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Shekhar, Roquet-Banères F, Anand A, Kremer L, Kumar V. Rational design and microwave-promoted synthesis of triclosan-based dimers: targeting InhA for anti-mycobacterial profiling. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240676. [PMID: 39392739 PMCID: PMC11461061 DOI: 10.1098/rsos.240676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/02/2024] [Accepted: 08/06/2024] [Indexed: 10/13/2024]
Abstract
A set of alkyl-/1H-1,2,3-triazole-based dimers was strategically designed and synthesized to evaluate their in vitro anti-mycobacterial activities against Mycobacterium tuberculosis and the non-tuberculous Mycobacterium abscessus strains. Systematic variations in the nature (alkyl/1H-1,2,3-triazole) and positioning of the linker were implemented based on the docking scores observed in the binding sites identified in the crystal structures of InhA from M. tuberculosis and M. abscessus. However, the in vitro evaluation results revealed that the synthesized compounds did not exhibit inhibitory effects on the growth of mycobacteria, even at the highest tested concentrations. The elevated lipophilicity values determined through ADMET studies for these synthesized dimers might be a contributing factor to their poor activity profiles.
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Affiliation(s)
- Shekhar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab143005, India
| | - Francoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Amit Anand
- Department of Chemistry, Khalsa College, Amritsar, Punjab143005, India
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
- INSERM, IRIM, 34293 Montpellier, France
| | - Vipan Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, Punjab143005, India
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2
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Kamera S, Sharma VK, Prasad V B, Garlapati A. Identification of potential inhibitors of Mtb InhA: a pharmacoinformatics approach. J Biomol Struct Dyn 2024; 42:7957-7971. [PMID: 37526169 DOI: 10.1080/07391102.2023.2242499] [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: 10/20/2022] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
The emergence of superbugs of multi-drug resistant (MDR/RR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (Mtb) strains at a faster rate is posing a serious threat to Tuberculosis (TB) control worldwide. Mtb enoyl-acyl carrier protein reductase (InhA) is a well-established target of the front-line anti-TB prodrug Isoniazid (INH), which requires activation by Catalase-peroxidase enzyme (KatG) in order to inhibit InhA enzyme, that is crucial for the biosynthesis of the mycobacterial cell wall. Currently, due to widespread resistance to this drug, it is necessary to identify new clinical candidates that directly inhibit InhA enzyme and do not require activation by KatG, thereby circumventing most of the resistance mechanisms. In the present study, high-throughput virtual screening of ASINEX database was carried out to identify potential direct inhibitors of Mtb InhA. Best twenty compounds with good binding energies ranging between -12.36 and -9.27 kcal/mol were selected as promising virtual screening hits. These molecules were subjected to ADME study followed by toxicity prediction. Finally, four top-ranked molecules which are structurally diverse and possess best binding affinity than the co-crystalized ligand have been chosen for MD simulation studies followed by MM-GBSA analysis to validate and ensure the stability of hits in the active site of the enzyme. Based on the 100 ns MD simulation studies and binding free energy estimates, three hit molecules B244, B369, and B310 could be considered as potential inhibitors for Mtb InhA, which are likely to be potent against INH-resistant Mtb strains after successful experimental validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sreelatha Kamera
- Medicinal Chemistry Division, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana, India
| | - Vishnu Kumar Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Bharatam Prasad V
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Achaiah Garlapati
- Medicinal Chemistry Division, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana, India
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3
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Kuralt V, Frlan R. Navigating the Chemical Space of ENR Inhibitors: A Comprehensive Analysis. Antibiotics (Basel) 2024; 13:252. [PMID: 38534687 DOI: 10.3390/antibiotics13030252] [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: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial resistance is a global health threat that requires innovative strategies against drug-resistant bacteria. Our study focuses on enoyl-acyl carrier protein reductases (ENRs), in particular FabI, FabK, FabV, and InhA, as potential antimicrobial agents. Despite their promising potential, the lack of clinical approvals for inhibitors such as triclosan and isoniazid underscores the challenges in achieving preclinical success. In our study, we curated and analyzed a dataset of 1412 small molecules recognized as ENR inhibitors, investigating different structural variants. Using advanced cheminformatic tools, we mapped the physicochemical landscape and identified specific structural features as key determinants of bioactivity. Furthermore, we investigated whether the compounds conform to Lipinski rules, PAINS, and Brenk filters, which are crucial for the advancement of compounds in development pipelines. Furthermore, we investigated structural diversity using four different representations: Chemotype diversity, molecular similarity, t-SNE visualization, molecular complexity, and cluster analysis. By using advanced bioinformatics tools such as matched molecular pairs (MMP) analysis, machine learning, and SHAP analysis, we were able to improve our understanding of the activity cliques and the precise effects of the functional groups. In summary, this chemoinformatic investigation has unraveled the FAB inhibitors and provided insights into rational antimicrobial design, seamlessly integrating computation into the discovery of new antimicrobial agents.
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Affiliation(s)
- Vid Kuralt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Frlan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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Tamhaev R, Grosjean E, Ahamed H, Chebaiki M, Rodriguez F, Recchia D, Degiacomi G, Pasca MR, Maveyraud L, Mourey L, Lherbet C. Exploring the plasticity of the InhA substrate-binding site using new diaryl ether inhibitors. Bioorg Chem 2024; 143:107032. [PMID: 38128204 DOI: 10.1016/j.bioorg.2023.107032] [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: 11/09/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a worldwide scourge with more than 10 million people affected yearly. Among the proteins essential for the survival of Mtb, InhA has been and is still clinically validated as a therapeutic target. A new family of direct diaryl ether inhibitors, not requiring prior activation by the catalase peroxidase enzyme KatG, has been designed with the ambition of fully occupying the InhA substrate-binding site. Thus, eleven compounds, featuring three pharmacophores within the same molecule, were synthesized. One of them, 5-(((4-(2-hydroxyphenoxy)benzyl)(octyl)amino)methyl)-2-phenoxyphenol (compound 21), showed good inhibitory activity against InhA with IC50 of 0.70 µM. The crystal structure of compound 21 in complex with InhA/NAD+ showed how the molecule fills the substrate-binding site as well as the minor portal of InhA. This study represents a further step towards the design of new inhibitors of InhA.
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Affiliation(s)
- Rasoul Tamhaev
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Emeline Grosjean
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Hikmat Ahamed
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Mélina Chebaiki
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Frédéric Rodriguez
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Deborah Recchia
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Giulia Degiacomi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
| | - Christian Lherbet
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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5
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Chebaiki M, Delfourne E, Tamhaev R, Danoun S, Rodriguez F, Hoffmann P, Grosjean E, Goncalves F, Azéma-Despeyroux J, Pál A, Korduláková J, Preuilh N, Britton S, Constant P, Marrakchi H, Maveyraud L, Mourey L, Lherbet C. Discovery of new diaryl ether inhibitors against Mycobacterium tuberculosis targeting the minor portal of InhA. Eur J Med Chem 2023; 259:115646. [PMID: 37482022 DOI: 10.1016/j.ejmech.2023.115646] [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: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) affects 10 million people each year and the emergence of resistant TB augurs for a growing incidence. In the last 60 years, only three new drugs were approved for TB treatment, for which resistances are already emerging. Therefore, there is a crucial need for new chemotherapeutic agents capable of eradicating TB. Enzymes belonging to the type II fatty acid synthase system (FAS-II) are involved in the biosynthesis of mycolic acids, cell envelope components essential for mycobacterial survival. Among them, InhA is the primary target of isoniazid (INH), one of the most effective compounds to treat TB. INH acts as a prodrug requiring activation by the catalase-peroxidase KatG, whose mutations are the major cause for INH resistance. Herein, a new series of direct InhA inhibitors were designed based on a molecular hybridization approach. They exhibit potent inhibitory activities of InhA and, for some of them, good antitubercular activities. Moreover, they display a low toxicity on human cells. A study of the mechanism of action of the most effective molecules shows that they inhibit the biosynthesis of mycolic acids. The X-ray structures of two InhA/NAD+/inhibitor complexes have been obtained showing a binding mode of a part of the molecule in the minor portal, rarely seen in the InhA structures reported so far.
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Affiliation(s)
- Mélina Chebaiki
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Evelyne Delfourne
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Rasoul Tamhaev
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Saïda Danoun
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Frédéric Rodriguez
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Pascal Hoffmann
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Emeline Grosjean
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Fernanda Goncalves
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Joëlle Azéma-Despeyroux
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Adrián Pál
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215, Bratislava, Slovakia
| | - Nadège Preuilh
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Patricia Constant
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
| | - Christian Lherbet
- Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.
