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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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Alcaraz M, Edwards TE, Kremer L. New therapeutic strategies for Mycobacterium abscessus pulmonary diseases - untapping the mycolic acid pathway. Expert Rev Anti Infect Ther 2023; 21:813-829. [PMID: 37314394 PMCID: PMC10529309 DOI: 10.1080/14787210.2023.2224563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Treatment options against Mycobacterium abscessus infections are very limited. New compounds are needed to cure M. abscessus pulmonary diseases. While the mycolic acid biosynthetic pathway has been largely exploited for the treatment of tuberculosis, this metabolic process has been overlooked in M. abscessus, although it offers many potential drug targets for the treatment of this opportunistic pathogen. AREAS COVERED Herein, the authors review the role of the MmpL3 membrane protein and the enoyl-ACP reductase InhA involved in the transport and synthesis of mycolic acids, respectively. They discuss their importance as two major vulnerable drug targets in M. abscessus and report the activity of MmpL3 and InhA inhibitors. In particular, they focus on NITD-916, a direct InhA inhibitor against M. abscessus, particularly warranted in the context of multidrug resistance. EXPERT OPINION There is an increasing body of evidence validating the mycolic acid pathway as an attractive drug target to be further exploited for M. abscessus lung disease treatments. The NITD-916 studies provide a proof-of-concept that direct inhibitors of InhA are efficient in vitro, in macrophages and in zebrafish. Future work is now required to improve the activity and pharmacological properties of these inhibitors and their evaluation in pre-clinical models.
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Affiliation(s)
- Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Thomas E. Edwards
- UCB BioSciences, Bainbridge Island, WA 98109 USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109 USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
- INSERM, IRIM, 34293 Montpellier, France
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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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New InhA Inhibitors Based on Expanded Triclosan and Di-Triclosan Analogues to Develop a New Treatment for Tuberculosis. Pharmaceuticals (Basel) 2021; 14:ph14040361. [PMID: 33919737 PMCID: PMC8070701 DOI: 10.3390/ph14040361] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) has reinforced the need for the development of new anti-TB drugs. The first line drug isoniazid inhibits InhA. This is a prodrug requiring activation by the enzyme KatG. Mutations in KatG have largely contributed to clinical isoniazid resistance. We aimed to design new 'direct' InhA inhibitors that obviate the need for activation by KatG, circumventing pre-existing resistance. In silico molecular modelling was used as part of a rational structure-based drug-design approach involving inspection of protein crystal structures of InhA:inhibitor complexes, including the broad spectrum antibiotic triclosan (TCS). One crystal structure exhibited the unusual presence of two triclosan molecules within the Mycobacterium tuberculosis InhA binding site. This became the basis of a strategy for the synthesis of novel inhibitors. A series of new, flexible ligands were designed and synthesised, expanding on the triclosan structure. Low Minimum Inhibitory Concentrations (MICs) were obtained for benzylphenyl compounds (12, 43 and 44) and di-triclosan derivative (39), against Mycobacterium bovis BCG although these may also be inhibiting other enzymes. The ether linked di-triclosan derivative (38) displayed excellent in vitro isolated enzyme inhibition results comparable with triclosan, but at a higher MIC (125 µg mL-1). These compounds offer good opportunities as leads for further optimisation.
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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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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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Javed E, Guthrie JD, Neu J, Chirayath GS, Huo S. Introducing an α-Keto Ester Functional Group through Pt-Catalyzed Direct C-H Acylation with Ethyl Chlorooxoacetate. ACS OMEGA 2020; 5:8393-8402. [PMID: 32309750 PMCID: PMC7161214 DOI: 10.1021/acsomega.0c00982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Platinum-catalyzed selective C-H acylation of 2-aryloxypyridines with ethyl chlorooxoacetate provides an efficient way of introducing an α-keto ester functional group. The reaction is oxidant-free, additive-free, and, more significantly, free of any decarbonylative side reactions. The reaction tolerates a variety of substituents from strongly electron-donating to strongly electron-withdrawing groups. Double acylation is feasible for 2-phenoxypyridine and its derivatives with only one substituent at the para position. Although the reaction of 2-(2-methylphenoxy)pyridine with ethyl malonyl chloride did not produce the desired β-keto ester, the reaction with ethyl succinyl chloride proceeded smoothly to give the γ-keto ester. Ethyl chlorooxoacetate is much more reactive than ethyl succinyl chloride in this Pt-catalyzed C-H acylation reaction.
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Affiliation(s)
- Erman Javed
- Department of Chemistry, East
Carolina University, Greenville, North Carolina 27858, United States
| | | | - Justin Neu
- Department of Chemistry, East
Carolina University, Greenville, North Carolina 27858, United States
| | - George S. Chirayath
- Department of Chemistry, East
Carolina University, Greenville, North Carolina 27858, United States
| | - Shouquan Huo
- Department of Chemistry, East
Carolina University, Greenville, North Carolina 27858, United States
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8
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Tiwari AP, Giliyar VB, Shenoy GG, Eshwara VK. Identifying the Structural Features of Diphenyl Ether Analogues for InhA Inhibition: A 2D and 3D QSAR Based Study. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666190611153933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Background:
Enoyl acyl carrier protein reductase (InhA) is a validated target for
Mycobacterium. It is an enzyme which is associated with the biosynthesis of mycolic acids in type II
fatty acid synthase system. Mycobacterial cell wall majorly comprises mycolic acids, which are
responsible for virulence of the microorganism. Several diphenyl ether derivatives have been known
to be direct inhibitors of InhA.
Objective:
In the present work, a Quantitative Structure Activity Relationship (QSAR) study was
performed to identify the structural features of diphenyl ether analogues which contribute to InhA
inhibitory activity in a favourable way.
Method:
Both 2D and 3D QSAR models were built and compared. Several fingerprint based 2D
QSAR models were generated and their relationship with the structural features was studied. Models
which corroborated the inhibitory activity of the molecules with their structural features were
selected and studied in detail.
Results:
A 2D-QSAR model, with dendritic fingerprints having regression coefficient, for test set
molecules Q2 =0.8132 and for the training set molecules, R2 =0.9607 was obtained. Additionally, an
atom-based 3D-QSAR model with Q2 =0.7697 and R2 =0.9159 was also constructed.
Conclusion:
The data reported by various models provides guidance for the designing of structurally
new diphenyl ether inhibitors with potential activity against InhA of M. tuberculosis.
