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Canales CSC, Pavan AR, Dos Santos JL, Pavan FR. In silico drug design strategies for discovering novel tuberculosis therapeutics. Expert Opin Drug Discov 2024; 19:471-491. [PMID: 38374606 DOI: 10.1080/17460441.2024.2319042] [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: 11/08/2023] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments. AREAS COVERED In this review, the authors explore recent advancements in tuberculosis drug discovery enabled by in silico tools. The main objectives of this review article are to highlight emerging drug candidates identified through in silico methods and to provide an update on the therapeutic targets associated with Mycobacterium tuberculosis. EXPERT OPINION These in silico methods have not only streamlined the drug discovery process but also opened up new horizons for finding novel drug candidates and repositioning existing ones. The continued advancements in these fields hold great promise for more efficient, ethical, and successful drug development in the future.
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Affiliation(s)
- Christian S Carnero Canales
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- School of Pharmacy, biochemistry and biotechnology, Santa Maria Catholic University, Arequipa, Perú
| | - Aline Renata Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
| | | | - Fernando Rogério Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
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2
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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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3
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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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4
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Zhang Q, Han J, Zhu Y, Yu F, Hu X, Tong HHY, Liu H. Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays. J Comput Aided Mol Des 2023; 37:695-706. [PMID: 37642861 DOI: 10.1007/s10822-023-00530-4] [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: 05/09/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) continues to spread worldwide and remains one of the leading causes of death among infectious diseases. The enoyl-acyl carrier protein reductase (InhA) belongs to FAS-II family and is essential for the formation of the Mycobacterium tuberculosis cell wall. Recent years, InhA direct inhibitors have been extensively studied to overcome MDR-TB. However, there are still no inhibitors that have entered clinical research. Here, the ensemble docking-based virtual screening along with biological assay were used to identify potent InhA direct inhibitors from Chembridge, Chemdiv, and Specs. Ultimately, 34 compounds were purchased and first assayed for the binding affinity, of which four compounds can bind InhA well with KD values ranging from 48.4 to 56.2 µM. Among them, compound 9,222,034 has the best inhibitory activity against InhA enzyme with an IC50 value of 18.05 µM. In addition, the molecular dynamic simulation and binding free energy calculation indicate that the identified compounds bind to InhA with "extended" conformation. Residue energy decomposition shows that residues such as Tyr158, Met161, and Met191 have higher energy contributions in the binding of compounds. By analyzing the binding modes, we found that these compounds can bind to a hydrophobic sub-pocket formed by residues Tyr158, Phe149, Ile215, Leu218, etc., resulting in extensive van der Waals interactions. In summary, this study proposed an efficient strategy for discovering InhA direct inhibitors through ensemble docking-based virtual screening, and finally identified four active compounds with new skeletons, which can provide valuable information for the discovery and optimization of InhA direct inhibitors.
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Affiliation(s)
- Qianqian Zhang
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Jianting Han
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Yongchang Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Xiaopeng Hu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China.
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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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Özcan E, Vagolu SK, Gündüz MG, Stevanovic M, Kökbudak Z, Tønjum T, Nikodinovic-Runic J, Çetinkaya Y, Doğan ŞD. Novel Quinoline-Based Thiosemicarbazide Derivatives: Synthesis, DFT Calculations, and Investigation of Antitubercular, Antibacterial, and Antifungal Activities. ACS OMEGA 2023; 8:40140-40152. [PMID: 37929089 PMCID: PMC10620885 DOI: 10.1021/acsomega.3c03018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023]
Abstract
The discovery of new antimicrobial agents as a means of treating drug-resistant microbial pathogens is of utmost significance to overcome their immense risk to human well-being. The current investigation involves the development, synthesis, and assessment of the antimicrobial efficacy of novel quinoline derivatives incorporating a thiosemicarbazide functionality. To design the target compounds (QST1-QST14), we applied the molecular hybridization approach to link various thiosemicarbazides to the quinoline core with a sulfonyl group. Upon the synthesis and completion of structural characterization via spectroscopic techniques (1H NMR, 13C NMR, 15N NMR, IR, and HRMS), the title molecules were extensively evaluated for their potential antitubercular, antibacterial, and antifungal activities. N-(3-Chlorophenyl)-2-(quinolin-8-ylsulfonyl)hydrazine-1-carbothioamide (QST4), the most effective compound against Mycobacterium tuberculosis H37Rv, was also tested on isoniazid-resistant clinical isolates with katG and inhA promoter mutations. Based on molecular docking studies, QST4 was also likely to demonstrate its antimycobacterial activity through inhibition of the InhA enzyme. Furthermore, three derivatives (QST3, QST4, and QST10) with preferable antimicrobial and drug-like profiles were also shown to be nontoxic against human embryonic kidney (HEK) cells. All compounds were optimized by the density functional theory method using B3LYP with the 6-31+G(d,p) basis set. Structural analysis, natural bond orbital calculations of donor-acceptor interactions, molecular electrostatic potential analysis, and frontier molecular orbital analysis were carried out. Quantum chemical descriptors and charges on the atoms were determined to compare the strengths of the intramolecular hydrogen bonds formed and their stabilities. We determined that the sulfur atom forms a stronger intramolecular hydrogen bond than the nitrogen, oxygen, and fluorine atoms in these sulfonyl thiosemicarbazide derivatives.