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6
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Bieri C, Esmel A, Keita M, Owono LCO, Dali B, Megnassan E, Miertus S, Frecer V. Structure-Based Design and Pharmacophore-Based Virtual Screening of Combinatorial Library of Triclosan Analogues Active against Enoyl-Acyl Carrier Protein Reductase of Plasmodium falciparum with Favourable ADME Profiles. Int J Mol Sci 2023; 24:ijms24086916. [PMID: 37108083 PMCID: PMC10139228 DOI: 10.3390/ijms24086916] [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: 03/12/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Cost-effective therapy of neglected and tropical diseases such as malaria requires everlasting drug discovery efforts due to the rapidly emerging drug resistance of the plasmodium parasite. We have carried out computational design of new inhibitors of the enoyl-acyl carrier protein reductase (ENR) of Plasmodium falciparum (PfENR) using computer-aided combinatorial and pharmacophore-based molecular design. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) complexation QSAR model was developed for triclosan-based inhibitors (TCL) and a significant correlation was established between the calculated relative Gibbs free energies of complex formation (∆∆Gcom) between PfENR and TCL and the observed inhibitory potencies of the enzyme (IC50exp) for a training set of 20 known TCL analogues. Validation of the predictive power of the MM-PBSA QSAR model was carried out with the generation of 3D QSAR pharmacophore (PH4). We obtained a reasonable correlation between the relative Gibbs free energy of complex formation ∆∆Gcom and IC50exp values, which explained approximately 95% of the PfENR inhibition data: pIC50exp=-0.0544×∆∆Gcom+6.9336,R2=0.95. A similar agreement was established for the PH4 pharmacophore model of the PfENR inhibition (pIC50exp=0.9754×pIC50pre+0.1596, R2=0.98). Analysis of enzyme-inhibitor binding site interactions suggested suitable building blocks to be used in a virtual combinatorial library of 33,480 TCL analogues. Structural information derived from the complexation model and the PH4 pharmacophore guided us through in silico screening of the virtual combinatorial library of TCL analogues to finally identify potential new TCL inhibitors effective at low nanomolar concentrations. Virtual screening of the library by PfENR-PH4 led to a predicted IC50pre value for the best inhibitor candidate as low as 1.9 nM. Finally, the stability of PfENR-TCLx complexes and the flexibility of the active conformation of the inhibitor for selected top-ranking TCL analogues were checked with the help of molecular dynamics. This computational study resulted in a set of proposed new potent inhibitors with predicted antimalarial effects and favourable pharmacokinetic profiles that act on a novel pharmacological target, PfENR.
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Affiliation(s)
- Cecile Bieri
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Akori Esmel
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Luc Calvin Owono Owono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
| | - Brice Dali
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (Now Nangui Abrogoua), Abidjan 02, Côte d'Ivoire
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
- International Centre for Theoretical Physics, Strada Costiera 11, I-34151 Trieste, Italy
- Laboratoire de Cristallographie-Physique Moléculaire, Université De Cocody, Abidjan 22, Côte d'Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, Université De Cocody, Abidjan 22, Côte d'Ivoire
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
| | - Vladimir Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, SK-83232 Bratislava, Slovakia
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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8
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Trifluoromethylcinnamanilide Michael Acceptors for Treatment of Resistant Bacterial Infections. Int J Mol Sci 2022; 23:ijms232315090. [PMID: 36499415 PMCID: PMC9737391 DOI: 10.3390/ijms232315090] [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: 10/31/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
A series of thirty-two anilides of 3-(trifluoromethyl)cinnamic acid (series 1) and 4-(trifluoromethyl)cinnamic acid (series 2) was prepared by microwave-assisted synthesis. All the compounds were tested against reference strains Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212 and resistant clinical isolates of methicillin-resistant S. aureus (MRSA) and vancomycin-resistant E. faecalis (VRE). All the compounds were evaluated in vitro against Mycobacterium smegmatis ATCC 700084 and M. marinum CAMP 5644. (2E)-3-[3-(Trifluoromethyl)phenyl]-N-[4-(trifluoromethyl)phenyl]prop-2-enamide (1j), (2E)-N-(3,5-dichlorophenyl)-3-[3-(trifluoromethyl)phenyl]prop-2-enamide (1o) and (2E)-N-[3-(trifluoromethyl)phenyl]-3-[4-(trifluoromethyl)-phenyl]prop-2-enamide (2i), (2E)-N-[3,5-bis(trifluoromethyl)phenyl]-3-[4-(trifluoromethyl)phenyl]-prop-2-enamide (2p) showed antistaphylococcal (MICs/MBCs 0.15-5.57 µM) as well as anti-enterococcal (MICs/MBCs 2.34-44.5 µM) activity. The growth of M. marinum was strongly inhibited by compounds 1j and 2p in a MIC range from 0.29 to 2.34 µM, while all the agents of series 1 showed activity against M. smegnatis (MICs ranged from 9.36 to 51.7 µM). The performed docking study demonstrated the ability of the compounds to bind to the active site of the mycobacterial enzyme InhA. The compounds had a significant effect on the inhibition of bacterial respiration, as demonstrated by the MTT assay. The compounds showed not only bacteriostatic activity but also bactericidal activity. Preliminary in vitro cytotoxicity screening was assessed using the human monocytic leukemia cell line THP-1 and, except for compound 2p, all effective agents did show insignificant cytotoxic effect. Compound 2p is an interesting anti-invasive agent with dual (cytotoxic and antibacterial) activity, while compounds 1j and 1o are the most interesting purely antibacterial compounds within the prepared molecules.
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9
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Abdelaziz OA, Othman DIA, Abdel-Aziz MM, Badr SMI, Eisa HM. Novel diaryl ether derivatives as InhA inhibitors: Design, synthesis and antimycobacterial activity. Bioorg Chem 2022; 129:106125. [PMID: 36126606 DOI: 10.1016/j.bioorg.2022.106125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022]
Abstract
A new series of triclosan (TCL)-mimicking diaryl ether derivatives 7-25 were synthesized and evaluated as inhibitors of enoyl acyl carrier protein reductase InhA enzyme. In addition, these derivatives were screened as inhibitors of drug-susceptible (DS), multidrug-resistant (MDR), and extensive drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains. Most compounds exihibted superior anti-TB activities and improved ClogP compared to TCL as a standard drug. The present work has led to the identification of compounds 14, 19 and 24 which possess remarkable activities against DS, MDR and XDR MTB strains with MIC values of 1.95, 3.9 and 15.63 µg/ml, respectively for compound 14, 1.95, 3.9 and 7.81 µg/ml, respectively for compound 19 and 0.98, 1.95 and 3.9 µg/ml, respectively for compound 24. Most compounds did not exhibit toxicity to HePG2 normal cell line. Compounds 14, 19 and 24, presenting the best MIC values, were further evaluated as inhibitors of InhA enzyme. They showed high binding affinities in the micromolar range with IC50 values of 1.33, 0.6, and 0.29 µM for compounds 14, 19, and 24, respectively. Furthermore, molecular docking approach was utilized to understand the difference in bioactivities between the new compounds. In particular, the results revealed strong binding interactions and high docking scores of compounds 14, 19 and 24, which could correlate with their high activities. Mainly, the molecular modelling study of compound 24 provides an excellent platform for understanding the molecular mechanism regarding InhA inhibition. Thus, compound 24 could be a lead compound for future development of new antitubercular drugs.
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Affiliation(s)
- Ola A Abdelaziz
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Dina I A Othman
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Marwa M Abdel-Aziz
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Sahar M I Badr
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Hassan M Eisa
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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10
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Hanwarinroj C, Thongdee P, Sukchit D, Taveepanich S, Kamsri P, Punkvang A, Ketrat S, Saparpakorn P, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. In silico design of novel quinazoline-based compounds as potential Mycobacterium tuberculosis PknB inhibitors through 2D and 3D-QSAR, molecular dynamics simulations combined with pharmacokinetic predictions. J Mol Graph Model 2022; 115:108231. [PMID: 35667143 DOI: 10.1016/j.jmgm.2022.108231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 05/14/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
Serine/threonine protein kinase B (PknB) is essential to Mycobacterium tuberculosis (M. tuberculosis) cell division and metabolism and a potential anti-tuberculosis drug target. Here we apply Hologram Quantitative Structure Activity Relationship (HQSAR) and three-dimensional QSAR (Comparative Molecular Similarity Indices Analysis (CoMSIA)) methods to investigate structural requirements for PknB inhibition by a series of previously described quinazoline derivatives. PknB binding of quinazolines was evaluated by molecular dynamics (MD) simulations of the catalytic domain and binding energies calculated by Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) methods. Evaluation of a training set against experimental data showed both HQSAR and CoMSIA models to reliably predict quinazoline binding to PknB, and identified the quinazoline core and overall hydrophobicity as the major contributors to affinity. Calculated binding energies also agreed with experiment, and MD simulations identified hydrogen bonds to Glu93 and Val95, and hydrophobic interactions with Gly18, Phe19, Gly20, Val25, Thr99 and Met155, as crucial to PknB binding. Based on these results, additional quinazolines were designed and evaluated in silico, with HQSAR and CoMSIA models identifying sixteen compounds, with predicted PknB binding superior to the template, whose activity spectra and physicochemical, pharmacokinetic, and anti-M. tuberculosis properties were assessed. Compound, D060, bearing additional ortho- and meta-methyl groups on its R2 substituent, was superior to template regarding PknB inhibition and % caseum fraction unbound, and equivalent in other aspects, although predictions identified hepatotoxicity as a likely issue with the quinazoline series. These data provide a structural basis for rational design of quinazoline derivatives with more potent PknB inhibitory activity as candidate anti-tuberculosis agents.
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Affiliation(s)
- Chayanin Hanwarinroj
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Paptawan Thongdee
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Darunee Sukchit
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Somjintana Taveepanich
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Sombat Ketrat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, 21210, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Prasat Kittakoop
- Chulabhorn Research Institute, 10210, Bangkok, Thailand; Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, 10210, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok, 10210, Thailand
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand.