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Affiliation(s)
- Ashutosh Prasad Tiwari
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Varadaraj Bhat Giliyar
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Gurypur Gautham Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Vandana Kalwaja Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, India
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Kouman KC, Keita M, Kre N’Guessan R, Owono Owono LC, Megnassan E, Frecer V, Miertus S. Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles. Int J Mol Sci 2019; 20:ijms20194730. [PMID: 31554227 PMCID: PMC6802012 DOI: 10.3390/ijms20194730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/24/2023] Open
Abstract
Background: During the previous decade a new class of benzamide-based inhibitors of 2-trans enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (Mt) with unusual binding mode have emerged. Here we report in silico design and evaluation of novel benzamide InhA-Mt inhibitors with favorable predicted pharmacokinetic profiles. Methods: By using in situ modifications of the crystal structure of N-benzyl-4-((heteroaryl)methyl) benzamide (BHMB)-InhA complex (PDB entry 4QXM), 3D models of InhA-BHMBx complexes were prepared for a training set of 19 BHMBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the BHMB1-19, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation (∆∆HMM) of InhA-BHMBx complexes with the IC50exp. Further, taking into account the solvent effect and entropy changes upon ligand, binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of BHMBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds containing benzamide scaffolds. The VCL filtered by Lipinski’s rule-of-five was screened by the PH4 model to identify new BHMB analogs. Results: Gas phase QSAR model: −log10(IC50exp) = pIC50exp = −0.2465 × ∆∆HMM + 7.95503, R2 = 0.94; superior aqueous phase QSAR model: pIC50exp = −0.2370 × ∆∆Gcom + 7.8783, R2 = 0.97 and PH4 pharmacophore model: pIC50exp = 1.0013 × pIC50exp − 0.0085, R2 = 0.95. The VCL of more than 114 thousand BHMBs was filtered down to 73,565 analogs Lipinski’s rule. The five-point PH4 screening retained 90 new and potent BHMBs with predicted inhibitory potencies IC50pre up to 65 times lower than that of BHMB1 (IC50exp = 20 nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to current anti-tuberculotics. Conclusions: Combined use of QSAR models that considered binding of the BHMBs to InhA, pharmacophore model, and ADME properties helped to recognize bound active conformation of the benzamide inhibitors, permitted in silico screening of VCL of compounds sharing benzamide scaffold and identification of new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles.
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Affiliation(s)
- Koffi Charles Kouman
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Raymond Kre N’Guessan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Luc Calvin Owono Owono
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Laboratoire de Cristallographie—Physique Moléculaire, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Correspondence: ; Tel.: +225-02-36-30-08
| | - Vladimir Frecer
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, SK-83232 Bratislava, Slovakia
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
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10
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In Silico Repositioning of Cannabigerol as a Novel Inhibitor of the Enoyl Acyl Carrier Protein (ACP) Reductase (InhA). Molecules 2019; 24:molecules24142567. [PMID: 31311157 PMCID: PMC6680637 DOI: 10.3390/molecules24142567] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022] Open
Abstract
Cannabigerol (CBG) and cannabichromene (CBC) are non-psychoactive cannabinoids that have raised increasing interest in recent years. These compounds exhibit good tolerability and low toxicity, representing promising candidates for drug repositioning. To identify novel potential therapeutic targets for CBG and CBC, an integrated ligand-based and structure-based study was performed. The results of the analysis led to the identification of CBG as a low micromolar inhibitor of the Enoyl acyl carrier protein (ACP) reductase (InhA) enzyme.
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11
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Ničković VP, Vujnović-Živković ZN, Trajković R, Krtinić D, Ristić L, Radović M, Ćirić Z, Sokolović D, Veselinović AM. In silico studies and the design of novel agents for the treatment of systemic tuberculosis. J Biomol Struct Dyn 2018; 37:3198-3205. [DOI: 10.1080/07391102.2018.1511476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Rada Trajković
- Faculty of Medicine, University of Pristina, Kosovska Mitrovica, Serbia
| | - Dane Krtinić
- Department for Pharmacology and Toxicology, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Lidija Ristić
- Department for Internal Medicine, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Milan Radović
- Department for Internal Medicine, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Zorica Ćirić
- Department for Internal Medicine, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Dušan Sokolović
- Department of Biochemistry, Faculty of Medicine, University of Nis, Nis, Serbia
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12
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Huo S. Platinum in Chemistry: An Adventure from Phosphorescent Materials to Catalytic C−H Functionalization. CHEM REC 2018; 18:1583-1595. [DOI: 10.1002/tcr.201800019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/18/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Shouquan Huo
- Department of ChemistryEast Carolina University Greenville, North Carolina 27858 USA
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13
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Vosátka R, Krátký M, Vinšová J. Triclosan and its derivatives as antimycobacterial active agents. Eur J Pharm Sci 2018; 114:318-331. [DOI: 10.1016/j.ejps.2017.12.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/06/2017] [Accepted: 12/17/2017] [Indexed: 12/16/2022]
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14
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Neckles C, Eltschkner S, Cummings JE, Hirschbeck M, Daryaee F, Bommineni GR, Zhang Z, Spagnuolo L, Yu W, Davoodi S, Slayden RA, Kisker C, Tonge PJ. Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase. Biochemistry 2017; 56:1865-1878. [PMID: 28225601 DOI: 10.1021/acs.biochem.6b01048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the drug-target residence time require knowledge of both the ground and transition states on the inhibition reaction coordinate, and we have determined the structure-kinetic relationship for 22 ethyl- or hexyl-substituted diphenyl ethers that are slow-binding inhibitors of bpFabI1, the enoyl-ACP reductase FabI1 from Burkholderia pseudomallei. Analysis of enzyme inhibition using a two-dimensional kinetic map demonstrates that the ethyl and hexyl diphenyl ethers fall into two distinct clusters. Modifications to the ethyl diphenyl ether B ring result in changes to both on and off rates, where residence times of up to ∼700 min (∼11 h) are achieved by either ground state stabilization (PT444) or transition state destabilization (slower on rate) (PT404). By contrast, modifications to the hexyl diphenyl ether B ring result in residence times of 300 min (∼5 h) through changes in only ground state stabilization (PT119). Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure-kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. Finally, we demonstrate that three compounds with residence times on bpFabI1 from 118 min (∼2 h) to 670 min (∼11 h) have in vivo efficacy in an acute B. pseudomallei murine infection model using the virulent B. pseudomallei strain Bp400.