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Affiliation(s)
- Esma Özcan
- Department
of Chemistry, Faculty of Science, Erciyes
University, 38039 Kayseri, Turkey
- Department
of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Siva Krishna Vagolu
- Unit
for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
| | - Miyase Gözde Gündüz
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| | - Milena Stevanovic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Zülbiye Kökbudak
- Department
of Chemistry, Faculty of Science, Erciyes
University, 38039 Kayseri, Turkey
| | - Tone Tønjum
- Unit
for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
- Unit for
Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0316 Oslo, Norway
| | - Jasmina Nikodinovic-Runic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Yasin Çetinkaya
- Department
of Chemistry, Faculty of Science, Atatürk
University, 25240 Erzurum, Turkey
| | - Şengül Dilem Doğan
- Department
of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
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7
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Davoodi S, Daryaee F, Iuliano JN, Collado JT, He Y, Pollard AC, Gil AA, Aramini JM, Tonge PJ. Evaluating the Impact of the Tyr158 p Ka on the Mechanism and Inhibition of InhA, the Enoyl-ACP Reductase from Mycobacterium tuberculosis. Biochemistry 2023; 62:1943-1952. [PMID: 37270808 PMCID: PMC10329767 DOI: 10.1021/acs.biochem.2c00606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
InhA, the Mycobacterium tuberculosis enoyl-ACP reductase, is a target for the tuberculosis (TB) drug isoniazid (INH). InhA inhibitors that do not require KatG activation avoid the most common mechanism of INH resistance, and there are continuing efforts to fully elucidate the enzyme mechanism to drive inhibitor discovery. InhA is a member of the short-chain dehydrogenase/reductase superfamily characterized by a conserved active site Tyr, Y158 in InhA. To explore the role of Y158 in the InhA mechanism, this residue has been replaced by fluoroTyr residues that increase the acidity of Y158 up to ∼3200-fold. Replacement of Y158 with 3-fluoroTyr (3-FY) and 3,5-difluoroTyr (3,5-F2Y) has no effect on kcatapp/KMapp nor on the binding of inhibitors to the open form of the enzyme (Kiapp), whereas both kcatapp/KMapp and Kiapp are altered by seven-fold for the 2,3,5-trifluoroTyr variant (2,3,5-F3Y158 InhA). 19F NMR spectroscopy suggests that 2,3,5-F3Y158 is ionized at neutral pH indicating that neither the acidity nor ionization state of residue 158 has a major impact on catalysis or on the binding of substrate-like inhibitors. In contrast, Ki*app is decreased 6- and 35-fold for the binding of the slow-onset inhibitor PT504 to 3,5-F2Y158 and 2,3,5-F3Y158 InhA, respectively, indicating that Y158 stabilizes the closed form of the enzyme adopted by EI*. The residence time of PT504 is reduced ∼four-fold for 2,3,5-F3Y158 InhA compared to wild-type, and thus, the hydrogen bonding interaction of the inhibitor with Y158 is an important factor in the design of InhA inhibitors with increased residence times on the enzyme.
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Affiliation(s)
- Shabnam Davoodi
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - James N. Iuliano
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Jinnette Tolentino Collado
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Yongle He
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Alyssa C. Pollard
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Agnieszka A. Gil
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - James M. Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, United States
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
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8
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Reddy BRS, Babu KS, Mulakayala N, Gajulapalli VPR. Synthesis of Novel 5‐Oxo‐1,2,4‐Oxadiazole Derivatives as Antitubercular Agents and Their Molecular Docking Study toward Enoyl Reductase (InhA) Enzyme. ChemistrySelect 2023. [DOI: 10.1002/slct.202204093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - K Sudakar Babu
- Department of Chemistry Sri Krishnadevaraya University Anantapur 515055 India
| | - Naveen Mulakayala
- Department of Chemistry Sri Krishnadevaraya University Anantapur 515055 India
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Trawally M, Demir-Yazıcı K, İpek Dingis-Birgül S, Kaya K, Akdemir A, Güzel-Akdemir Ö. Dithiocarbamates and dithiocarbonates containing 6-nitrosaccharin scaffold: Synthesis, antimycobacterial activity and in silico target prediction using ensemble docking-based reverse virtual screening. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Synthesis, characterization, anti-tuberculosis activity and molecular modeling studies of thiourea derivatives bearing aminoguanidine moiety. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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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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Koçak Aslan E, Han Mİ, Krishna VS, Tamhaev R, Dengiz C, Doğan ŞD, Lherbet C, Mourey L, Tønjum T, Gündüz MG. Isoniazid Linked to Sulfonate Esters via Hydrazone Functionality: Design, Synthesis, and Evaluation of Antitubercular Activity. Pharmaceuticals (Basel) 2022; 15:ph15101301. [PMID: 36297413 PMCID: PMC9609273 DOI: 10.3390/ph15101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 01/24/2023] Open
Abstract
Isoniazid (INH) is one of the key molecules employed in the treatment of tuberculosis (TB), the most deadly infectious disease worldwide. However, the efficacy of this cornerstone drug has seriously decreased due to emerging INH-resistant strains of Mycobacterium tuberculosis (Mtb). In the present study, we aimed to chemically tailor INH to overcome this resistance. We obtained thirteen novel compounds by linking INH to in-house synthesized sulfonate esters via a hydrazone bridge (SIH1-SIH13). Following structural characterization by FTIR, 1H NMR, 13C NMR, and HRMS, all compounds were screened for their antitubercular activity against Mtb H37Rv strain and INH-resistant clinical isolates carrying katG and inhA mutations. Additionally, the cytotoxic effects of SIH1-SIH13 were assessed on three different healthy host cell lines; HEK293, IMR-90, and BEAS-2B. Based on the obtained data, the synthesized compounds appeared as attractive antimycobacterial drug candidates with low cytotoxicity. Moreover, the stability of the hydrazone moiety in the chemical structure of the final compounds was confirmed by using UV/Vis spectroscopy in both aqueous medium and DMSO. Subsequently, the compounds were tested for their inhibitory activities against enoyl acyl carrier protein reductase (InhA), the primary target enzyme of INH. Although most of the synthesized compounds are hosted by the InhA binding pocket, SIH1-SIH13 do not primarily show their antitubercular activities by direct InhA inhibition. Finally, in silico determination of important physicochemical parameters of the molecules showed that SIH1-SIH13 adhered to Lipinski's rule of five. Overall, our study revealed a new strategy for modifying INH to cope with the emerging drug-resistant strains of Mtb.
