyzánské náměstí 7 , 70200 Ostrava , Czech Republic
| | - Jana Korduláková
- Faculty of Natural Sciences, Department of Biochemistry , Comenius University in Bratislava , Mlynská Dolina, Ilkovičova 6 , 842 15 Bratislava , Slovakia
| | - Kateřina Vávrová
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Petr Pávek
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Věra Klimešová
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Alexandr Hrabálek
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
| | - Katarína Mikušová
- Faculty of Natural Sciences, Department of Biochemistry , Comenius University in Bratislava , Mlynská Dolina, Ilkovičova 6 , 842 15 Bratislava , Slovakia
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Králové , Charles University , Akademika Heyrovského 1203 , 50005 Hradec Králové , Czech Republic
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Bahuguna A, Rawat DS. An overview of new antitubercular drugs, drug candidates, and their targets. Med Res Rev 2019; 40:263-292. [PMID: 31254295 DOI: 10.1002/med.21602] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
The causative agent of tuberculosis (TB), Mycobacterium tuberculosis and more recently totally drug-resistant strains of M. tuberculosis, display unique mechanisms to survive in the host. A four-drug treatment regimen was introduced 40 years ago but the emergence of multidrug-resistance and more recently TDR necessitates the identification of new targets and drugs for the cure of M. tuberculosis infection. The current efforts in the drug development process are insufficient to completely eradicate the TB epidemic. For almost five decades the TB drug development process remained stagnant. The last 10 years have made sudden progress giving some new and highly promising drugs including bedaquiline, delamanid, and pretomanid. Many of the candidates are repurposed compounds, which were developed to treat other infections but later, exhibited anti-TB properties also. Each class of drug has a specific target and a definite mode of action. These targets are either involved in cell wall biosynthesis, protein synthesis, DNA/RNA synthesis, or metabolism. This review discusses recent progress in the discovery of newly developed and Food and Drug Administration approved drugs as well as repurposed drugs, their targets, mode of action, drug-target interactions, and their structure-activity relationship.
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Affiliation(s)
| | - Diwan S Rawat
- Department of Chemistry, University of Delhi, Delhi, India
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32
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Spaggiari D, Desfontaine V, Cruchon S, Guinchard S, Vocat A, Blattes E, Pitteloud J, Ciullini L, Bardinet C, Ivanyuk A, Makarov V, Ryabova O, Buclin T, Cole ST, Decosterd LA. Development and validation of a multiplex UHPLC-MS/MS method for the determination of the investigational antibiotic against multi-resistant tuberculosis macozinone (PBTZ169) and five active metabolites in human plasma. PLoS One 2019; 14:e0217139. [PMID: 31150423 PMCID: PMC6544242 DOI: 10.1371/journal.pone.0217139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/07/2019] [Indexed: 12/31/2022] Open
Abstract
The emergence of Mycobacterium tuberculosis strains resistant to current first-line antibiotic regimens constitutes a major global health threat. New treatments against multidrug-resistant tuberculosis (MDR-TB) are thus eagerly needed in particular in countries with a high MDR-TB prevalence. In this context, macozinone (PBTZ169), a promising drug candidate with an unique mode of action and highly potent in vitro tuberculocidal properties against MDR Mycobacterium strains, has now reached the clinical phase and has been notably tested in healthy male volunteers in Switzerland. To that endeavor, a multiplex UHPLC-MS/MS method has been developed for the sensitive and accurate human plasma levels determination of PBTZ169 along with five metabolites retaining in vitro anti-TB activity. Plasma protein precipitation with methanol was carried out as a simplified sample clean-up procedure followed by direct injection of the undiluted supernatant for the bioanalysis of the six analytes within 5 min, using 1.8 μm reversed-phase chromatography coupled to triple quadrupole mass spectrometry employing electrospray ionization in the positive mode. Stable isotopically-labelled PBTZ169 was used as internal standard (ISTD), while metabolites could be reliably quantified using two unlabeled chemical analogues selected as ISTD from a large in-house analogous compounds library. The overall methodology was fully validated according to current recommendations (FDA, EMEA) for bioanalytical methods, which include selectivity, carryover, qualitative and quantitative matrix effect, extraction recovery, process efficiency, trueness, precision, accuracy profiles, method and instrument detection limits, integrity to dilution, anticoagulant comparison and short- and long-term stabilities. Stability studies on the reduced metabolite H2-PBTZ169 have shown no significant impact on the actual PBTZ169 concentrations determined with the proposed assay. This simplified, rapid, sensitive and robust methodology has been applied to the bioanalysis of human plasma samples collected within the frame of a phase I clinical study in healthy volunteers receiving PBTZ169.
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Affiliation(s)
- Dany Spaggiari
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Vincent Desfontaine
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Sandra Cruchon
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Sylvie Guinchard
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Emilyne Blattes
- Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland
| | - Jeff Pitteloud
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Lorenzo Ciullini
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Carine Bardinet
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Anton Ivanyuk
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Vadim Makarov
- Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland
- Federal Research Center “Fundamentals of Biotechnology RAS”, Moscow, Russia
| | - Olga Ryabova
- Federal Research Center “Fundamentals of Biotechnology RAS”, Moscow, Russia
| | - Thierry Buclin
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Stewart T. Cole
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
- Innovative Medicines for Tuberculosis (IM4TB), Lausanne, Switzerland
| | - Laurent A. Decosterd
- Laboratory & Service of Clinical Pharmacology, Department of Laboratories, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Nosova EV, Batanova OA, Lipunova GN, Kotovskaya SK, Slepukhin PA, Kravchenko MA, Charushin VN. SYNTHESIS AND ANTITUBERCULAR EVALUATION OF FLUORINATED 2-CYCLOALKYLIMINO SUBSTITUTED 1,3-BENZOTHIAZIN-4-ONES. J Fluor Chem 2019. [DOI: 10.1016/j.jfluchem.2019.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Zhang G, Howe M, Aldrich CC. Spirocyclic and Bicyclic 8-Nitrobenzothiazinones for Tuberculosis with Improved Physicochemical and Pharmacokinetic Properties. ACS Med Chem Lett 2019; 10:348-351. [PMID: 30891138 PMCID: PMC6421526 DOI: 10.1021/acsmedchemlett.8b00634] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
8-Nitrobenzothiazinones (BTZs) typified by the second-generation analogue PBTZ169 are a new class of antitubercular agents. The activity of BTZs and lipophilicity are tightly coupled since the molecular target DprE1 is located in the mycobacterial cell envelope. A series of analogues was designed to address the notorious insolubility of the BTZs while preserving the required lipophilicity. This was accomplished by decreasing the molecular planarity and symmetry through bioisosteric replacement of the piperazine moiety of PBTZ169 with spirocyclic and bicyclic diamines. Several promising compounds with improved aqueous solubilities were identified with potent antitubercular activity. Compound 5 was identified as the most promising candidate based on its excellent antitubercular activity (MIC of 32 nM), more than 1000-fold improvement in solubility, 2-fold lower clearance in mouse and human microsomes relative to PBTZ169, and promising pharmacokinetic parameters.
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Affiliation(s)
- Gang Zhang
- State
Key Laboratory of Bioactive Substances and Function of Natural Medicine,
Institute of Materia Medica, Peking Union
Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Michael Howe
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Courtney C. Aldrich
- State
Key Laboratory of Bioactive Substances and Function of Natural Medicine,
Institute of Materia Medica, Peking Union
Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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