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Affiliation(s)
- Carla Neckles
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Sandra Eltschkner
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Jason E Cummings
- Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research and Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-0922, United States
| | - Maria Hirschbeck
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Fereidoon Daryaee
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Gopal R Bommineni
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Zhuo Zhang
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lauren Spagnuolo
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Weixuan Yu
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Shabnam Davoodi
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Richard A Slayden
- Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research and Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-0922, United States
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Peter J Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
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15
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Saharan VD, Mahajan SS. Development of gallic acid formazans as novel enoyl acyl carrier protein reductase inhibitors for the treatment of tuberculosis. Bioorg Med Chem Lett 2017; 27:808-815. [PMID: 28117201 DOI: 10.1016/j.bmcl.2017.01.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/09/2016] [Accepted: 01/10/2017] [Indexed: 01/16/2023]
Abstract
The enoyl acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (MTB) is an attractive target for developing novel antitubercular agents. A series of gallic acid formazans, were computationally designed and docked into the active site of InhA to understand their binding mode and potential to inhibit InhA. Nine compounds from the designed series were identified as potential InhA inhibitors, on the basis of good Glide score. These compounds were synthesized in the laboratory and evaluated for in vitro antitubercular activity against drug-sensitive and multi-drug resistant strains of MTB. Out of nine compounds, three compounds exhibited the most promising MIC of <2μM against the sensitive strain of MTB, H37Rv. The compounds were evaluated against five resistant strains of MTB. Most of the compounds exhibited activity superior to the standard, linezolid, against all these resistant strains. The mechanism of action of these compounds was concluded to be InhA inhibition, through InhA enzyme inhibition study. Insignificant cytotoxicity of these compounds was observed on RAW 264.7 cell line. Inactivity of all these compounds against gram positive and gram negative bacteria indicated their specificity against MTB. The compounds were further analyzed for ADME properties and showed potential as good oral drug candidates. The results clearly identified some novel, selective and specific InhA inhibitors against sensitive and resistant strains of MTB.
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Affiliation(s)
- Vanita D Saharan
- Department of Pharmaceutical Chemistry, C.U. Shah College of Pharmacy, S.N.D.T. Women's University, Sir Vithaldas Vidyavihar, Juhu Tara Road, Santacruz (West), Mumbai 400049, India.
| | - Supriya S Mahajan
- Department of Pharmaceutical Chemistry, C.U. Shah College of Pharmacy, S.N.D.T. Women's University, Sir Vithaldas Vidyavihar, Juhu Tara Road, Santacruz (West), Mumbai 400049, India
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16
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Štular T, Lešnik S, Rožman K, Schink J, Zdouc M, Ghysels A, Liu F, Aldrich CC, Haupt VJ, Salentin S, Daminelli S, Schroeder M, Langer T, Gobec S, Janežič D, Konc J. Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction. J Med Chem 2016; 59:11069-11078. [PMID: 27936766 DOI: 10.1021/acs.jmedchem.6b01277] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug discovery is usually focused on a single protein target; in this process, existing compounds that bind to related proteins are often ignored. We describe ProBiS plugin, extension of our earlier ProBiS-ligands approach, which for a given protein structure allows prediction of its binding sites and, for each binding site, the ligands from similar binding sites in the Protein Data Bank. We developed a new database of precalculated binding site comparisons of about 290000 proteins to allow fast prediction of binding sites in existing proteins. The plugin enables advanced viewing of predicted binding sites, ligands' poses, and their interactions in three-dimensional graphics. Using the InhA query protein, an enoyl reductase enzyme in the Mycobacterium tuberculosis fatty acid biosynthesis pathway, we predicted its possible ligands and assessed their inhibitory activity experimentally. This resulted in three previously unrecognized inhibitors with novel scaffolds, demonstrating the plugin's utility in the early drug discovery process.
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Affiliation(s)
- Tanja Štular
- National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Samo Lešnik
- National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Julia Schink
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Mitja Zdouc
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
| | - An Ghysels
- Center for Molecular Modeling, Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Feng Liu
- AAT Bioquest, Inc. , 520 Mercury Drive, Sunnyvale, California 94085, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - V Joachim Haupt
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Simone Daminelli
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden , 01307 Dresden, Germany
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Janez Konc
- National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska , Glagoljaška 8, SI-6000 Koper, Slovenia
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17
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Knudson SE, Cummings JE, Bommineni GR, Pan P, Tonge PJ, Slayden RA. Formulation studies of InhA inhibitors and combination therapy to improve efficacy against Mycobacterium tuberculosis. Tuberculosis (Edinb) 2016; 101:8-14. [PMID: 27865404 DOI: 10.1016/j.tube.2016.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
Abstract
Previously, structure-based drug design was used to develop substituted diphenyl ethers with potency against the Mycobacterium tuberculosis (Mtb) enoyl-ACP reductase (InhA), however, the highly lipophilic centroid compound, SB-PT004, lacked sufficient efficacy in the acute murine Mtb infection model. A next generation series of compounds were designed with improved specificity, potency against InhA, and reduced cytotoxicity in vitro, but these compounds also had limited solubility. Accordingly, solubility and pharmacokinetics studies were performed to develop formulations for this class and other experimental drug candidates with high logP values often encountered in drug discovery. Lead diphenyl ethers were formulated in co-solvent and Self-Dispersing Lipid Formulations (SDLFs) and evaluated in a rapid murine Mtb infection model that assesses dissemination to and bacterial burden in the spleen. In vitro synergy studies were performed with the lead diphenyl ether compounds, SB-PT070 and SB-PT091, and rifampin (RIF), which demonstrated an additive effect, and that guided the in vivo studies. Combinatorial therapy in vivo studies with these compounds delivered in our Self-Micro Emulsifying Drug Delivery System (SMEDDS) resulted in an additional 1.4 log10 CFU reduction in the spleen of animals co-treated with SB-PT091 and RIF and an additional 1.7 log10 reduction in the spleen with animals treated with both SB-PT070 and RIF.
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Affiliation(s)
- Susan E Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jason E Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Gopal R Bommineni
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Pan Pan
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Peter J Tonge
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Richard A Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA.
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18
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Rožman K, Sosič I, Fernandez R, Young RJ, Mendoza A, Gobec S, Encinas L. A new 'golden age' for the antitubercular target InhA. Drug Discov Today 2016; 22:492-502. [PMID: 27663094 DOI: 10.1016/j.drudis.2016.09.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
Abstract
The increasing prevalence of multidrug-resistant strains of Mycobacterium tuberculosis is the main contributing factor in unfavorable outcomes in the treatment of tuberculosis. Studies suggest that direct inhibitors of InhA, an enoyl-ACP-reductase, might yield promising clinical candidates that can be developed into new antitubercular drugs. In this review, we describe the application of different hit-identification strategies to InhA, which clearly illustrate the druggability of its active site through distinct binding mechanisms. We further characterize four classes of InhA inhibitors that show novel binding modes, and provide evidence of their successful target engagement as well as their in vivo activity.
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Affiliation(s)
- Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Raquel Fernandez
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Robert J Young
- GlaxoSmithKline Medicines Research Centre, Stevenage, Herfordshire SG1 2NY, UK
| | - Alfonso Mendoza
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Lourdes Encinas
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain.