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Affiliation(s)
- Ebru Koçak Aslan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
| | - Muhammed İhsan Han
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
| | - Rasoul Tamhaev
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France
| | - Cagatay Dengiz
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
- Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
- Correspondence:
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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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14
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Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Derivatives as the Direct InhA Inhibitors and the Hotspot Residues of InhA. Int J Mol Sci 2022; 23:ijms231710102. [PMID: 36077494 PMCID: PMC9456180 DOI: 10.3390/ijms231710102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Given the current epidemic of multidrug-resistant tuberculosis, there is an urgent need to develop new drugs to combat drug-resistant tuberculosis. Direct inhibitors of the InhA target do not require activation and thus can overcome drug resistance caused by mutations in drug-activating enzymes. In this work, the binding thermodynamic and kinetic information of InhA to its direct inhibitors, phenoxyphenol derivatives, were explored through multiple computer-aided drug design (CADD) strategies. The results show that the van der Waals interactions were the main driving force for protein–ligand binding, among which hydrophobic residues such as Tyr158, Phe149, Met199 and Ile202 have high energy contribution. The AHRR pharmacophore model generated by multiple ligands demonstrated that phenoxyphenol derivatives inhibitors can form pi–pi stacking and hydrophobic interactions with InhA target. In addition, the order of residence time predicted by random acceleration molecular dynamics was consistent with the experimental values. The intermediate states of these inhibitors could form hydrogen bonds and van der Waals interactions with surrounding residues during dissociation. Overall, the binding and dissociation mechanisms at the atomic level obtained in this work can provide important theoretical guidance for the development of InhA direct inhibitors with higher activity and proper residence time.
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15
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Dutta A, Trivedi P, Gehlot PS, Gogoi D, Hazarika R, Chetia P, Kumar A, Chaliha AK, Chaturvedi V, Sarma D. Design and Synthesis of Quinazolinone-Triazole Hybrids as Potent Anti-Tubercular Agents. ACS APPLIED BIO MATERIALS 2022; 5:4413-4424. [PMID: 36053225 DOI: 10.1021/acsabm.2c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A straightforward and convenient methodology has been developed for the reaction of 2-aminobenzamide and carbonyls affording 2,3-dihydroquinazolin-4(1H)-ones using aqueous solution of [C12Py][FeCl3Br]. The developed methodology was applied for the synthesis of 25 quinazolinone-triazole hybrids followed by evaluation of their in vitro anti-tubercular (TB) activity. The results revealed that 8 quinazolinone-triazole hybrids displayed promising activity having MIC values of 0.78-12.5 μg/mL. The compound 3if with MIC 0.78 μg/mL was found to be the lead nominee among the series, better than Ethambutol, a first line anti-TB drug and comparable with Rifampicin. The active compounds with MIC values ≤ 6.25 μg/mL were subjected to in vitro cytotoxicity and found nontoxic. In drug-drug interaction, compounds 3ia and 3ii interacted synergistically with all the three anti-TB drugs, INH, RFM, and EMB. Other 3 compounds interacted either in synergistic or additive manners. Important information on the binding interaction of the target compounds with the active sites of 1DQY Antigen 85C from Mycobacterium tuberculosis and Enoyl acyl carrier protein reductase (InhA) enzymes was obtained from molecular docking studies. Screening of the drug-likeness properties and bioactivity score indicates that synthesized molecules could be projected as potential drug candidates. Based on the current study, quinazolinone-triazole hybrids framework can be useful in drug development for TB.
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Affiliation(s)
- Apurba Dutta
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Priyanka Trivedi
- Biochemistry Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
| | - Praveen Singh Gehlot
- AcSIR, Salt and Marine Chemicals Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Dipshikha Gogoi
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Roktopol Hazarika
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Pankaj Chetia
- Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Arvind Kumar
- AcSIR, Salt and Marine Chemicals Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Amrita Kashyap Chaliha
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam 786004, India
| | - Vinita Chaturvedi
- Biochemistry Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
| | - Diganta Sarma
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam 786004, India
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16
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Keleş Atıcı R, Doğan ŞD, Gündüz MG, Krishna VS, Chebaiki M, Homberset H, Lherbet C, Mourey L, Tønjum T. Urea derivatives carrying a thiophenylthiazole moiety: Design, synthesis, and evaluation of antitubercular and InhA inhibitory activities. Drug Dev Res 2022; 83:1292-1304. [PMID: 35769019 DOI: 10.1002/ddr.21958] [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: 01/06/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/05/2022]
Abstract
The recent emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) has complicated and significantly slowed efforts to eradicate and/or reduce the worldwide incidence of life-threatening acute and chronic cases of tuberculosis. To overcome this setback, researchers have increased the intensity of their work to identify new small-molecule compounds that are expected to remain efficacious antimicrobials against Mtb. Here, we describe our effort to apply the principles of molecular hybridization to synthesize 16 compounds carrying thiophene and thiazole rings beside the core urea functionality (TTU1-TTU16). Following extensive structural characterization, the obtained compounds were initially evaluated for their antimycobacterial activity against Mtb H37Rv. Subsequently, three derivatives standing out with their anti-Mtb activity profiles and low cytotoxicity (TTU5, TTU6, and TTU12) were tested on isoniazid-resistant clinical isolates carrying katG and inhA mutations. Additionally, due to their pharmacophore similarities to the well-known InhA inhibitors, the molecules were screened for their enoyl acyl carrier protein reductase (InhA) inhibitory potentials. Molecular docking studies were performed to support the experimental enzyme inhibition data. Finally, drug-likeness of the selected compounds was established by theoretical calculations of physicochemical descriptors.