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11
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Younis MH, Mohammed ER, Mohamed AR, Abdel-Aziz MM, Georgey HH, Abdel Gawad NM. Design, Synthesis and Anti-Mycobacterium tuberculosis Evaluation of New Thiazolidin-4-one and Thiazolo[3,2-a][1,3,5]triazine Derivatives. Bioorg Chem 2022; 124:105807. [DOI: 10.1016/j.bioorg.2022.105807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022]
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12
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Raghu MS, Kumar CBP, Kumar KY, Prashanth MK, Alshahrani MY, Ahmad I, Jain R. Design, synthesis and molecular docking studies of imidazole and benzimidazole linked ethionamide derivatives as inhibitors of InhA and antituberculosis agents. Bioorg Med Chem Lett 2022; 60:128604. [PMID: 35123004 DOI: 10.1016/j.bmcl.2022.128604] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 12/31/2022]
Abstract
To explore effective antituberculosis agents, a new class of imidazoles and benzimidazoles linked ethionamide analogs were designed and synthesized. The elemental analysis, 1H NMR, 13C NMR and mass spectral data were used to characterize all of the novel analogs. In vitro activity against Mycobacterium tuberculosis (Mtb) H37Rv was assessed for all of the target compounds. The hydroxy and nitrile moieties on the imidazole ring, as well as the hydroxy and methoxy groups on the benzimidazole ring connected to the ethionamide side chain, were shown to be advantageous. In our cell viability experiment against the Vero cell line, all of the compounds were non-cytotoxic even at 100 μM. To confirm the powerful analogs target identification, we investigated their in vitro inhibitory action on an M. tuberculosis InhA over-expressing (Mtb InhA-OE) strain, which yielded MICs nearly twice those of the Mtb H37Rv strain. Furthermore, the results of molecular docking confirmed the experimental findings. Additionally, the molecules were evaluated in silico for ADMET and drug similarity features. The experimental observation enables the newly generated ethionamide derivatives to be attractive candidates for the creation of newer and better anti-TB agents.
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Affiliation(s)
- M S Raghu
- Department of Chemistry, New Horizon College of Engineering, Bengaluru 560 103, India
| | - C B Pradeep Kumar
- Department of Chemistry, Malnad College of Engineering, Hassan 573 202, India
| | - K Yogesh Kumar
- Department of Chemistry, School of Engineering and Technology, Jain University, Ramanagara, 562 112, India
| | - M K Prashanth
- Department of Chemistry, B N M Institute of Technology, Bengaluru 560 070, India.
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 9088, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 9088, Saudi Arabia
| | - Ranjana Jain
- Department of Training & Placement, Jain University, Ramanagara, 562 112, India
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13
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Perveen S, Sharma R. Screening approaches and therapeutic targets: The two driving wheels of tuberculosis drug discovery. Biochem Pharmacol 2022; 197:114906. [PMID: 34990594 DOI: 10.1016/j.bcp.2021.114906] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease, infecting a quarter of world's population. Drug resistant TB further exacerbates the grim scenario of the drying TB drug discovery pipeline. The limited arsenal to fight TB presses the need for thorough efforts for identifying promising hits to combat the disease. The review highlights the efforts in the field of tuberculosis drug discovery, with an emphasis on massive drug screening campaigns for identifying novel hits against Mtb in both industry and academia. As an intracellular pathogen, mycobacteria reside in a complicated intracellular environment with multiple factors at play. Here, we outline various strategies employed in an effort to mimic the intracellular milieu for bringing the screening models closer to the actual settings. The review also focuses on the novel targets and pathways that could aid in target-based drug discovery in TB. The recent high throughput screening efforts resulting in the identification of potent hits against Mtb has been summarized in this article. There is a pressing need for effective screening strategies and approaches employing innovative tools and recent technologies; including nanotechnology, gene-editing tools such as CRISPR-cas system, host-directed bacterial killing and high content screening to augment the TB drug discovery pipeline with safer and shorter drug regimens.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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14
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Elsayed ZM, Eldehna WM, Abdel-Aziz MM, El Hassab MA, Elkaeed EB, Al-Warhi T, Abdel-Aziz HA, Abou-Seri SM, Mohammed ER. Development of novel isatin-nicotinohydrazide hybrids with potent activity against susceptible/resistant Mycobacterium tuberculosis and bronchitis causing-bacteria. J Enzyme Inhib Med Chem 2021; 36:384-393. [PMID: 33406941 PMCID: PMC7801109 DOI: 10.1080/14756366.2020.1868450] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/19/2023] Open
Abstract
Joining the global fight against Tuberculosis, the world's most deadly infectious disease, herein we present the design and synthesis of novel isatin-nicotinohydrazide hybrids (5a-m and 9a-c) as promising anti-tubercular and antibacterial agents. The anti-tubercular activity of the target hybrids was evaluated against drug-susceptible M. tuberculosis strain (ATCC 27294) where hybrids 5d, 5g and 5h were found to be as potent as INH with MIC = 0.24 µg/mL, also the activity was evaluated against Isoniazid/Streptomycin resistant M. tuberculosis (ATCC 35823) where compounds 5g and 5h showed excellent activity (MIC = 3.9 µg/mL). Moreover, the target hybrids were examined against six bronchitis causing-bacteria. Most derivatives exhibited excellent antibacterial activity. K. pneumonia emerged as the most sensitive strain with MIC range: 0.49-7.81 µg/mL. Furthermore, a molecular docking study has proposed DprE1 as a probable enzymatic target for herein reported isatin-nicotinohydrazide hybrids, and explored the binding interactions within the vicinity of DprE1 active site.
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Affiliation(s)
- Zainab M. Elsayed
- Faculty of Pharmacy, Scientific Research and Innovation Support Unit, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Wagdy M. Eldehna
- Faculty of Pharmacy, Scientific Research and Innovation Support Unit, Kafrelsheikh University, Kafrelsheikh, Egypt
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Marwa M. Abdel-Aziz
- The Regional Center for Mycology & Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Mahmoud A. El Hassab
- Department of Pharmaceutical Chemistry, School of Pharmacy, Badr University in Cairo, Badr City, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Saudi Arabia
- Faculty of Pharmacy (Boys), Department of Pharmaceutical Organic Chemistry, Al-Azhar University, Cairo, Egypt
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hatem A. Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Giza, Egypt
| | - Sahar M. Abou-Seri
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Cairo University, Cairo, Egypt
| | - Eman R. Mohammed
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Cairo University, Cairo, Egypt
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15
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Crystal structures, DFT calculations and Hirshfeld surface analysis of two (E)-3-(aryl)-1-(naphthalen-1-yl)prop-2-en-1-one chalcone derivatives, potential Mycobacterium tuberculosis Enoyl ACP reductase (InhA) inhibitors and optical materials: conformational differences within the prop-2-en-1-one unit. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Phanumartwiwath A, Kesornpun C, Sureram S, Hongmanee P, Pungpo P, Kamsri P, Punkvang A, Eurtivong C, Kittakoop P, Ruchirawat S. Antitubercular and antibacterial activities of isoxazolines derived from natural products: Isoxazolines as inhibitors of Mycobacterium tuberculosis InhA. JOURNAL OF CHEMICAL RESEARCH 2021. [DOI: 10.1177/17475198211047801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Isoxazoline derivatives of the natural products eugenol, 1’- S-acetoxychavicol acetate and sclareol are prepared through 1,3-dipolar cycloaddition reactions in an aqueous buffered system. The compounds are evaluated for their antitubercular and antibacterial activities. Compounds 2, 2a and 3f display strong antitubercular activity with minimum inhibitory concentration values of 26.68, 17.89 and 14.58 µM, respectively. Furthermore, derivative 3f exhibits antibacterial activity against Bacillus cereus (minimum inhibitory concentration value of 29.16 µM). Isoxazoline derivatives of 1’- S-acetoxychavicol acetate demonstrate improvements in cytotoxicity, and derivative 3f of sclareol demonstrates improved antitubercular and antibacterial activities. Isoxazolines derived from natural products exhibit Mycobacterium tuberculosis enoyl-acyl carrier protein reductase (InhA) inhibitory activity, and molecular modelling predicts that they form hydrogen bonding and hydrophobic interactions with NADH and with the key residues of the InhA binding site.