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19
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Bommineni GR, Kapilashrami K, Cummings JE, Lu Y, Knudson SE, Gu C, Walker SG, Slayden RA, Tonge PJ. Thiolactomycin-Based Inhibitors of Bacterial β-Ketoacyl-ACP Synthases with in Vivo Activity. J Med Chem 2016; 59:5377-90. [PMID: 27187871 DOI: 10.1021/acs.jmedchem.6b00236] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
β-Ketoacyl-ACP synthases (KAS) are key enzymes involved in the type II bacterial fatty acid biosynthesis (FASII) pathway and are putative targets for antibacterial discovery. Several natural product KAS inhibitors have previously been reported, including thiolactomycin (TLM), which is produced by Nocardia spp. Here we describe the synthesis and characterization of optically pure 5R-thiolactomycin (TLM) analogues that show improved whole cell activity against bacterial strains including methicillin-resistant Staphylococcus aureus (MRSA) and priority pathogens such as Francisella tularensis and Burkholderia pseudomallei. In addition, we identify TLM analogues with in vivo efficacy against MRSA and Klebsiella pneumoniae in animal models of infection.
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Affiliation(s)
| | | | - Jason E Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | | | - Susan E Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | | | | | - Richard A Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
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20
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Neckles C, Pschibul A, Lai CT, Hirschbeck M, Kuper J, Davoodi S, Zou J, Liu N, Pan P, Shah S, Daryaee F, Bommineni GR, Lai C, Simmerling C, Kisker C, Tonge PJ. Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia pestis FabV Enoyl-ACP Reductase. Biochemistry 2016; 55:2992-3006. [PMID: 27136302 DOI: 10.1021/acs.biochem.5b01301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The enoyl-ACP reductase (ENR) catalyzes the last reaction in the elongation cycle of the bacterial type II fatty acid biosynthesis (FAS-II) pathway. While the FabI ENR is a well-validated drug target in organisms such as Mycobacterium tuberculosis and Staphylococcus aureus, alternate ENR isoforms have been discovered in other pathogens, including the FabV enzyme that is the sole ENR in Yersinia pestis (ypFabV). Previously, we showed that the prototypical ENR inhibitor triclosan was a poor inhibitor of ypFabV and that inhibitors based on the 2-pyridone scaffold were more potent [Hirschbeck, M. (2012) Structure 20 (1), 89-100]. These studies were performed with the T276S FabV variant. In the work presented here, we describe a detailed examination of the mechanism and inhibition of wild-type ypFabV and the T276S variant. The T276S mutation significantly reduces the affinity of diphenyl ether inhibitors for ypFabV (20-fold → 100-fold). In addition, while T276S ypFabV generally displays an affinity for 2-pyridone inhibitors higher than that of the wild-type enzyme, the 4-pyridone scaffold yields compounds with similar affinity for both wild-type and T276S ypFabV. T276 is located at the N-terminus of the helical substrate-binding loop, and structural studies coupled with site-directed mutagenesis reveal that alterations in this residue modulate the size of the active site portal. Subsequently, we were able to probe the mechanism of time-dependent inhibition in this enzyme family by extending the inhibition studies to include P142W ypFabV, a mutation that results in a gain of slow-onset inhibition for the 4-pyridone PT156.
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Affiliation(s)
| | - Annica Pschibul
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | | | - Maria Hirschbeck
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
| | | | | | | | | | | | | | | | - Cristina Lai
- William A. Shine Great Neck South High School , Great Neck, New York 11020, United States
| | | | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany
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21
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Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PLoS Negl Trop Dis 2016; 10:e0004300. [PMID: 26735851 PMCID: PMC4703370 DOI: 10.1371/journal.pntd.0004300] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/21/2015] [Indexed: 12/16/2022] Open
Abstract
Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105 compounds and several functional relations among 1.67 105 proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature. Neglected tropical diseases are human infectious diseases that are often associated with poverty. Historically, lack of interest from the pharmaceutical industry resulted in the lack of good drugs to combat the majority of the pathogens that cause these diseases. Recently, the availability of open chemical information has increased with the advent of public domain chemical resources and the release of data from high throughput screening assays. Our aim in this work was to make use of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to prioritize and identify candidate drug targets in neglected pathogen proteomes, and drug-like bioactive molecules to foster drug development against neglected diseases. Our approach to the problem relied on applying bioinformatics and computational biology strategies to model large datasets spanning complete proteomes and extensive chemical information from publicly available sources. As a result, we were able to prioritize drug targets and identify potential targets for orphan bioactive drugs.
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Affiliation(s)
- Ariel José Berenstein
- Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Paula Magariños
- Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
| | - Ariel Chernomoretz
- Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernán Agüero
- Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
- * E-mail: ,
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22
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Kouassi AF, Kone M, Keita M, Esmel A, Megnassan E, N'Guessan YT, Frecer V, Miertus S. Computer-Aided Design of Orally Bioavailable Pyrrolidine Carboxamide Inhibitors of Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Pharmacokinetic Profiles. Int J Mol Sci 2015; 16:29744-71. [PMID: 26703572 PMCID: PMC4691139 DOI: 10.3390/ijms161226196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 11/16/2022] Open
Abstract
We have carried out a computational structure-based design of new potent pyrrolidine carboxamide (PCAMs) inhibitors of enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (MTb). Three-dimensional (3D) models of InhA-PCAMx complexes were prepared by in situ modification of the crystal structure of InhA-PCAM1 (Protein Data Bank (PDB) entry code: 4U0J), the reference compound of a training set of 20 PCAMs with known experimental inhibitory potencies (IC50(exp)). First, we built a gas phase quantitative structure-activity relationships (QSAR) model, linearly correlating the computed enthalpy of the InhA-PCAM complex formation and the IC50(exp). Further, taking into account the solvent effect and loss of inhibitor entropy upon enzyme binding led to a QSAR model with a superior linear correlation between computed Gibbs free energies (ΔΔGcom) of InhA-PCAM complex formation and IC50(exp) (pIC50(exp) = -0.1552·ΔΔGcom + 5.0448, R² = 0.94), which was further validated with a 3D-QSAR pharmacophore model generation (PH4). Structural information from the models guided us in designing of a virtual combinatorial library (VL) of more than 17 million PCAMs. The VL was adsorption, distribution, metabolism and excretion (ADME) focused and reduced down to 1.6 million drug like orally bioavailable analogues and PH4 in silico screened to identify new potent PCAMs with predicted IC50(pre) reaching up to 5 nM. Combining molecular modeling and PH4 in silico screening of the VL resulted in the proposed novel potent antituberculotic agent candidates with favorable pharmacokinetic profiles.
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Affiliation(s)
- Affiba Florance Kouassi
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
| | - Mawa Kone
- Laboratoire de Chimie Organique et des Substances Naturelles, University of Cocody-Felix Houphouët-Boigny, Avenue de l'Université, Abidjan 22, Cote D'Ivoire.
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
| | - Akori Esmel
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée, University of Abobo Adjamé-Nangui Abrogoua, Autoroute d'Abobo, Abidjan 02, Cote D'Ivoire.
- Laboratoire de Chimie Organique et des Substances Naturelles, University of Cocody-Felix Houphouët-Boigny, Avenue de l'Université, Abidjan 22, Cote D'Ivoire.