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Affiliation(s)
- Rüveyde Keleş Atıcı
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Melina Chebaiki
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
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17
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Hopf FSM, Roth CD, de Souza EV, Galina L, Czeczot AM, Machado P, Basso LA, Bizarro CV. Bacterial Enoyl-Reductases: The Ever-Growing List of Fabs, Their Mechanisms and Inhibition. Front Microbiol 2022; 13:891610. [PMID: 35814645 PMCID: PMC9260719 DOI: 10.3389/fmicb.2022.891610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Enoyl-ACP reductases (ENRs) are enzymes that catalyze the last step of the elongation cycle during fatty acid synthesis. In recent years, new bacterial ENR types were discovered, some of them with structures and mechanisms that differ from the canonical bacterial FabI enzymes. Here, we briefly review the diversity of structural and catalytic properties of the canonical FabI and the new FabK, FabV, FabL, and novel ENRs identified in a soil metagenome study. We also highlight recent efforts to use the newly discovered Fabs as targets for drug development and consider the complex evolutionary history of this diverse set of bacterial ENRs.
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Affiliation(s)
- Fernanda S. M. Hopf
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida D. Roth
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Eduardo V. de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiza Galina
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexia M. Czeczot
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano V. Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Cristiano V. Bizarro,
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18
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Rethinking the MtInhA tertiary and quaternary structure flexibility: a molecular dynamics view. J Mol Model 2022; 28:140. [PMID: 35534695 DOI: 10.1007/s00894-022-05135-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/30/2022] [Indexed: 10/18/2022]
Abstract
Flexibility and function are related properties in the study of protein dynamics. Flexibility reflects in the conformational potential of proteins and thus in their functionalities. The presence of interactions between protein-ligands and protein-protein complexes, substrates, and environmental changes can alter protein plasticity, acting from the rearrangement of the side chains of amino acids to the folding/unfolding of large structural motifs. To evaluate the effects of the flexibility in protein systems, we defined the enzyme 2-trans-enoyl-ACP (CoA) reductase from Mycobacterium tuberculosis, or MtInhA, as our target system. MtInhA is biologically active as a tetramer in solution; however, computational studies commonly use the monomer justifying the independence of its active sites due to their distances. However, differences in flexibility between tertiary and quaternary structures could present impact on the size of the active site, influencing the drug discovery process. In this study, we investigated the influence of flexibility restrictions in A- and B-loops of the MtInhA in order to suggest a monomeric structure that describes the conformational behavior of the tetrameric system. Overall, we observed that simulations where restrictions were applied to the A- and B-loops present a more similar behavior to the native structure when compared to unrestricted simulations. Therefore, our work presents a monomeric model of MtInhA, which has conformational characteristics of the biologically active structure. Thus, the data obtained in this work can be applied to the MtInhA system for the generation of more reliable flexible models for molecular docking experiments, and also for the performance of longer simulations by molecular dynamics and with a lower computational cost.
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19
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Koçak Aslan E, Krishna VS, Armaković SJ, Armaković S, Şahin O, Tønjum T, Gündüz MG. Linking azoles to isoniazid via hydrazone bridge: Synthesis, crystal structure determination, antitubercular evaluation and computational studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Mandelic acid-based spirothiazolidinones targeting M. tuberculosis: Synthesis, in vitro and in silico investigations. Bioorg Chem 2022; 121:105688. [DOI: 10.1016/j.bioorg.2022.105688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/09/2022] [Accepted: 02/13/2022] [Indexed: 01/01/2023]
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21
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Songsiriritthigul C, Hanwarinroj C, Pakamwong B, Srimanote P, Suttipanta N, Sureram S, Suttisintong K, Kamsri P, Punkvang A, Spencer J, Kittakoop P, Pungpo P. Inhibition of Mycobacterium tuberculosis InhA by 3-nitropropanoic acid. Proteins 2021; 90:898-904. [PMID: 34677871 DOI: 10.1002/prot.26268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022]
Abstract
3-Nitropropanoic acid (3NP), a bioactive fungal natural product, was previously demonstrated to inhibit growth of Mycobacterium tuberculosis. Here we demonstrate that 3NP inhibits the 2-trans-enoyl-acyl carrier protein reductase (InhA) from Mycobacterium tuberculosis with an IC50 value of 71 μM, and present the crystal structure of the ternary InhA-NAD+ -3NP complex. The complex contains the InhA substrate-binding loop in an ordered, open conformation with Tyr158, a catalytically important residue whose orientation defines different InhA substrate/inhibitor complex conformations, in the "out" position. 3NP occupies a hydrophobic binding site adjacent to the NAD+ cofactor and close to that utilized by the diphenyl ether triclosan, but binds predominantly via electrostatic and water-mediated hydrogen-bonding interactions with the protein backbone and NAD+ cofactor. The identified mode of 3NP binding provides opportunities to improve inhibitory activity toward InhA.