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Affiliation(s)
- Anuchit Phanumartwiwath
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
- College of Public Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Chatchakorn Eurtivong
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
| | - Prasat Kittakoop
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
| | - Somsak Ruchirawat
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
- Chulabhorn Research Institute, Bangkok, Thailand
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17
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Sundararajan S, Muniyan R. Latent tuberculosis: interaction of virulence factors in Mycobacterium tuberculosis. Mol Biol Rep 2021; 48:6181-6196. [PMID: 34351540 DOI: 10.1007/s11033-021-06611-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains a prominent health concern worldwide. Besides extensive research and vaccinations available, attempts to control the pandemic are cumbersome due to the complex physiology of Mycobacterium tuberculosis (Mtb). Alongside the emergence of drug-resistant TB, latent TB has worsened the condition. The tubercle bacilli are unusually behaved and successful with its strategies to modulate genes to evade host immune system and persist within macrophages. Under latent/unfavorable conditions, Mtb conceals itself from immune system and modulates its genes. Among many intracellular modulated genes, important are those involved in cell entry, fatty acid degradation, mycolic acid synthesis, phagosome acidification inhibition, inhibition of phagosome-lysosome complex and chaperon protein modulation. Though the study on these genes date back to early times of TB, an insight on their inter-relation within and to newly evolved genes are still required. This review focuses on the findings and discussions on these genes, possible mechanism, credibility as target for novel drugs and repurposed drugs and their interaction that enables Mtb in survival, pathogenesis, resistance and latency.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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18
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Jayaraman M, Loganathan L, Muthusamy K, Ramadas K. Virtual screening assisted discovery of novel natural products to inhibit the catalytic mechanism of Mycobacterium tuberculosis InhA. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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19
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New InhA Inhibitors Based on Expanded Triclosan and Di-Triclosan Analogues to Develop a New Treatment for Tuberculosis. Pharmaceuticals (Basel) 2021; 14:ph14040361. [PMID: 33919737 PMCID: PMC8070701 DOI: 10.3390/ph14040361] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) has reinforced the need for the development of new anti-TB drugs. The first line drug isoniazid inhibits InhA. This is a prodrug requiring activation by the enzyme KatG. Mutations in KatG have largely contributed to clinical isoniazid resistance. We aimed to design new 'direct' InhA inhibitors that obviate the need for activation by KatG, circumventing pre-existing resistance. In silico molecular modelling was used as part of a rational structure-based drug-design approach involving inspection of protein crystal structures of InhA:inhibitor complexes, including the broad spectrum antibiotic triclosan (TCS). One crystal structure exhibited the unusual presence of two triclosan molecules within the Mycobacterium tuberculosis InhA binding site. This became the basis of a strategy for the synthesis of novel inhibitors. A series of new, flexible ligands were designed and synthesised, expanding on the triclosan structure. Low Minimum Inhibitory Concentrations (MICs) were obtained for benzylphenyl compounds (12, 43 and 44) and di-triclosan derivative (39), against Mycobacterium bovis BCG although these may also be inhibiting other enzymes. The ether linked di-triclosan derivative (38) displayed excellent in vitro isolated enzyme inhibition results comparable with triclosan, but at a higher MIC (125 µg mL-1). These compounds offer good opportunities as leads for further optimisation.
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20
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Eltschkner S, Kehrein J, Le TA, Davoodi S, Merget B, Basak S, Weinrich JD, Schiebel J, Tonge PJ, Engels B, Sotriffer C, Kisker C. A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure. ACS Infect Dis 2021; 7:746-758. [PMID: 33710875 DOI: 10.1021/acsinfecdis.0c00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enoyl-acyl carrier protein (ACP) reductase (ENR) is a key enzyme within the bacterial fatty-acid synthesis pathway. It has been demonstrated that small-molecule inhibitors carrying the diphenylether (DPE) scaffold bear a great potential for the development of highly specific and effective drugs against this enzyme class. Interestingly, different substitution patterns of the DPE scaffold have been shown to lead to varying effects on the kinetic and thermodynamic behavior toward ENRs from different organisms. Here, we investigated the effect of a 4'-pyridone substituent in the context of the slow tight-binding inhibitor SKTS1 on the inhibition of the Staphylococcus aureus enoyl-ACP-reductase saFabI and the closely related isoenzyme from Mycobacterium tuberculosis, InhA, and explored a new interaction site of DPE inhibitors within the substrate-binding pocket. Using high-resolution crystal structures of both complexes in combination with molecular dynamics (MD) simulations, kinetic measurements, and quantum mechanical (QM) calculations, we provide evidence that the 4'-pyridone substituent adopts different tautomeric forms when bound to the two ENRs. We furthermore elucidate the structural determinants leading to significant differences in the residence time of SKTS1 on both enzymes.
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Affiliation(s)
- Sandra Eltschkner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Thien Anh Le
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
- Department of Experimental Physics 5 (Biophysics), University of Würzburg, 97074 Würzburg, Germany
| | - Shabnam Davoodi
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Benjamin Merget
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Sneha Basak
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jonas D. Weinrich
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
- Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johannes Schiebel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Peter J. Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
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21
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Atukuri D, Gunjal R, Holagundi N, Korlahalli B, Gangannavar S, Akkasali K. Contribution of N-heterocycles towards anti-tubercular drug discovery (2014-2019); predicted and reengineered molecular frameworks. Drug Dev Res 2021; 82:767-783. [PMID: 33660325 DOI: 10.1002/ddr.21809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 11/08/2022]
Abstract
Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis, responsible for high death frequency every year all over the world. In this regard, efficient drug-design and discovery towards the prevention of M.tb H37 Rv is of prime concern. Prevention of the infection may include vaccination, and the treatment comprises anti-TB drug regimen. However, the vaccine decreases the risk of tuberculosis infection only to some extent, while drug-resistance limits the efficacy of the existing anti-TB agents. Much improvement has to be achieved to overcome pitfalls such as side effects, high-toxicity, low bioavailability, pharmacokinetics and pharmacodynamics, and hence forth in clinical therapeutics. Amongst heterocyclic compounds, N-heterocycles played a pivotal role in drug-design and discovery. A wide range of microbial diseases are being treated by the N-heterocyclic drugs. The present review comprises description of anti-TB effects of the N-heterocycles such as indoles, triazoles, thiazoles, and pyrazoles. The potent anti-TB activity exerted by the derivatives of these heterocycles is evaluated critically alongside emphasizing structure-activity relationship. Besides, docking studies supporting anti-TB activity is supplemented. Alongside this, based on the potent heterocyclic molecules, the molecular frameworks are designed that would bring about enhanced M. tb H37 Rv inhibitory potencies.
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Affiliation(s)
- Dorababu Atukuri
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | - Rutu Gunjal
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | - Nagaraj Holagundi
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
| | | | | | - Kirankumar Akkasali
- Department of Chemistry, SRMPP Govt. First Grade College, Huvinahadagali, India
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Shawon J, Khan AM, Shahriar I, Halim MA. Improving the binding affinity and interaction of 5-Pentyl-2-Phenoxyphenol against Mycobacterium Enoyl ACP reductase by computational approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Quantitative structure-activity relationship (QSAR) and molecular docking of xanthone derivatives as anti-tuberculosis agents. J Clin Tuberc Other Mycobact Dis 2020; 21:100203. [PMID: 33294629 PMCID: PMC7695880 DOI: 10.1016/j.jctube.2020.100203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Quantitative structure–activity relationship (QSAR) and molecular docking approach were carried out to design novel anti-tuberculosis agents based on xanthone derivatives. QSAR designed new compounds were calculated by Austin Model 1 (AM1) methods and analysis of multi-linear regression (MLR). The result showed that the best model as follows: Log IC50 = 3.113 + 11.627 qC1 + 15.955 qC4 + 11.702 qC9, this result has appropriate some statistical parameters (PRESS = 2.11, r2 = 0.730, SEE = 0. 3545, R = 0.6827, FCal/FTab = 4.68), and being used to design a potential anti-tuberculosis drugs with substituted amide, sulfoxide, and carboxylate group xanthone scaffold by a number of their inhibitory concentration (IC50). The mechanism action of sulfonamide substituted on the xanthone scaffold as anti-tuberculosis was carried out using molecular docking. Docking inhibition studies were carried out on MTB C171Q receptor (4C6X.pdb) as KasA inhibitors using by the discovery studio. Based on the binding interaction showed, the sulfonamide substituted xanthone has potential being the anti-tuberculosis drugs by KasA inhibitor for target drug activity.
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Fernández de Luco J, Recio-Balsells AI, Ghiano DG, Bortolotti A, Belardinelli JM, Liu N, Hoffmann P, Lherbet C, Tonge PJ, Tekwani B, Morbidoni HR, Labadie GR. Exploring the chemical space of 1,2,3-triazolyl triclosan analogs for discovery of new antileishmanial chemotherapeutic agents. RSC Med Chem 2020; 12:120-128. [PMID: 34046604 DOI: 10.1039/d0md00291g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 01/02/2023] Open
Abstract
Triclosan and isoniazid are known antitubercular compounds that have proven to be also active against Leishmania parasites. On these grounds, a collection of 37 diverse 1,2,3-triazoles based on the antitubercular molecules triclosan and 5-octyl-2-phenoxyphenol (8PP) were designed in search of novel structures with leishmanicidal activity and prepared using different alkynes and azides. The 37 compounds were assayed against Leishmania donovani, the etiological agent of leishmaniasis, yielding some analogs with activity at micromolar concentrations and against M. tuberculosis H37Rv resulting in scarce active compounds with an MIC of 20 μM. To study the mechanism of action of these catechols, we analyzed the inhibition activity of the library on the M. tuberculosis enoyl-ACP reductase (ENR) InhA, obtaining poor inhibition of the enzyme. The cytotoxicity against Vero cells was also tested, resulting in none of the compounds being cytotoxic at concentrations of up to 20 μM. Derivative 5f could be considered a valuable starting point for future antileishmanial drug development. The validation of a putative leishmanial InhA orthologue as a therapeutic target needs to be further investigated.