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
| | - Yao Thomas N'Guessan
- Laboratoire de Chimie Organique et des Substances Naturelles, University of Cocody-Felix Houphouët-Boigny, Avenue de l'Université, Abidjan 22, Cote D'Ivoire.
| | - Vladimir Frecer
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
- Faculty of Pharmacy, Comenius University in Bratislava, Bratislava SK-83232, Slovakia.
- International Centre for Applied Research and Sustainable Technology, Bratislava SK-84104, Slovakia.
| | - Stanislav Miertus
- International Centre for Science and High Technology, UNIDO, Area Science Park, Trieste I-34012, Italy.
- International Centre for Applied Research and Sustainable Technology, Bratislava SK-84104, Slovakia.
- Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava SK-91701, Slovakia.
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23
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Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors. Int J Mol Sci 2015; 16:23695-722. [PMID: 26457706 PMCID: PMC4632722 DOI: 10.3390/ijms161023695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/18/2015] [Accepted: 09/08/2015] [Indexed: 12/22/2022] Open
Abstract
Molecular dynamics (MD) simulations of 12 aqueous systems of the NADH-dependent enoyl-ACP reductase from Mycobacterium tuberculosis (InhA) were carried out for up to 20–40 ns using the GROMACS 4.5 package. Simulations of the holoenzyme, holoenzyme-substrate, and 10 holoenzyme-inhibitor complexes were conducted in order to gain more insight about the secondary structure motifs of the InhA substrate-binding pocket. We monitored the lifetime of the main intermolecular interactions: hydrogen bonds and hydrophobic contacts. Our MD simulations demonstrate the importance of evaluating the conformational changes that occur close to the active site of the enzyme-cofactor complex before and after binding of the ligand and the influence of the water molecules. Moreover, the protein-inhibitor total steric (ELJ) and electrostatic (EC) interaction energies, related to Gly96 and Tyr158, are able to explain 80% of the biological response variance according to the best linear equation, pKi = 7.772 − 0.1885 × Gly96 + 0.0517 × Tyr158 (R2 = 0.80; n = 10), where interactions with Gly96, mainly electrostatic, increase the biological response, while those with Tyr158 decrease. These results will help to understand the structure-activity relationships and to design new and more potent anti-TB drugs.
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24
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Borah AJ, Yan G, Wang L. RhIII-Catalyzed Olefination of 2-Aryloxypyridines Using 2-Pyridyloxyl as the Removable Directing Group. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Yu W, Neckles C, Chang A, Bommineni GR, Spagnuolo L, Zhang Z, Liu N, Lai C, Truglio J, Tonge PJ. A [(32)P]NAD(+)-based method to identify and quantitate long residence time enoyl-acyl carrier protein reductase inhibitors. Anal Biochem 2015; 474:40-9. [PMID: 25684450 PMCID: PMC4454744 DOI: 10.1016/j.ab.2014.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 01/26/2023]
Abstract
The classical methods for quantifying drug-target residence time (tR) use loss or regain of enzyme activity in progress curve kinetic assays. However, such methods become imprecise at very long residence times, mitigating the use of alternative strategies. Using the NAD(P)H-dependent FabI enoyl-acyl carrier protein (enoyl-ACP) reductase as a model system, we developed a Penefsky column-based method for direct measurement of tR, where the off-rate of the drug was determined with radiolabeled [adenylate-(32)P]NAD(P(+)) cofactor. In total, 23 FabI inhibitors were analyzed, and a mathematical model was used to estimate limits to the tR values of each inhibitor based on percentage drug-target complex recovery following gel filtration. In general, this method showed good agreement with the classical steady-state kinetic methods for compounds with tR values of 10 to 100 min. In addition, we were able to identify seven long tR inhibitors (100-1500 min) and to accurately determine their tR values. The method was then used to measure tR as a function of temperature, an analysis not previously possible using the standard kinetic approach due to decreased NAD(P)H stability at elevated temperatures. In general, a 4-fold difference in tR was observed when the temperature was increased from 25 to 37 °C.
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Affiliation(s)
- Weixuan Yu
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Carla Neckles
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Andrew Chang
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Gopal Reddy Bommineni
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Lauren Spagnuolo
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Zhuo Zhang
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Nina Liu
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA
| | - Christina Lai
- Great Neck South High School, Great Neck, NY 11020, USA
| | - James Truglio
- Great Neck South High School, Great Neck, NY 11020, USA
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11790, USA.
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26
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Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ. A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA. J Chem Inf Model 2015; 55:645-59. [PMID: 25636146 DOI: 10.1021/ci500672v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Isoniazid (INH) is usually administered to treat latent Mycobacterium tuberculosis (Mtb) infections and is used in combination therapy to treat active tuberculosis (TB). Unfortunately, resistance to this drug is hampering its clinical effectiveness. INH is a prodrug that must be activated by Mtb catalase-peroxidase (KatG) before it can inhibit InhA (Mtb enoyl-acyl-carrier-protein reductase). Isoniazid-resistant cases of TB found in clinical settings usually involve mutations in or deletion of katG, which abrogate INH activation. Compounds that inhibit InhA without requiring prior activation by KatG would not be affected by this resistance mechanism and hence would display continued potency against these drug-resistant isolates of Mtb. Virtual screening experiments versus InhA in the GO Fight Against Malaria (GO FAM) project were designed to discover new scaffolds that display base-stacking interactions with the NAD cofactor. GO FAM experiments included targets from other pathogens, including Mtb, when they had structural similarity to a malaria target. Eight of the 16 soluble compounds identified by docking against InhA plus visual inspection were modest inhibitors and did not require prior activation by KatG. The best two inhibitors discovered are both fragment-sized compounds and displayed Ki values of 54 and 59 μM, respectively. Importantly, the novel inhibitors discovered have low structural similarity to known InhA inhibitors and thus help expand the number of chemotypes on which future medicinal chemistry efforts can be focused. These new fragment hits could eventually help advance the fight against INH-resistant Mtb strains, which pose a significant global health threat.
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Affiliation(s)
- Alexander L Perryman
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Sean Ekins
- ⊥Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States.,#Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Stefano Forli
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | | | - Arthur J Olson
- †Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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27
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Wang H, Lu Y, Liu L, Kim SW, Hooker JM, Fowler JS, Tonge PJ. Radiosynthesis and biological evaluation of a novel enoyl-ACP reductase inhibitor for Staphylococcus aureus. Eur J Med Chem 2014; 88:66-73. [PMID: 25217335 DOI: 10.1016/j.ejmech.2014.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 11/18/2022]
Abstract
The pharmacokinetics (PK) and pharmacodynamics (PD) of PT119, a potent Staphylococcus aureus enoyl-ACP reductase (saFabI) inhibitor with a Ki value of 0.01 nM and a residence time of 750 min on the enzyme target, has been evaluated in mice. PT119 was found to have promising antibacterial activity in two different S. aureus infection models: it caused a 3 log reduction in the CFU's in a mouse thigh muscle infection model and increased the survival rate from 0% to 50% in a mouse systemic infection model. PT119 was then radiolabeled with carbon-11 to evaluate its biodistribution and PK in both healthy and S. aureus infected mice using positron emission tomography (PET). The biodistribution of [11C]PT119 and/or its labeled metabolites did not differ significantly between the healthy group and the infected group, and PT119 was found to distribute equally between serum and tissue during the ∼1 h of analysis permitted by the carbon-11 half life. This approach provides important data for PK/PD modeling and is the first step in identifying radiotracers that can non-invasively image bacterial infection in vivo.