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Affiliation(s)
- Chomphunuch Songsiriritthigul
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand.,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Chayanin Hanwarinroj
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | - Bongkochawan Pakamwong
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | - Potjanee Srimanote
- Faculty of Allied Health Sciences, Thammasat University, Khlong Nueng, Pathumthani, Thailand
| | - Nitima Suttipanta
- Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | | | - Khomson Suttisintong
- National Nanotechnology Center, National Science and Technology Development Agency, Pathumthani, 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
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Bangkok, Thailand.,Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), CHE, Ministry of Education, Bangkok, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, Thailand
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22
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Prasad MS, Bhole RP, Khedekar PB, Chikhale RV. Mycobacterium enoyl acyl carrier protein reductase (InhA): A key target for antitubercular drug discovery. Bioorg Chem 2021; 115:105242. [PMID: 34392175 DOI: 10.1016/j.bioorg.2021.105242] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Enoyl acyl carrier protein reductase (InhA) is a key enzyme involved in fatty acid synthesis mainly mycolic acid biosynthesis that is a part of NADH dependent acyl carrier protein reductase family. The aim of the present literature is to underline the different scaffolds or enzyme inhibitors that inhibit mycolic acid biosynthesis mainly cell wall synthesis by inhibiting enzyme InhA. Various scaffolds were identified based on the screening technologies like high throughput screening, encoded library technology, fragment-based screening. The compounds studied include indirect inhibitors (Isoniazid, Ethionamide, Prothionamide) and direct inhibitors (Triclosan/Diphenyl ethers, Pyrrolidine Carboxamides, Pyrroles, Acetamides, Thiadiazoles, Triazoles) with better efficacy against drug resistance. Out of the several scaffolds studied, pyrrolidine carboxamides were found to be the best molecules targeting InhA having good bioavailability properties and better MIC. This review provides with a detailed information, analysis, structure activity relationship and useful insight on various scaffolds as InhA inhibitors.
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Affiliation(s)
- Mayuri S Prasad
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MS, India
| | - Ritesh P Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, Maharashtra, India
| | - Pramod B Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MS, India.
| | - Rupesh V Chikhale
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom.
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23
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Cazzaniga G, Mori M, Chiarelli LR, Gelain A, Meneghetti F, Villa S. Natural products against key Mycobacterium tuberculosis enzymatic targets: Emerging opportunities for drug discovery. Eur J Med Chem 2021; 224:113732. [PMID: 34399099 DOI: 10.1016/j.ejmech.2021.113732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/15/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
For centuries, natural products (NPs) have served as powerful therapeutics against a variety of human ailments. Nowadays, they still represent invaluable resources for the treatment of many diseases, including bacterial infections. After nearly three decades since the World Health Organization's (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. Nature has always provided a virtually unlimited source of bioactive molecules, which have inspired the development of new drugs. NPs are characterized by an exceptional chemical and structural diversity, the result of millennia of evolutionary responses to various stimuli. Thanks to their favorable structural features and their enzymatic origin, they are naturally prone to bind proteins and exhibit bioactivities. Furthermore, their worldwide distribution and ease of accessibility has contributed to promote investigations on their activity. Overall, these characteristics make NPs excellent models for the design of novel therapeutics. This review offers a critical and comprehensive overview of the most promising NPs, isolated from plants, fungi, marine species, and bacteria, endowed with inhibitory properties against traditional and emerging mycobacterial enzymatic targets. A selection of 86 compounds is here discussed, with a special emphasis on their biological activity, structure-activity relationships, and mechanism of action. Our study corroborates the antimycobacterial potential of NPs, substantiating their relevance in future drug discovery and development efforts.
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Affiliation(s)
- Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Laurent Roberto Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, via A. Ferrata 9, 27100, Pavia, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
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24
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Venugopala KN, Deb PK, Pillay M, Chopra D, Chandrashekharappa S, Morsy MA, Aldhubiab BE, Attimarad M, Nair AB, Sreeharsha N, Kandeel M, Venugopala R, Mohanlall V. 4-Aryl-1,4-Dihydropyridines as Potential Enoyl-Acyl Carrier Protein Reductase Inhibitors: Antitubercular Activity and Molecular Docking Study. Curr Top Med Chem 2021; 21:295-306. [PMID: 33138763 DOI: 10.2174/1568026620666201102121606] [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: 08/18/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculosis remains one of the most deadly infectious diseases worldwide due to the emergence of multi-drug resistance (MDR) and extensively drug resistance (XDR) strains of Mycobacterium tuberculosis (MTB). AIMS Currently, available drugs are getting resistant and toxic. Hence, there is an urgent need for the development of potent molecules to treat tuberculosis. MATERIALS AND METHODS Herein, the screening of a total of eight symmetrical 1,4-dihydropyridine (1,4- DHP) derivatives (4a-4h) was carried out for whole-cell anti-TB activity against the susceptible H37Rv and MDR strains of MTB. RESULTS AND DISCUSSION Most of the compounds exhibited moderate to excellent activity against the susceptible H37Rv. Moreover, the most promising compound 4f (against H37Rv) having paratrifluoromethyl phenyl group at 4-position and bis para-methoxy benzyl ester group at 3- and 5- positions of 1,4-dihydropyridine pharmacophore, exhibited no toxicity, but demonstrated weak activity against MTB strains resistant to isoniazid and rifampicin. In light of the inhibitory profile of the title compounds, enoyl-acyl carrier protein reductase (InhA) appeared to be the appropriate molecular target. A docking study of these derivatives against InhA receptor revealed favorable binding interactions. Further, in silico predicted ADME properties of these compounds 4a-4h were found to be in the acceptable ranges, including satisfactory Lipinski's rule of five, thereby indicating their potential as drug-like molecules. CONCLUSION In particular, the 1,4-DHP derivative 4f can be considered an attractive lead molecule for further exploration and development of more potent anti-TB agents as InhA inhibitors.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman 19392, Jordan