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Affiliation(s)
- Julia Fernández de Luco
- Instituto de Química Rosario, UNR, CONICET Suipacha 531 S2002LRK Rosario Argentina +54 341 4370477 +54 341 4370477
| | - Alejandro I Recio-Balsells
- Instituto de Química Rosario, UNR, CONICET Suipacha 531 S2002LRK Rosario Argentina +54 341 4370477 +54 341 4370477
| | - Diego G Ghiano
- Instituto de Química Rosario, UNR, CONICET Suipacha 531 S2002LRK Rosario Argentina +54 341 4370477 +54 341 4370477
| | - Ana Bortolotti
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario Santa Fe 3100 S2002KTR Rosario Argentina
| | - Juán Manuel Belardinelli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario Santa Fe 3100 S2002KTR Rosario Argentina
| | - Nina Liu
- Department of Chemistry, Institute of Chemical Biology & Drug Discovery, Stony Brook University Stony Brook NY 11794 USA
| | - Pascal Hoffmann
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III 118 Route de Narbonne 31062 Toulouse Cedex 9 France
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III 118 Route de Narbonne 31062 Toulouse Cedex 9 France
| | - Peter J Tonge
- Department of Chemistry, Institute of Chemical Biology & Drug Discovery, Stony Brook University Stony Brook NY 11794 USA
| | - Babu Tekwani
- National Center for Natural Products Research & Department of Biomolecular Sciences, School of Pharmacy, University of Mississippi MS 38677 USA
| | - Héctor R Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario Santa Fe 3100 S2002KTR Rosario Argentina .,Consejo de Investigaciones, Universidad Nacional de Rosario Argentina
| | - Guillermo R Labadie
- Instituto de Química Rosario, UNR, CONICET Suipacha 531 S2002LRK Rosario Argentina +54 341 4370477 +54 341 4370477.,Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Suipacha 531 S2002LRK Rosario Argentina
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Tiwari AP, Sridhar B, Boshoff HI, Arora K, Gautham Shenoy G, Vandana KE, Varadaraj Bhat G. Design, synthesis, in silico and in vitro evaluation of novel diphenyl ether derivatives as potential antitubercular agents. Mol Divers 2020; 24:1265-1279. [PMID: 31506871 PMCID: PMC11177332 DOI: 10.1007/s11030-019-09990-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/24/2019] [Indexed: 11/28/2022]
Abstract
Diphenyl ether derivatives inhibit mycobacterial cell wall synthesis by inhibiting an enzyme, enoyl-acyl carrier protein reductase (InhA), which catalyses the last step in the fatty acid synthesis cycle of genus Mycobacterium. To select and validate a protein crystal structure of enoyl-acyl carrier protein reductase of Mycobacterium tuberculosis for designing inhibitors using molecular modelling, a cross-docking and correlation study was performed. A series of novel 1-(3-(3-hydroxy-4-phenoxyphenyl)-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl) ethan-1-ones were synthesized from this model and screened for their antitubercular activity against M. tuberculosis H37Rv. Compound PYN-8 showed good antitubercular activity on M. tuberculosis H37Rv (MIC = 4-7 µM) and Mycobacterium bovis (% inhibition at 10 µM = 95.91%). Cytotoxicity of all the synthesized derivatives was assessed using various cell lines, and they were found to be safe. Structure of PYN-8 was also confirmed by single-crystal X-ray diffraction. The molecular modelling studies also corroborated the biological activity of the compounds. Further, in silico findings revealed that all these tested compounds exhibited good ADME properties and drug likeness and thus may be considered as potential candidates for further drug development.
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Affiliation(s)
- Ashutosh Prasad Tiwari
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - B Sridhar
- X-ray Crystallography Division, CSIR - Indian Institute of Chemical Technology, Hyderabad, 500607, India
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - G Gautham Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - K E Vandana
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, India
| | - G Varadaraj Bhat
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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Armstrong T, Lamont M, Lanne A, Alderwick LJ, Thomas NR. Inhibition of Mycobacterium tuberculosis InhA: Design, synthesis and evaluation of new di-triclosan derivatives. Bioorg Med Chem 2020; 28:115744. [PMID: 33007556 DOI: 10.1016/j.bmc.2020.115744] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 11/25/2022]
Abstract
Multi-drug resistant tuberculosis (MDR-TB) represents a growing problem for global healthcare systems. In addition to 1.3 million deaths in 2018, the World Health Organisation reported 484,000 new cases of MDR-TB. Isoniazid is a key anti-TB drug that inhibits InhA, a crucial enzyme in the cell wall biosynthesis pathway and identical in Mycobacterium tuberculosis and M. bovis. Isoniazid is a pro-drug which requires activation by the enzyme KatG, mutations in KatG prevent activation and confer INH-resistance. 'Direct inhibitors' of InhA are attractive as they would circumvent the main clinically observed resistance mechanisms. A library of new 1,5-triazoles, designed to mimic the structures of both triclosan molecules uniquely bound to InhA have been synthesised. The inhibitory activity of these compounds was evaluated using isolated enzyme assays with 2 (5-chloro-2-(4-(5-(((4-(4-chloro-2-hydroxyphenoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) exhibiting an IC50 of 5.6 µM. Whole-cell evaluation was also performed, with 11 (5-chloro-2-(4-(5-(((4-(cyclopropylmethoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) showing the greatest potency, with an MIC99 of 12.9 µM against M. bovis.
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Affiliation(s)
- Tom Armstrong
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Malcolm Lamont
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Alice Lanne
- Institute of Microbiology and Infection, School of Bioscience, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology and Infection, School of Bioscience, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Neil R Thomas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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Venkatesh N, Sundergoud S, Swamy MK, Veerasomaiah P. Microwave-Assisted Synthesis and Antimicrobial Activity of Novel Pyrazole–Indanone Hybrid Analogs. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020090213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ghiano DG, Recio-Balsells A, Bortolotti A, Defelipe LA, Turjanski A, Morbidoni HR, Labadie GR. New one-pot synthesis of anti-tuberculosis compounds inspired on isoniazid. Eur J Med Chem 2020; 208:112699. [PMID: 32927391 DOI: 10.1016/j.ejmech.2020.112699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
A library of thirty N-substituted tosyl N'-acryl-hydrazones was prepared with p-toluenesulfonyl hydrazide, methyl propiolate and different aldehydes in a one-pot synthesis via an aza-Michael reaction. The scope of the reaction was studied, including aliphatic, isoprenylic, aromatic and carbocyclic aldehydes. The prepared collection was tested against Mycobacterium tuberculosis H37Rv. Nine analogs of the collection showed Minimum Inhibitory Concentration ≤10 μM, of which the most active members (MIC of 1.25 μM) were exclusively E isomers. In order to validate the mechanism of action of the most active acrylates, we tested their activity on a M. tuberculosis InhA over-expressing strain obtaining MIC that consistently doubled those obtained on the wild type strain. Additionally, the binding mode of those analogs on M. tuberculosis InhA was investigated by docking simulations. The results displayed a hydrogen bond interaction between the sulfonamide and Ile194 and the carbonyl of the methyl ester with Tyr 158 (both critical residues in the interaction with the fatty acyl chain substrate), where the main differences on the binding mode relays on the hydrophobicity of the nitrogen substituent. Additionally, chemoinformatic analysis was performed to evaluate in silico possible cytotoxicity risk and ADME-Tox profile. Based on their simple preparation and interesting antimycobacterial activity profile, the newly prepared aza-acrylates are promising candidates for antitubercular drug development.
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Affiliation(s)
- Diego G Ghiano
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina
| | | | - Ana Bortolotti
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, S2002KTR, Rosario, Argentina
| | - Lucas A Defelipe
- IQUIBICEN-CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Adrián Turjanski
- IQUIBICEN-CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - Héctor R Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Santa Fe 3100, S2002KTR, Rosario, Argentina; Consejo de Investigaciones Científicas, Universidad Nacional de Rosario, Argentina
| | - Guillermo R Labadie
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina; Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina.
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Tayo AD, Djoumbissie A, Golngar D, Fomuta TR, Kuate Tagne AC, Anguile JJ, Ngoune J, Eleuterio Á. Syntheses, characterization and DFT studies of two new homo-dinuclear zinc(II) complexes based on pyrazole and 3,5-dimethylpyrazole ligands. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1796987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | | | - Djimassingar Golngar
- Department of Chemistry, Mongo Polytechnique University Institute (IUPM), Mongo, Chad
| | | | | | - Jean Jacques Anguile
- Department of Chemistry, University of Sciences & Techniques of Masuku, Franceville, Gabon
| | - Jean Ngoune
- Department of Chemistry, University of Dschang, Dschang, Cameroon
| | - Álvarez Eleuterio
- Instituto de Investigaciones Químicas- CSIC, Universidad de Sevilla, Sevilla, Spain
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Faïon L, Djaout K, Frita R, Pintiala C, Cantrelle FX, Moune M, Vandeputte A, Bourbiaux K, Piveteau C, Herledan A, Biela A, Leroux F, Kremer L, Blaise M, Tanina A, Wintjens R, Hanoulle X, Déprez B, Willand N, Baulard AR, Flipo M. Discovery of the first Mycobacterium tuberculosis MabA (FabG1) inhibitors through a fragment-based screening. Eur J Med Chem 2020; 200:112440. [PMID: 32505086 DOI: 10.1016/j.ejmech.2020.112440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis (M.tb), the etiologic agent of tuberculosis, remains the leading cause of death from a single infectious agent worldwide. The emergence of drug-resistant M.tb strains stresses the need for drugs acting on new targets. Mycolic acids are very long chain fatty acids playing an essential role in the architecture and permeability of the mycobacterial cell wall. Their biosynthesis involves two fatty acid synthase (FAS) systems. Among the four enzymes (MabA, HadAB/BC, InhA and KasA/B) of the FAS-II cycle, MabA (FabG1) remains the only one for which specific inhibitors have not been reported yet. The development of a new LC-MS/MS based enzymatic assay allowed the screening of a 1280 fragment-library and led to the discovery of the first small molecules that inhibit MabA activity. A fragment from the anthranilic acid series was optimized into more potent inhibitors and their binding to MabA was confirmed by 19F ligand-observed NMR experiments.