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Affiliation(s)
- Hui Wang
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yang Lu
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Li Liu
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sung Won Kim
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jacob M Hooker
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Joanna S Fowler
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Peter J Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA.
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28
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Holas O, Ondrejcek P, Dolezal M. Mycobacterium tuberculosisenoyl-acyl carrier protein reductase inhibitors as potential antituberculotics: development in the past decade. J Enzyme Inhib Med Chem 2014; 30:629-48. [DOI: 10.3109/14756366.2014.959512] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Stec J, Vilchèze C, Lun S, Perryman AL, Wang X, Freundlich JS, Bishai W, Jacobs WR, Kozikowski AP. Biological evaluation of potent triclosan-derived inhibitors of the enoyl-acyl carrier protein reductase InhA in drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. ChemMedChem 2014; 9:2528-37. [PMID: 25165007 PMCID: PMC4213240 DOI: 10.1002/cmdc.201402255] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Indexed: 11/09/2022]
Abstract
New triclosan (TRC) analogues were evaluated for their activity against the enoyl-acyl carrier protein reductase InhA in Mycobacterium tuberculosis (Mtb). TRC is a well-known inhibitor of InhA, and specific modifications to its positions 5 and 4' afforded 27 derivatives; of these compounds, seven derivatives showed improved potency over that of TRC. These analogues were active against both drug-susceptible and drug-resistant Mtb strains. The most active compound in this series, 4-(n-butyl)-1,2,3-triazolyl TRC derivative 3, had an MIC value of 0.6 μg mL(-1) (1.5 μM) against wild-type Mtb. At a concentration equal to its MIC, this compound inhibited purified InhA by 98 %, and showed an IC50 value of 90 nM. Compound 3 and the 5-methylisoxazole-modified TRC 14 were able to inhibit the biosynthesis of mycolic acids. Furthermore, mc(2) 4914, an Mtb strain overexpressing inhA, was found to be less susceptible to compounds 3 and 14, supporting the notion that InhA is the likely molecular target of the TRC derivatives presented herein.
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Affiliation(s)
- Jozef Stec
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States, Fax: +1-312-996-7107
- Department of Pharmaceutical Sciences, College of Pharmacy, Chicago State University, 9501 S. King Drive, Chicago, Illinois 60628, United States
| | - Catherine Vilchèze
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Shichun Lun
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD 21231-1044, United States
| | - Alexander L. Perryman
- Center for Emerging & Re-emerging Pathogens, Division of Infectious, Diseases, Department of Medicine, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
| | - Xin Wang
- Center for Emerging & Re-emerging Pathogens, Division of Infectious, Diseases, Department of Medicine, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
| | - Joel S. Freundlich
- Center for Emerging & Re-emerging Pathogens, Division of Infectious, Diseases, Department of Medicine, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
- Department of Pharmacology and Physiology, Rutgers University-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, United States
| | - William Bishai
- Center for Tuberculosis Research, Department of Medicine, Division of Infectious Disease, Johns Hopkins School of Medicine, Baltimore, MD 21231-1044, United States
| | - William R. Jacobs
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Alan P. Kozikowski
- Drug Discovery Program, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States, Fax: +1-312-996-7107
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30
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Punkvang A, Kamsri P, Saparpakorn P, Hannongbua S, Wolschann P, Irle S, Pungpo P. Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation. Chem Biol Drug Des 2014; 86:91-101. [PMID: 25354564 DOI: 10.1111/cbdd.12465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 01/03/2023]
Abstract
Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity.
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Affiliation(s)
- Auradee Punkvang
- Faculty of Science, Nakhon Phanom University, Muang, Nakhon Phanom, 48000, Thailand
| | - Pharit Kamsri
- Department of Chemistry, Ubon Ratchathani University, 85 Sthollmark Road, Warinchamrap, Ubonratchathani, 34190, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Peter Wolschann
- Institute for Theoretical Chemistry, University of Vienna, Vienna, A-1090, Austria.,Department of Pharmaceutical Technology and Biopharmaceutics, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Stephan Irle
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Pornpan Pungpo
- Department of Chemistry, Ubon Ratchathani University, 85 Sthollmark Road, Warinchamrap, Ubonratchathani, 34190, Thailand
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31
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Rynearson KD, Charrette B, Gabriel C, Moreno J, Boerneke MA, Dibrov SM, Hermann T. 2-Aminobenzoxazole ligands of the hepatitis C virus internal ribosome entry site. Bioorg Med Chem Lett 2014; 24:3521-5. [PMID: 24930829 PMCID: PMC4114401 DOI: 10.1016/j.bmcl.2014.05.088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 01/08/2023]
Abstract
2-Aminobenzoxazoles have been synthesized as ligands for the hepatitis C virus (HCV) internal ribosome entry site (IRES) RNA. The compounds were designed to explore the less basic benzoxazole system as a replacement for the core scaffold in previously discovered benzimidazole viral translation inhibitors. Structure-activity relationships in the target binding of substituted benzoxazole ligands were investigated.
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Affiliation(s)
- Kevin D Rynearson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Brian Charrette
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Christopher Gabriel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Jesus Moreno
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Mark A Boerneke
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Sergey M Dibrov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States.
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32
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Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study. J Mol Model 2014; 20:2319. [PMID: 24935113 DOI: 10.1007/s00894-014-2319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.
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33
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Kamsri P, Koohatammakun N, Srisupan A, Meewong P, Punkvang A, Saparpakorn P, Hannongbua S, Wolschann P, Prueksaaroon S, Leartsakulpanich U, Pungpo P. Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:473-488. [PMID: 24785640 DOI: 10.1080/1062936x.2014.898690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor-enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents.