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | | | - Mohamed A Morsy
- Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia 61511, Egypt
| | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Rashmi Venugopala
- Department of Public Health Medicine, University of KwaZulu-Natal, Howard College Campus, Durban 4001, South Africa
| | - Viresh Mohanlall
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
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25
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Venugopala KN, Chandrashekharappa S, Deb PK, Tratrat C, Pillay M, Chopra D, Al-Shar'i NA, Hourani W, Dahabiyeh LA, Borah P, Nagdeve RD, Nayak SK, Padmashali B, Morsy MA, Aldhubiab BE, Attimarad M, Nair AB, Sreeharsha N, Haroun M, Shashikanth S, Mohanlall V, Mailavaram R. Anti-tubercular activity and molecular docking studies of indolizine derivatives targeting mycobacterial InhA enzyme. J Enzyme Inhib Med Chem 2021; 36:1472-1487. [PMID: 34210233 PMCID: PMC8259857 DOI: 10.1080/14756366.2021.1919889] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A series of 1,2,3-trisubstituted indolizines (2a-2f, 3a-3d, and 4a-4c) were screened for in vitro whole-cell anti-tubercular activity against the susceptible H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 2b-2d, 3a-3d, and 4a-4c were active against the H37Rv-MTB strain with minimum inhibitory concentration (MIC) ranging from 4 to 32 µg/mL, whereas the indolizines 4a-4c, with ethyl ester group at the 4-position of the benzoyl ring also exhibited anti-MDR-MTB activity (MIC = 16-64 µg/mL). In silico docking study revealed the enoyl-acyl carrier protein reductase (InhA) and anthranilate phosphoribosyltransferase as potential molecular targets for the indolizines. The X-ray diffraction analysis of the compound 4b was also carried out. Further, a safety study (in silico and in vitro) demonstrated no toxicity for these compounds. Thus, the indolizines warrant further development and may represent a novel promising class of InhA inhibitors and multi-targeting agents to combat drug-sensitive and drug-resistant MTB strains.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | | | - Pran Kishore Deb
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Philadelphia University, Amman, Jordan
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Nizar A Al-Shar'i
- Faculty of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, Jordan University of Science and Technology, Irbid, Jordan
| | - Wafa Hourani
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Philadelphia University, Amman, Jordan
| | - Lina A Dahabiyeh
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, India
| | - Rahul D Nagdeve
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, India
| | - Susanta K Nayak
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, India
| | - Basavaraj Padmashali
- Department of Chemistry, School of Basic Science, Rani Channamma University, Belagavi, India
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Faculty of Medicine, Department of Pharmacology, Minia University, El-Minia, Egypt
| | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bangalore, India
| | - Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Sheena Shashikanth
- Department of Studies in Organic Chemistry, University of Mysore, Mysore, India
| | - Viresh Mohanlall
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
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26
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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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27
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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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28
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Popov A, Klimovich A, Styshova O, Moskovkina T, Shchekotikhin A, Grammatikova N, Dezhenkova L, Kaluzhny D, Deriabin P, Gerasimenko A, Udovenko A, Stonik V. Design, synthesis and biomedical evaluation of mostotrin, a new water soluble tryptanthrin derivative. Int J Mol Med 2020; 46:1335-1346. [PMID: 32945360 PMCID: PMC7447309 DOI: 10.3892/ijmm.2020.4693] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
Mostotrin (MT), a novel compound, at least five orders of magnitude more soluble in water than its mother substance, was designed and synthesised from tryptanthrin (TR). Its structure was established by nuclear magnetic resonance and mass spectrometry data and confirmed by X-ray analysis, revealing that MT is a pentacyclic product with an additional pseudo-cycle formed with the participation of one intramolecular hydrogen bond. Antimicrobial activity and cytotoxic action against tumour cells in vitro, as well as anti-tumour effects, acute toxicity and anti-inflammatory activities in vivo, were evaluated. Antimicrobial proper-ties of MT against Mycobacterium spp and Bacillus cereus ATCC 10702 appeared to be the same as that of TR, but against the other strains used it was weaker. Furthermore, MT exhibited 5-10 times higher cytotoxic activities against tumour cell lines HCT-116, MCF-7 and K-562 than TR, but was less toxic than TR (LD50 of MT was 375 mg/kg, while LD50 for TR was 75 mg/kg). Additionally, compounds MT and TR were studied in DNA binding tests. The quenching of its fluorescence on addition to DNA solution established MT to be capable of binding to DNA. Its anti-tumour action in vivo on mice with the ascitic form of Ehrlich carcinoma was promising, particularly with joint application of MT and the antitumour drug doxorubicin. In this model, the survival and life span for the doxorubicin and 1 co-treatment group were significantly higher compared to doxorubicin treatment alone. The compound MT showed a lower immunosuppressive effect than TR at the early stages of inflammation induced in mice by LPS from E. coli (MT hardly inhibited the release of IL-1, IL-2, or INF-γ). These results demonstrated that MT is a perspective hit compound for drug development. In our opinion, further evaluation on the biological effects of MT and its synthetic analogues could lead to safer and more effective anti-tumour and anti-tuberculosis agents than TR itself. MT has also the prospect of application in combination with known anti-tumour drugs for the treatment of oncological diseases.