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Affiliation(s)
- Léo Faïon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Catalin Pintiala
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Francois-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Alexandre Vandeputte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Kevin Bourbiaux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France; INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France
| | - Mickael Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France
| | - Abdalkarim Tanina
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Xavier Hanoulle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
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Padmini T, Bhikshapathi D, Suresh K, Kulkarni R, Kamal BR. Novel Aminopyrazole Tagged Hydrazones as Anti-Tubercular Agents: Synthesis and Molecular Docking Studies. Med Chem 2020; 17:344-351. [PMID: 32407282 DOI: 10.2174/1573406416666200514084747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pyrazole derivatives have been reported to possess numerous pharmacological activities viz., anti-inflammatory, antipsychotic, etc. Our group has disclosed that pyrazole benzamides display potent antibacterial and anti-tubercular activities. OBJECTIVE Synthesis of new pyrazole acetamides which possess hydrazone group to be evaluated for antitubercular activity. METHODS The key intermediate 5-aminopyrazole was synthesized with the known procedure, which is then converted into chloroacetamide. This compound than resulted in hydrazine derivative and finally converted into aromatic hydrazones. All the compounds were screened for antitubercular activity. RESULTS All the synthesized compounds have been characterized by their spectral data obtained and subjected to anti-tubercular activity. Among all the twenty tested compounds, three compounds, 5a5, 5b5 and 5b7 have demonstrated MIC value of 3.12 μg/mL against MTB H37Rv. Docking studies revealed important hydrogen bonding interactions with InhA. CONCLUSION Three compounds 5a5, 5b5 and 5b7 were found to be most potent among the series of compounds. Docking studies of compounds explained the presence of hydrogen bonding and π- π stacking interactions with InhA. Further synthesis of more such derivatives with optimized groups would produce compounds with more potent anti-tubercular activity.
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Affiliation(s)
| | - Darna Bhikshapathi
- Teegala Ram Reddy College of Pharmacy, Pragathi Colony, Meerpet, Hyderabad- 500097, Telangana, India
| | - Kandagatla Suresh
- Vijaya College of Pharmacy, Hayatnagar, Hyderabad-501511, Telangana, Hyderabad, India
| | - Ravindra Kulkarni
- Bharati Vidyapeeth's Poona College of Pharmacy, Erandwane, Pune-411038, Maharashtra, India
| | - Bigala R Kamal
- Research Supervisor, Mewar University, Chittorgarh, Rajasthan, India
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Economical synthesis strategy, characterization and theoretical study of the organic dye 3-oxo-3H-spiro [isobenzofuran-1,9′-xanthene]-3′,6′-diyl dibenzoate. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2782-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Sabbah M, Mendes V, Vistal RG, Dias DMG, Záhorszká M, Mikušová K, Korduláková J, Coyne AG, Blundell TL, Abell C. Fragment-Based Design of Mycobacterium tuberculosis InhA Inhibitors. J Med Chem 2020; 63:4749-4761. [PMID: 32240584 PMCID: PMC7232676 DOI: 10.1021/acs.jmedchem.0c00007] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tuberculosis (TB) remains a leading cause of mortality among infectious diseases worldwide. InhA has been the focus of numerous drug discovery efforts as this is the target of the first line pro-drug isoniazid. However, with resistance to this drug becoming more common, the aim has been to find new clinical candidates that directly inhibit this enzyme and that do not require activation by the catalase peroxidase KatG, thus circumventing the majority of the resistance mechanisms. In this work, the screening and validation of a fragment library are described, and the development of the fragment hits using a fragment growing strategy was employed, which led to the development of InhA inhibitors with affinities of up to 250 nM.
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Affiliation(s)
- Mohamad Sabbah
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Robert G Vistal
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David M G Dias
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Monika Záhorszká
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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de Ávila MB, Bitencourt-Ferreira G, de Azevedo WF. Structural Basis for Inhibition of Enoyl-[Acyl Carrier Protein] Reductase (InhA) from Mycobacterium tuberculosis. Curr Med Chem 2020; 27:745-759. [DOI: 10.2174/0929867326666181203125229] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Background::
The enzyme trans-enoyl-[acyl carrier protein] reductase (InhA) is a central
protein for the development of antitubercular drugs. This enzyme is the target for the pro-drug
isoniazid, which is catalyzed by the enzyme catalase-peroxidase (KatG) to become active.
Objective::
Our goal here is to review the studies on InhA, starting with general aspects and focusing on
the recent structural studies, with emphasis on the crystallographic structures of complexes involving
InhA and inhibitors.
Method::
We start with a literature review, and then we describe recent studies on InhA crystallographic
structures. We use this structural information to depict protein-ligand interactions. We also analyze the
structural basis for inhibition of InhA. Furthermore, we describe the application of computational
methods to predict binding affinity based on the crystallographic position of the ligands.
Results::
Analysis of the structures in complex with inhibitors revealed the critical residues responsible
for the specificity against InhA. Most of the intermolecular interactions involve the hydrophobic residues
with two exceptions, the residues Ser 94 and Tyr 158. Examination of the interactions has shown
that many of the key residues for inhibitor binding were found in mutations of the InhA gene in the
isoniazid-resistant Mycobacterium tuberculosis. Computational prediction of the binding affinity for
InhA has indicated a moderate uphill relationship with experimental values.
Conclusion::
Analysis of the structures involving InhA inhibitors shows that small modifications on
these molecules could modulate their inhibition, which may be used to design novel antitubercular
drugs specific for multidrug-resistant strains.
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Affiliation(s)
- Maurício Boff de Ávila
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Gabriela Bitencourt-Ferreira
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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Kienle M, Eisenring P, Stoessel B, Horlacher OP, Hasler S, van Colen G, Hartkoorn RC, Vocat A, Cole ST, Altmann KH. Synthesis and Structure–Activity Relationship Studies of C2-Modified Analogs of the Antimycobacterial Natural Product Pyridomycin. J Med Chem 2020; 63:1105-1131. [DOI: 10.1021/acs.jmedchem.9b01457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Maryline Kienle
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Patrick Eisenring
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Barbara Stoessel
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Oliver P. Horlacher
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Samuel Hasler
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Gwénaëlle van Colen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
| | - Ruben C. Hartkoorn
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stewart T. Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zurich, Switzerland
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37
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Design, synthesis, evaluation, and molecular dynamic simulation of triclosan mimic diphenyl ether derivatives as antitubercular and antibacterial agents. Struct Chem 2020. [DOI: 10.1007/s11224-019-01478-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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38
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Sahoo J, Sahoo CR, Nandini Sarangi PK, Prusty SK, Padhy RN, Paidesetty SK. Molecules with versatile biological activities bearing antipyrinyl nucleus as pharmacophore. Eur J Med Chem 2020; 186:111911. [DOI: 10.1016/j.ejmech.2019.111911] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/06/2019] [Accepted: 11/24/2019] [Indexed: 02/06/2023]
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Kamsri P, Hanwarinroj C, Phusi N, Pornprom T, Chayajarus K, Punkvang A, Suttipanta N, Srimanote P, Suttisintong K, Songsiriritthigul C, Saparpakorn P, Hannongbua S, Rattanabunyong S, Seetaha S, Choowongkomon K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Chen Z, Zhu W, Blood RA, Takebayashi Y, Hinchliffe P, Mulholland AJ, Spencer J, Pungpo P. Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography. J Chem Inf Model 2019; 60:226-234. [PMID: 31820972 DOI: 10.1021/acs.jcim.9b00918] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The enoyl-acyl carrier protein reductase InhA of Mycobacterium tuberculosis is an attractive, validated target for antituberculosis drug development. Moreover, direct inhibitors of InhA remain effective against InhA variants with mutations associated with isoniazid resistance, offering the potential for activity against MDR isolates. Here, structure-based virtual screening supported by biological assays was applied to identify novel InhA inhibitors as potential antituberculosis agents. High-speed Glide SP docking was initially performed against two conformations of InhA differing in the orientation of the active site Tyr158. The resulting hits were filtered for drug-likeness based on Lipinski's rule and avoidance of PAINS-like properties and finally subjected to Glide XP docking to improve accuracy. Sixteen compounds were identified and selected for in vitro biological assays, of which two (compounds 1 and 7) showed MIC of 12.5 and 25 μg/mL against M. tuberculosis H37Rv, respectively. Inhibition assays against purified recombinant InhA determined IC50 values for these compounds of 0.38 and 0.22 μM, respectively. A crystal structure of the most potent compound, compound 7, bound to InhA revealed the inhibitor to occupy a hydrophobic pocket implicated in binding the aliphatic portions of InhA substrates but distant from the NADH cofactor, i.e., in a site distinct from those occupied by the great majority of known InhA inhibitors. This compound provides an attractive starting template for ligand optimization aimed at discovery of new and effective compounds against M. tuberculosis that act by targeting InhA.