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Affiliation(s)
- P Kamsri
- a Department of Chemistry, Faculty of Science , Ubon Ratchathani University , Ubonratchathani , Thailand
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34
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Li HJ, Lai CT, Pan P, Yu W, Liu N, Bommineni GR, Garcia-Diaz M, Simmerling C, Tonge PJ. A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA. ACS Chem Biol 2014; 9:986-93. [PMID: 24527857 PMCID: PMC4004265 DOI: 10.1021/cb400896g] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/14/2014] [Indexed: 01/01/2023]
Abstract
Slow-onset enzyme inhibitors are of great interest for drug discovery programs since the slow dissociation of the inhibitor from the drug-target complex results in sustained target occupancy leading to improved pharmacodynamics. However, the structural basis for slow-onset inhibition is often not fully understood, hindering the development of structure-kinetic relationships and the rational optimization of drug-target residence time. Previously we demonstrated that slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA correlated with motions of a substrate-binding loop (SBL) near the active site. In the present work, X-ray crystallography and molecular dynamics simulations have been used to map the structural and energetic changes of the SBL that occur upon enzyme inhibition. Helix-6 within the SBL adopts an open conformation when the inhibitor structure or binding kinetics is substrate-like. In contrast, slow-onset inhibition results in large-scale local refolding in which helix-6 adopts a closed conformation not normally populated during substrate turnover. The open and closed conformations of helix-6 are hypothesized to represent the EI and EI* states on the two-step induced-fit reaction coordinate for enzyme inhibition. These two states were used as the end points for nudged elastic band molecular dynamics simulations resulting in two-dimensional potential energy profiles that reveal the barrier between EI and EI*, thus rationalizing the binding kinetics observed with different inhibitors. Our findings indicate that the structural basis for slow-onset kinetics can be understood once the structures of both EI and EI* have been identified, thus providing a starting point for the rational control of enzyme-inhibitor binding kinetics.
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Affiliation(s)
- Huei-Jiun Li
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Cheng-Tsung Lai
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Pan Pan
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Weixuan Yu
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Nina Liu
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Gopal R. Bommineni
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Miguel Garcia-Diaz
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Peter J. Tonge
- Institute for Chemical
Biology and Drug Discovery, Laufer Center for Physical and
Quantitative Biology and Department of Chemistry, Graduate Program in Biochemistry
and Structural Biology, and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
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Pan P, Knudson S, Bommineni GR, Li HJ, Lai CT, Liu N, Garcia-Diaz M, Simmerling C, Patil SS, Slayden RA, Tonge PJ. Time-dependent diaryl ether inhibitors of InhA: structure-activity relationship studies of enzyme inhibition, antibacterial activity, and in vivo efficacy. ChemMedChem 2014; 9:776-91. [PMID: 24616444 PMCID: PMC4126670 DOI: 10.1002/cmdc.201300429] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 11/07/2022]
Abstract
The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl-ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. In the present work, we demonstrate that two time-dependent B-ring modified diaryl ether InhA inhibitors have antibacterial activity in a mouse model of TB infection when delivered by intraperitoneal injection. We propose that the efficacy of these compounds is related to their residence time on the enzyme, and to identify structural features that modulate drug-target residence time in this system, we have explored the inhibition of InhA by a series of B-ring modified analogues. Seven ortho-substituted compounds were found to be time-dependent inhibitors of InhA, where the slow step leading to the final enzyme-inhibitor complex (EI*) is thought to correlate with closure and ordering of the InhA substrate binding loop. A detailed mechanistic understanding of the molecular basis for residence time in this system will facilitate the development of InhA inhibitors with improved in vivo activity.
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Affiliation(s)
- Pan Pan
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Susan Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-2025
| | - Gopal R. Bommineni
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Huei-Jiun Li
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Cheng-Tsung Lai
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
- Biochemistry and Structural Biology, Stony Brook, NY 11794-3400
| | - Nina Liu
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | - Miguel Garcia-Diaz
- Pharmacological Sciences Graduate Program, Stony Brook University, Stony Brook, NY 11794-3400
| | - Carlos Simmerling
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
| | | | - Richard A. Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-2025
| | - Peter J. Tonge
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook, NY 11794-3400
- Biochemistry and Structural Biology, Stony Brook, NY 11794-3400
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Belardinelli JM, Morbidoni HR. Recycling and refurbishing old antitubercular drugs: the encouraging case of inhibitors of mycolic acid biosynthesis. Expert Rev Anti Infect Ther 2014; 11:429-40. [DOI: 10.1586/eri.13.24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Walsh K, Sneddon HF, Moody CJ. An efficient method for the synthesis of heteroaryl C–O bonds in the absence of added transition metal catalysts. RSC Adv 2014. [DOI: 10.1039/c4ra04851b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Wang Y, Ma S. Recent Advances in Inhibitors of Bacterial Fatty Acid Synthesis Type II (FASII) System Enzymes as Potential Antibacterial Agents. ChemMedChem 2013; 8:1589-608. [DOI: 10.1002/cmdc.201300209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/30/2013] [Indexed: 12/25/2022]
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40
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Chang A, Schiebel J, Yu W, Bommineni GR, Pan P, Baxter MV, Khanna A, Sotriffer CA, Kisker C, Tonge PJ. Rational optimization of drug-target residence time: insights from inhibitor binding to the Staphylococcus aureus FabI enzyme-product complex. Biochemistry 2013; 52:4217-28. [PMID: 23697754 DOI: 10.1021/bi400413c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug-target kinetics has recently emerged as an especially important facet of the drug discovery process. In particular, prolonged drug-target residence times may confer enhanced efficacy and selectivity in the open in vivo system. However, the lack of accurate kinetic and structural data for a series of congeneric compounds hinders the rational design of inhibitors with decreased off-rates. Therefore, we chose the Staphylococcus aureus enoyl-ACP reductase (saFabI)--an important target for the development of new anti-staphylococcal drugs--as a model system to rationalize and optimize the drug-target residence time on a structural basis. Using our new, efficient, and widely applicable mechanistically informed kinetic approach, we obtained a full characterization of saFabI inhibition by a series of 20 diphenyl ethers complemented by a collection of 9 saFabI-inhibitor crystal structures. We identified a strong correlation between the affinities of the investigated saFabI diphenyl ether inhibitors and their corresponding residence times, which can be rationalized on a structural basis. Because of its favorable interactions with the enzyme, the residence time of our most potent compound exceeds 10 h. In addition, we found that affinity and residence time in this system can be significantly enhanced by modifications predictable by a careful consideration of catalysis. Our study provides a blueprint for investigating and prolonging drug-target kinetics and may aid in the rational design of long-residence-time inhibitors targeting the essential saFabI enzyme.
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Affiliation(s)
- Andrew Chang
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
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Suzuki H, Utsunomiya I, Shudo K, Fukuhara N, Iwaki T, Yasukata T. Antibacterial oxazolidinone analogues having a N-hydroxyacetyl-substituted seven-membered [1,2,5]triazepane or [1,2,5]oxadiazepane C-ring unit. Eur J Med Chem 2013; 63:811-25. [DOI: 10.1016/j.ejmech.2013.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/27/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
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42
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Chen T, Huang Q, Luo Y, Hu Y, Lu W. Cu-mediated selective O-arylation on C-6 substituted pyridin-2-ones. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2012.12.126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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43
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Lee JH, Deng L. Asymmetric approach toward chiral cyclohex-2-enones from anisoles via an enantioselective isomerization by a new chiral diamine catalyst. J Am Chem Soc 2012; 134:18209-12. [PMID: 23043531 PMCID: PMC3492513 DOI: 10.1021/ja308623n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A 3-step asymmetric approach toward the optically active chiral cyclohex-2-enones from anisoles has been developed. The crucial asymmetric induction step is an unprecedented catalytic enantioselective isomerization of β,γ-unsaturated cyclohex-3-en-1-ones to the corresponding α,β-unsaturated chiral enones. This new asymmetric transformation was realized by cooperative iminium-base catalysis with an electronically tunable new organic catalyst. The synthetic utility of this methodology is highlighted by the enantioselective total synthesis of (-)-isoacanthodoral.