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Affiliation(s)
- Alexander Popov
- Department of Biotechnology, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of The Russian Academy of Sciences, Vladivostok 69022, Russia
| | - Anna Klimovich
- Department of Biotechnology, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of The Russian Academy of Sciences, Vladivostok 69022, Russia
| | - Olga Styshova
- Department of Biotechnology, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of The Russian Academy of Sciences, Vladivostok 69022, Russia
| | - Taisiya Moskovkina
- School of Natural Sciences, Far Eastern Federal University, Vladivostok 690920, Russia
| | - Andrey Shchekotikhin
- Department of Chemical Transformation of Antibiotics, Gauze Research Institute for The Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow 119435, Russia
| | - Natalia Grammatikova
- Department of Chemical Transformation of Antibiotics, Gauze Research Institute for The Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow 119435, Russia
| | - Lyubov Dezhenkova
- Department of Chemical Transformation of Antibiotics, Gauze Research Institute for The Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow 119435, Russia
| | - Dmitry Kaluzhny
- Department of DNA‑protein Interactions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Peter Deriabin
- Department of DNA‑protein Interactions, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Andrey Gerasimenko
- Department of of X‑ray Analysis, Institute of Chemistry, Far Eastern Branch of The Russian Academy of Sciences, Vladivostok 69022, Russia
| | - Anatoly Udovenko
- Department of of X‑ray Analysis, Institute of Chemistry, Far Eastern Branch of The Russian Academy of Sciences, Vladivostok 69022, Russia
| | - Valentin Stonik
- Department of Biotechnology, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of The Russian Academy of Sciences, Vladivostok 69022, Russia
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29
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Doğan ŞD, Gündüz MG, Doğan H, Krishna VS, Lherbet C, Sriram D. Design and synthesis of thiourea-based derivatives as Mycobacterium tuberculosis growth and enoyl acyl carrier protein reductase (InhA) inhibitors. Eur J Med Chem 2020; 199:112402. [DOI: 10.1016/j.ejmech.2020.112402] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/16/2020] [Accepted: 04/27/2020] [Indexed: 01/30/2023]
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30
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Ibrahim TS, Taher ES, Samir E, M. Malebari A, Khayyat AN, Mohamed MFA, Bokhtia RM, AlAwadh MA, Seliem IA, Asfour HZ, Alhakamy NA, Panda SS, AL-Mahmoudy AMM. In Vitro Antimycobacterial Activity and Physicochemical Characterization of Diaryl Ether Triclosan Analogues as Potential InhA Reductase Inhibitors. Molecules 2020; 25:molecules25143125. [PMID: 32650556 PMCID: PMC7397076 DOI: 10.3390/molecules25143125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 11/29/2022] Open
Abstract
Two sets of diphenyl ether derivatives incorporating five-membered 1,3,4-oxadiazoles, and their open-chain aryl hydrazone analogs were synthesized in good yields. Most of the synthesized compounds showed promising in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv. Three diphenyl ether derivatives, namely hydrazide 3, oxadiazole 4 and naphthylarylidene 8g exhibited pronounced activity with minimum inhibitory concentrations (MICs) of 0.61, 0.86 and 0.99 μg/mL, respectively compared to triclosan (10 μg/mL) and isoniazid (INH) (0.2 μg/mL). Compounds 3, 4, and 8g showed the InhA reductase enzyme inhibition with higher IC50 values (3.28–4.23 µM) in comparison to triclosan (1.10 µM). Correlation between calculated physicochemical parameters and biological activity has been discussed which justifies a strong correlation with respect to the inhibition of InhA reductase enzyme. Molecular modeling and drug-likeness studies showed good agreement with the obtained biological evaluation. The structural and experimental information concerning these three InhA inhibitors will likely contribute to the lead optimization of new antibiotics for M. tuberculosis.
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Affiliation(s)
- Tarek S. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.M.); (A.N.K.); (M.A.A.)
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (R.M.B.); (I.A.S.); (A.M.M.A.-M.)
- Correspondence: (T.S.I.); (S.S.P.)
| | - Ehab S. Taher
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt;
| | - Ebtihal Samir
- Physical Chemistry, Department of Analytical Chemistry, Faculty of Pharmacy, Deraya University, New Minia 61519, Egypt;
| | - Azizah M. Malebari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.M.); (A.N.K.); (M.A.A.)
| | - Ahdab N. Khayyat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.M.); (A.N.K.); (M.A.A.)
| | - Mamdouh F. A. Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, Sohag 82524, Egypt;
| | - Riham M. Bokhtia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (R.M.B.); (I.A.S.); (A.M.M.A.-M.)
- Department of Chemistry & Physics, Augusta University, Augusta, GA 30912, USA
| | - Mohammed A. AlAwadh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.M.M.); (A.N.K.); (M.A.A.)
| | - Israa A. Seliem
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (R.M.B.); (I.A.S.); (A.M.M.A.-M.)
- Department of Chemistry & Physics, Augusta University, Augusta, GA 30912, USA
| | - Hani Z. Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Nabil A. Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Siva S. Panda
- Department of Chemistry & Physics, Augusta University, Augusta, GA 30912, USA
- Correspondence: (T.S.I.); (S.S.P.)
| | - Amany M. M. AL-Mahmoudy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (R.M.B.); (I.A.S.); (A.M.M.A.-M.)