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Affiliation(s)
- Pharit Kamsri
- Division of Chemistry, Faculty of Science , Nakhon Phanom University , 48000 Nakhon Phanom , Thailand
| | | | | | | | | | - Auradee Punkvang
- Division of Chemistry, Faculty of Science , Nakhon Phanom University , 48000 Nakhon Phanom , Thailand
| | | | - Potjanee Srimanote
- Faculty of Allied Health Sciences , Thammasat University , Rangsit Campus , 12120 Pathumthani , Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center , National Science and Technology Development Agency , Thailand Science Park , 12120 Pathumthani , Thailand
| | | | | | | | | | | | | | - Sanya Sureram
- Chulabhorn Research Institute , 10210 Bangkok , Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute , 10210 Bangkok , Thailand.,Chulabhorn Graduate Institute, Chemical Biology Program , Chulabhorn Royal Academy , 10210 Bangkok , Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), CHE , Ministry of Education , 10300 Bangkok , Thailand
| | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital , Mahidol University , 10400 Bangkok , Thailand
| | - Pitak Santanirand
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital , Mahidol University , 10400 Bangkok , Thailand
| | - Zhaoqiang Chen
- State Key Laboratory of Drug Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica , 201203 Shanghai , China
| | - Weiliang Zhu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica , 201203 Shanghai , China
| | - Rosemary A Blood
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , BS8 1TS Bristol , United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
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40
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First triclosan-based macrocyclic inhibitors of InhA enzyme. Bioorg Chem 2019; 95:103498. [PMID: 31855823 DOI: 10.1016/j.bioorg.2019.103498] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 01/07/2023]
Abstract
Two macrocyclic derivatives based on the triclosan frame were designed and synthesized as inhibitors of Mycobacterium tuberculosis InhA enzyme. One of the two molecules M02 displayed promising inhibitory activity against InhA enzyme with an IC50 of 4.7 μM. Molecular docking studies of these two compounds were performed and confirmed that M02 was more efficient as inhibitor of InhA activity. These molecules are the first macrocyclic direct inhibitors of InhA enzyme able to bind into the substrate pocket. Furthermore, these biaryl ether compounds exhibited antitubercular activities comparable to that of triclosan against M. tuberculosis H37Rv strain.
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Kouman KC, Keita M, Kre N’Guessan R, Owono Owono LC, Megnassan E, Frecer V, Miertus S. Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles. Int J Mol Sci 2019; 20:ijms20194730. [PMID: 31554227 PMCID: PMC6802012 DOI: 10.3390/ijms20194730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/24/2023] Open
Abstract
Background: During the previous decade a new class of benzamide-based inhibitors of 2-trans enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (Mt) with unusual binding mode have emerged. Here we report in silico design and evaluation of novel benzamide InhA-Mt inhibitors with favorable predicted pharmacokinetic profiles. Methods: By using in situ modifications of the crystal structure of N-benzyl-4-((heteroaryl)methyl) benzamide (BHMB)-InhA complex (PDB entry 4QXM), 3D models of InhA-BHMBx complexes were prepared for a training set of 19 BHMBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the BHMB1-19, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation (∆∆HMM) of InhA-BHMBx complexes with the IC50exp. Further, taking into account the solvent effect and entropy changes upon ligand, binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of BHMBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds containing benzamide scaffolds. The VCL filtered by Lipinski’s rule-of-five was screened by the PH4 model to identify new BHMB analogs. Results: Gas phase QSAR model: −log10(IC50exp) = pIC50exp = −0.2465 × ∆∆HMM + 7.95503, R2 = 0.94; superior aqueous phase QSAR model: pIC50exp = −0.2370 × ∆∆Gcom + 7.8783, R2 = 0.97 and PH4 pharmacophore model: pIC50exp = 1.0013 × pIC50exp − 0.0085, R2 = 0.95. The VCL of more than 114 thousand BHMBs was filtered down to 73,565 analogs Lipinski’s rule. The five-point PH4 screening retained 90 new and potent BHMBs with predicted inhibitory potencies IC50pre up to 65 times lower than that of BHMB1 (IC50exp = 20 nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to current anti-tuberculotics. Conclusions: Combined use of QSAR models that considered binding of the BHMBs to InhA, pharmacophore model, and ADME properties helped to recognize bound active conformation of the benzamide inhibitors, permitted in silico screening of VCL of compounds sharing benzamide scaffold and identification of new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles.
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Affiliation(s)
- Koffi Charles Kouman
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Raymond Kre N’Guessan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Luc Calvin Owono Owono
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Laboratoire de Cristallographie—Physique Moléculaire, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Correspondence: ; Tel.: +225-02-36-30-08
| | - Vladimir Frecer
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, SK-83232 Bratislava, Slovakia
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
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In Silico Repositioning of Cannabigerol as a Novel Inhibitor of the Enoyl Acyl Carrier Protein (ACP) Reductase (InhA). Molecules 2019; 24:molecules24142567. [PMID: 31311157 PMCID: PMC6680637 DOI: 10.3390/molecules24142567] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022] Open
Abstract
Cannabigerol (CBG) and cannabichromene (CBC) are non-psychoactive cannabinoids that have raised increasing interest in recent years. These compounds exhibit good tolerability and low toxicity, representing promising candidates for drug repositioning. To identify novel potential therapeutic targets for CBG and CBC, an integrated ligand-based and structure-based study was performed. The results of the analysis led to the identification of CBG as a low micromolar inhibitor of the Enoyl acyl carrier protein (ACP) reductase (InhA) enzyme.
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Kini SG, Rathi E, Kumar A, Bhat V. Potentials of Diphenyl Ether Scaffold as a Therapeutic Agent: A Review. Mini Rev Med Chem 2019; 19:1392-1406. [PMID: 30864517 DOI: 10.2174/1389557519666190312150132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 11/22/2022]
Abstract
Diphenyl ethers (DPE) and its analogs have exhibited excellent potential for therapeutic and industrial applications. Since the 19th century, intensive research is perpetuating on the synthetic routes and biological properties of DPEs. Few well-known DPEs are Nimesulide, Fenclofenac, Triclosan, Sorafenib, MK-4965, and MK-1439 which have shown the potential of this moiety as a lead scaffold for different pharmacological properties. In this review, we recapitulate the diverse synthetic route of DPE moiety inclusive of merits and demerits over the classical synthetic route and how this moiety sparked an interest in researchers to discern the SAR (Structure Activity Relationship) for the development of diversified biological properties of DPEs such as antimicrobial, antifungal, antiinflammatory & antiviral activities.
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Affiliation(s)
- Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, MAHE, Manipal, Karnataka, 576104, India
| | - Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, MAHE, Manipal, Karnataka, 576104, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, MAHE, Manipal, Karnataka, 576104, India
| | - Varadaraj Bhat
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, MAHE, Manipal, Karnataka, 576104, India
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Duca G, Pogrebnoi S, Boldescu V, Aksakal F, Uncu A, Valica V, Uncu L, Negres S, Nicolescu F, Macaev F. Tryptanthrin Analogues as Inhibitors of Enoyl-acyl Carrier Protein Reductase: Activity against Mycobacterium tuberculosis, Toxicity, Modeling of Enzyme Binding. Curr Top Med Chem 2019; 19:609-619. [PMID: 30834838 DOI: 10.2174/1568026619666190304125740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/01/2018] [Accepted: 11/01/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND High numbers of infection with resistant forms of Micobacterium tuberculosis (Mtb) contribute to a constant growing demand in new highly active and effective therapeutics. Current drug discovery efforts directed towards new antituberculosis agents include the development of new inhibitors of enoyl-acyl carrier protein reductase (InhA) that do not require activation by the specific enzymes. Tryptanthrin is a known inhibitor of Mtb InhA and its analogues are investigated as potential agents with antimycobacterial efficiency. OBJECTIVE The main objective of the presented research was to develop a new group of tryptanthrin analogues with good inhibition properties against Mtb. METHODS Synthesis of new derivatives of 5H-[1,3,4]thiadiazolo[2,3- b]quinazolin-5-one and evaluation of their activity against Mtb, as well as acute and chronic toxicity studies were carried out. Molecular modeling studies were performed to investigate the binding mechanisms of the synthesized ligands with InhA. Binding energies and non-covalent interactions stabilizing the ligand-receptor complexes were obtained from the results of molecular docking. RESULTS The most active compound in the obtained series, 2-(propylthio)-5H-[1,3,4]thiadiazolo[2,3- b]quinazolin-5-one, exhibited the superior inhibition activity (up to 100%) against mycobacterial growth at MIC 6.5 µg/mL, showed good affinity to the InhA enzyme in docking studies and demonstrated a very low per oral toxicity in animals falling under the category 5 according to GHS classification. CONCLUSION 2-(propylthio)-5H-[1,3,4]thiadiazolo[2,3-b]quinazolin-5-one can be further explored for the development of a new series of compounds active against Mtb.