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Affiliation(s)
- Jung Hwa Lee
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
| | - Li Deng
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States
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44
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Hirschbeck MW, Kuper J, Lu H, Liu N, Neckles C, Shah S, Wagner S, Sotriffer CA, Tonge PJ, Kisker C. Structure of the Yersinia pestis FabV enoyl-ACP reductase and its interaction with two 2-pyridone inhibitors. Structure 2012; 20:89-100. [PMID: 22244758 DOI: 10.1016/j.str.2011.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 01/03/2023]
Abstract
The recently discovered FabV enoyl-ACP reductase, which catalyzes the last step of the bacterial fatty acid biosynthesis (FAS-II) pathway, is a promising but unexploited drug target against the reemerging pathogen Yersinia pestis. The structure of Y. pestis FabV in complex with its cofactor reveals that the enzyme features the common architecture of the short-chain dehydrogenase reductase superfamily, but contains additional structural elements that are mostly folded around the usually flexible substrate-binding loop, thereby stabilizing it in a very tight conformation that seals the active site. The structures of FabV in complex with NADH and two newly developed 2-pyridone inhibitors provide insights for the development of new lead compounds, and suggest a mechanism by which the substrate-binding loop opens to admit the inhibitor, a motion that could also be coupled to the interaction of FabV with the acyl-carrier protein substrate.
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Affiliation(s)
- Maria W Hirschbeck
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, Josef-Schneider-Strasse 2, University of Würzburg, D-97080 Würzburg, Germany
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45
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Yang Y, Wang Z, Yang J, Yang T, Pi W, Ang W, Lin Y, Liu Y, Li Z, Luo Y, Wei Y. Design, synthesis and evaluation of novel molecules with a diphenyl ether nucleus as potential antitubercular agents. Bioorg Med Chem Lett 2011; 22:954-7. [PMID: 22197389 DOI: 10.1016/j.bmcl.2011.12.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/29/2011] [Accepted: 12/03/2011] [Indexed: 02/05/2023]
Abstract
A series of compounds with a diphenyl ether nucleus were synthesized by incorporating various amines into the diphenyl ether scaffold with an amide bond. Their antitubercular activities were evaluated against Mycobacterium tuberculosis H(37)Rv by a microdilution method, with MIC values ranging from 4 to 64μg/mL. Through structure-activity relationship studies, the two chlorine atoms at 3 and 4 positions in the phenyl ring of R(2) group were found to play a significant role in the antitubercular activity. The most potent compound 6c showed an MIC value of 4μg/mL and a good safety profile in HepG2 cell line by the MTT assay. Compound 6c was further found to be effective in a murine model of BCG infection, providing a good lead for subsequent optimization.
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Affiliation(s)
- Yinghong Yang
- State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China; Department of Pharmaceutical and Bioengineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
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46
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Recent advances in the design and synthesis of heterocycles as anti-tubercular agents. Future Med Chem 2011; 2:1469-500. [PMID: 21426140 DOI: 10.4155/fmc.10.227] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Due to the unusual structure and chemical composition of the mycobacterial cell wall, effective tuberculosis (TB) treatment is difficult, making many antibiotics ineffective and hindering the entry of drugs. With approximately 33% of infection, TB is still the second most deadly infectious disease worldwide. The reasons for this are drug-resistant TB (multidrug resistant and extensively drug resistant), persistent infection (latent TB) and synergism of TB with HIV; furthermore no new chemical entity has emerged in last 40 years. New data available from the recently sequenced genome of the mycobacterium and the application of methods of modern drug design promise much for the fight against this disease. In this review, we present an introduction to TB, followed by an overview of new heterocyclic anti-tubercular moieties published during the last decade.
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Lu X, Huang K, You Q. Enoyl acyl carrier protein reductase inhibitors: a patent review (2006 - 2010). Expert Opin Ther Pat 2011; 21:1007-22. [PMID: 21651455 DOI: 10.1517/13543776.2011.581227] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Bacterial enoyl acyl carrier protein reductase (ENR) specificity reduces the double bond in enoyl thioester substrates in the final enzymatic step of the elongation cycle of the fatty acid synthase-II pathway. Its function is essential for bacterial organism survival, making it an attractive target for the development of novel antibiotics. The structural features and therapeutic potential of this enzyme have stimulated the rational design of ENR inhibitors, and important progress has been achieved to date. AREAS COVERED This review describes recent advances made in the search for ENR inhibitors, as reflected by patent applications filed from 2006 to 2010, together with an overview of the relevant literature. The first section of this paper provides a background of the biology of ENR, followed by a description of its structure and function. The main section describes the substrate specificities for ENR, and the structure-based rational design of patent inhibitors originating from different companies and academic groups. EXPERT OPINION The increase in the number of ENR inhibitors bodes well for the development of new therapeutics against multidrug-resistant bacteria. The challenge is now to improve the pharmacokinetic parameters of these inhibitors and translate them into clinical studies.
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Affiliation(s)
- Xiaoyun Lu
- Guangzhou Institutes of Biomedicine and Health, Key Laboratory of Regenerative Biology and Institute of Chemical Biology, Chinese Academy of Sciences, No. 190, Kaiyuan Avenue, Science Park, Guangzhou, 510530, China
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Ribeiro da Silva MAV, Lobo Ferreira AIMC, Cimas Á. Calorimetric and Computational Study of the Thermochemistry of Phenoxyphenols. J Org Chem 2011; 76:3754-64. [DOI: 10.1021/jo200018r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Manuel A. V Ribeiro da Silva
- Centro de Investigação em Química, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Ana I. M. C Lobo Ferreira
- Centro de Investigação em Química, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
| | - Álvaro Cimas
- Centro de Investigação em Química, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
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Jain AK, Veerasamy R, Vaidya A, Kashaw S, Mourya VK, Agrawal RK. QSAR analysis of B-ring-modified diaryl ether derivatives as a InhA inhibitors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9518-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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50
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Investigating the structural basis of arylamides to improve potency against M. tuberculosis strain through molecular dynamics simulations. Eur J Med Chem 2010; 45:5585-93. [DOI: 10.1016/j.ejmech.2010.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/13/2010] [Accepted: 09/04/2010] [Indexed: 11/18/2022]
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