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31
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Doğan H, Doğan ŞD, Gündüz MG, Krishna VS, Lherbet C, Sriram D, Şahin O, Sarıpınar E. Discovery of hydrazone containing thiadiazoles as Mycobacterium tuberculosis growth and enoyl acyl carrier protein reductase (InhA) inhibitors. Eur J Med Chem 2020; 188:112035. [PMID: 31951850 DOI: 10.1016/j.ejmech.2020.112035] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 11/28/2022]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is a serious infectious disease and remains a global health problem. There is an increasing need for the discovery of novel therapeutic agents for its treatment due to the emerging multi-drug resistance. Herein, we present the rational design and the synthesis of eighteen new thiadiazolylhidrazones (TDHs) which were synthesized by intramolecular oxidative N-S bond formation reaction of 2-benzylidene-N-(phenylcarbamothioyl)hydrazine-1-carboximidamide derivatives by phenyliodine(III) bis(trifluoroacetate) (PIFA) under mild conditions. The compounds were characterized by various spectral techniques including FTIR, 1H NMR, 13C NMR and HRMS. Furthermore, the proposed structure of TDH12 was resolved by single-crystal X-ray analysis. The compounds were evaluated for their in vitro antitubercular activity against M. tuberculosis H37Rv. Among them, some compounds exhibited remarkable antimycobacterial activity, MIC = 0.78-6.25 μg/mL, with low cytotoxicity. Additionally, the most active compounds were screened for their biological activities against M. tuberculosis in the nutrient starvation model. Enzyme inhibition assays and molecular docking studies revealed enoyl acyl carrier protein reductase (InhA) as the possible target enzyme of the compounds to show their antitubercular activities.
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Affiliation(s)
- Hilal Doğan
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey; Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039, Kayseri, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039, Kayseri, Turkey.
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, 06100, Ankara, Turkey
| | - Vagolu Siva Krishna
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, 500078, Hyderabad, India
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118, route de Narbonne, 236 Cours Eugène Cosserat, 31062, Toulouse Cedex, France
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani, 500078, Hyderabad, India
| | - Onur Şahin
- Scientific and Technological Research Application and Research Center, Sinop University, 57000 Sinop, Turkey
| | - Emin Sarıpınar
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey
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32
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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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33
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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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34
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Development of (4-methoxyphenyl)-1H-tetrazol-5-amine regioisomers as a new class of selective antitubercular agents. Eur J Med Chem 2019; 186:111882. [PMID: 31753514 DOI: 10.1016/j.ejmech.2019.111882] [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: 08/22/2019] [Revised: 11/01/2019] [Accepted: 11/11/2019] [Indexed: 01/06/2023]
Abstract
A series of halogenated (4-methoxyphenyl)-1H-tetrazol-5-amine regioisomers (1a-9a, 1b-9b) were synthesized from their corresponding thiourea analogues (1-9). The synthesis pathway was confirmed by an X-ray crystallographic studies of 1a, 1b and 5a. Title derivatives were tested for their in vitro antitubercular activity against standard, "wild-type" and atypical mycobacteria. The highest therapeutic potential was attributed to isomeric N-(bromophenyl)tetrazoles 8a and 9a. Their growth-inhibitory effect against multidrug-resistant Mycobacterium tuberculosis Spec. 210 was 8-16-fold stronger than that of the first-line tuberculostatics. Other new tetrazole-derived compounds were also more or equally effective towards that pathogen comparing to the established pharmaceuticals. Among non-tuberculous strains, Mycobacterium scrofulaceum was the most susceptible to the presence of the majority of tetrazole derivatives. The synergistic interaction was found between 9a and streptomycin, as well as the additivity of both 8a and 9a in pairs with isoniazid, rifampicin and ethambutol. None of the studied compounds displayed antibacterial or cytotoxic properties against normal and cancer cell lines, which indicated their highly selective antimycobacterial effects.
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Tarabini RF, Timmers LFSM, Sequeiros-Borja CE, Norberto de Souza O. The importance of the quaternary structure to represent conformational ensembles of the major Mycobacterium tuberculosis drug target. Sci Rep 2019; 9:13683. [PMID: 31548581 PMCID: PMC6757107 DOI: 10.1038/s41598-019-50213-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/03/2019] [Indexed: 12/29/2022] Open
Abstract
Flexibility is a feature intimately related to protein function, since conformational changes can be used to describe environmental changes, chemical modifications, protein-protein and protein-ligand interactions. In this study, we have investigated the influence of the quaternary structure of 2-trans-enoyl-ACP (CoA) reductase or InhA, from Mycobacterium tuberculosis, to its flexibility. We carried out classical molecular dynamics simulations using monomeric and tetrameric forms to elucidate the enzyme's flexibility. Overall, we observed statistically significant differences between conformational ensembles of tertiary and quaternary structures. In addition, the enzyme's binding site is the most affected region, reinforcing the importance of the quaternary structure to evaluate the binding affinity of small molecules, as well as the effect of single point mutations to InhA protein dynamics.
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Affiliation(s)
- Renata Fioravanti Tarabini
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Luís Fernando Saraiva Macedo Timmers
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade do Vale do Taquari -Univates, Rua Avelino Talini, 171 - Bairro Universitário, Lajeado, RS, Brazil.
| | - Carlos Eduardo Sequeiros-Borja
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil.,Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression, Laboratory of Biomolecular Interactions and Transport, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Osmar Norberto de Souza
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas (LABIO), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, 90619-900, Porto Alegre, RS, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil.
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36
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Shaikh MS, Kanhed AM, Chandrasekaran B, Palkar MB, Agrawal N, Lherbet C, Hampannavar GA, Karpoormath R. Discovery of novel N-methyl carbazole tethered rhodanine derivatives as direct inhibitors of Mycobacterium tuberculosis InhA. Bioorg Med Chem Lett 2019; 29:2338-2344. [DOI: 10.1016/j.bmcl.2019.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/31/2019] [Accepted: 06/12/2019] [Indexed: 01/06/2023]
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