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Affiliation(s)
- Gheorghe Duca
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of
| | - Serghei Pogrebnoi
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of
| | - Veaceslav Boldescu
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of
| | - Fatma Aksakal
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Andrei Uncu
- Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
| | - Vladimir Valica
- Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
| | - Livia Uncu
- Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
| | - Simona Negres
- Department of Pharmacology and Clinical Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Florica Nicolescu
- Department of Pharmacology and Clinical Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Fliur Macaev
- Laboratory of Organic Synthesis and Biopharmaceuticals, Institute of Chemistry, Chisinau, Moldova, Republic of.,Scientific Center for Drug Research, "Nicolae Testemitanu" State University of Medicine and Pharmacy, Chisinau, Moldova, Republic of
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Sun ZG, Xu YJ, Xu JF, Liu QX, Yang YS, Zhu HL. Introducing Broadened Antibacterial Activity to Rhodanine Derivatives Targeting Enoyl-Acyl Carrier Protein Reductase. Chem Pharm Bull (Tokyo) 2019; 67:125-129. [PMID: 30713272 DOI: 10.1248/cpb.c18-00663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Broadened antibacterial activity was introduced to rhodanine derivatives targeting Mycobacterial tuberculosis enoyl-acyl carrier protein reductase (Mtb InhA) by recruiting feature of xacins to bring DNA Gyrase B inhibitory capability. This is significant for preventing further bacterial injections in the tuberculosis treatment. The most potent compound Cy14 suggested comparable bioactivity (IC50 = 3.18 µM for Mtb InhA; IC50 = 10 nM for DNA Gyrase B) with positive controls. Structure-activity relationship discussion and molecular docking model revealed the significance of rhodanine moiety and derived methoxyl on meta-position, pointing out orientations for future modification.
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Affiliation(s)
- Zhi-Gang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University.,Central Laboratory, Linyi Central Hospital
| | - Yun-Jie Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Jian-Fei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Qi-Xing Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University
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Synthesis, characterization, DFT and antimicrobial studies of transition metal ion complexes of a new schiff base ligand, 5-methylpyrazole-3yl-N-(2́-hydroxyphenylamine)methyleneimine, (MPzOAP). J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.09.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
4-Formylpyrazoles are useful building blocks in organic synthesis. This review focuses on the applications of 4-formylpyrazoles to generate a large variety of organic compounds and heterocycles such as Schiff bases, pyrazolylpyrazolines, pyrazoloquinolinones, 4H-pyrazolopyran, pyrazolylbenzoxazole, pyrazolothiadiazepines, pyrazolyloxazolone, pyrazolyloxadiazolines, pyrazolylthiadiazolines, imidazolylpyrazoles, pyrazolopyridines, chromenopyrazolones, thiopyranothiazolylpyrazoles and many others. Many of these molecules exhibit excellent biological activities.
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Affiliation(s)
- Renu Bala
- Department of Chemistry, Akal College of Basic Sciences, Eternal University, Baru Sahib, District Sirmour, H.P.- 173101, India
| | - Poonam Kumari
- Department of Chemistry, Akal College of Basic Sciences, Eternal University, Baru Sahib, District Sirmour, H.P.- 173101, India
| | - Sumit Sood
- Department of Chemistry, Akal College of Basic Sciences, Eternal University, Baru Sahib, District Sirmour, H.P.- 173101, India
| | - Karan Singh
- Department of Chemistry, Akal College of Basic Sciences, Eternal University, Baru Sahib, District Sirmour, H.P.- 173101, India
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Ničković VP, Vujnović-Živković ZN, Trajković R, Krtinić D, Ristić L, Radović M, Ćirić Z, Sokolović D, Veselinović AM. In silico studies and the design of novel agents for the treatment of systemic tuberculosis. J Biomol Struct Dyn 2018; 37:3198-3205. [DOI: 10.1080/07391102.2018.1511476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Rada Trajković
- Faculty of Medicine, University of Pristina, Kosovska Mitrovica, Serbia
| | - Dane Krtinić
- Department for Pharmacology and Toxicology, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Lidija Ristić
- Department for Internal Medicine, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Milan Radović
- Department for Internal Medicine, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Zorica Ćirić
- Department for Internal Medicine, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Dušan Sokolović
- Department of Biochemistry, Faculty of Medicine, University of Nis, Nis, Serbia
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Kar SS, Bhat VG, Shenoy VP, Bairy I, Shenoy GG. Design, synthesis, and evaluation of novel diphenyl ether derivatives against drug-susceptible and drug-resistant strains of Mycobacterium tuberculosis. Chem Biol Drug Des 2018; 93:60-66. [PMID: 30118192 DOI: 10.1111/cbdd.13379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/25/2018] [Accepted: 07/22/2018] [Indexed: 11/30/2022]
Abstract
In our efforts to develop druggable diphenyl ethers as potential antitubercular agents, a series of novel diphenyl ether derivatives (5a-f, 6a-f) were designed and synthesized. The representative compounds showed promising in vitro activity against drug-susceptible, isoniazid-resistant, and multidrug-resistant strains of Mycobacterium tuberculosis with MIC values of 1.56 μg/ml (6b), 6.25 μg/ml (6a-d), and 3.125 μg/ml (6b-c), respectively. All the synthesized compounds exhibited satisfactory safety profile (CC50 > 300 μg/ml) against Vero and HepG2 cells. Reverse phase HPLC method was used to probe the physicochemical properties of the synthesized compounds. This series of compounds demonstrated comparatively low logP values. pKa values of representative compounds indicated that they were weak acids. Additionally, in vitro human liver microsomal stability assay confirmed that the synthesized compounds possessed acceptable stability under study conditions. The present study thus establishes compound 6b as the most promising antitubercular agent with acceptable drug-likeness.
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Affiliation(s)
- Sidhartha S Kar
- Department of Pharmaceutical Chemistry, Manipal Academy of Higher Education, Manipal College of Pharmaceutical Sciences, Manipal, India
| | - Varadaraj G Bhat
- Department of Pharmaceutical Chemistry, Manipal Academy of Higher Education, Manipal College of Pharmaceutical Sciences, Manipal, India
| | - Vishnu P Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Indira Bairy
- Melaka-Manipal Medical College, Manipal Academy of Higher Education, Manipal, India
| | - G Gautham Shenoy
- Department of Pharmaceutical Chemistry, Manipal Academy of Higher Education, Manipal College of Pharmaceutical Sciences, Manipal, India
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50
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De Paris R, Vahl Quevedo C, Ruiz DD, Gargano F, de Souza ON. A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model. BMC Bioinformatics 2018; 19:235. [PMID: 29929475 PMCID: PMC6013854 DOI: 10.1186/s12859-018-2222-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 05/29/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In the rational drug design process, an ensemble of conformations obtained from a molecular dynamics simulation plays a crucial role in docking experiments. Some studies have found that Fully-Flexible Receptor (FFR) models predict realistic binding energy accurately and improve scoring to enhance selectiveness. At the same time, methods have been proposed to reduce the high computational costs involved in considering the explicit flexibility of proteins in receptor-ligand docking. This study introduces a novel method to optimize ensemble docking-based experiments by reducing the size of an InhA FFR model at docking runtime and scaling docking workflow invocations on cloud virtual machines. RESULTS First, in order to find the most affordable cost-benefit pool of virtual machines, we evaluated the performance of the docking workflow invocations in different configurations of Azure instances. Second, we validated the gains obtained by the proposed method based on the quality of the Reduced Fully-Flexible Receptor (RFFR) models produced using AutoDock4.2. The analyses show that the proposed method reduced the model size by approximately 50% while covering at least 86% of the best docking results from the 74 ligands tested. Third, we tested our novel method using AutoDock Vina, a different docking software, and showed the positive accuracy achieved in the resulting RFFR models. Finally, our results demonstrated that the method proposed optimized ensemble docking experiments and is applicable to different docking software. In addition, it detected new binding modes, which would be unreachable if employing only the rigid structure used to generate the InhA FFR model. CONCLUSIONS Our results showed that the selective method is a valuable strategy for optimizing ensemble docking-based experiments using different docking software. The RFFR models produced by discarding non-promising snapshots from the original model are accurately shaped for a larger number of ligands, and the elapsed time spent in the ensemble docking experiments are considerably reduced.
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Affiliation(s)
- Renata De Paris
- Business Intelligence and Machine Learning Research Group—GPIN, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 628, Porto Alegre, RS, Brazil
| | - Christian Vahl Quevedo
- Business Intelligence and Machine Learning Research Group—GPIN, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 628, Porto Alegre, RS, Brazil
| | - Duncan D. Ruiz
- Business Intelligence and Machine Learning Research Group—GPIN, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 628, Porto Alegre, RS, Brazil
| | - Furia Gargano
- Bioinformatics and Biossystems Modeling and Simulation Lab—LABIO, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 602, Porto Alegre, RS, Brazil
| | - Osmar Norberto de Souza
- Bioinformatics and Biossystems Modeling and Simulation Lab—LABIO, School of Technology, PUCRS, Av. Ipiranga, 6681, Building 32, Room 602, Porto Alegre, RS, Brazil
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