1
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Alzain AA, Makki AA, Ibraheem W. Insights into the Inhibition of Mycolic Acid Synthesis by Cytosporone E Derivatives for Tuberculosis Treatment Via an In Silico Multi-target Approach. CHEMISTRY AFRICA 2023. [DOI: 10.1007/s42250-023-00605-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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2
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El-Shoukrofy MS, Atta A, Fahmy S, Sriram D, Mahran MA, Labouta IM. New tetrahydropyrimidine-1,2,3-triazole clubbed compounds: Antitubercular activity and Thymidine Monophosphate Kinase (TMPKmt) inhibition. Bioorg Chem 2023; 131:106312. [PMID: 36528922 DOI: 10.1016/j.bioorg.2022.106312] [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: 09/16/2022] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022]
Abstract
Two series of new tetrahydropyrimidine (THPM)-1,2,3-triazole clubbed compounds were designed, synthesized and screened for their antitubercular (anti-TB) activity against M. tuberculosis H37Rv strain using microplate alamar blue assay (MABA). The most active compounds 5c, 5d, 5e and 5f were further examined for their cytotoxicity against the growth of RAW 264.7 mouse macrophage cells using MTT assay. The four compounds showed safety profiles better than or comparable to that of ethambutol (EMB). These compounds were evaluated for their inhibition activity against mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt). Compounds 5c and 5e were the most potent exhibiting comparable inhibition activity to that of the natural substrate deoxythymidine monophosphate (dTMP). An in silico study was performed including docking of the most active compounds 5c and 5e into the TMPKmt (PDB: ID 1G3U) binding pocket in addition to prediction of their physicochemical and pharmacokinetic properties to explore the overall activity of these anti-TB candidates. Compounds 5c and 5e are promising anti-TB agents and TMPKmt inhibitors with acceptable oral bioavailability, physicochemical and pharmacokinetic properties.
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Affiliation(s)
- Mai S El-Shoukrofy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt.
| | - Amal Atta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Salwa Fahmy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Dharmarajan Sriram
- Medicinal Chemistry Research Laboratory, Pharmacy Group, Birla Institute of Technology and Science, Pilani 33031, India
| | - Mona A Mahran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Ibrahim M Labouta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
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3
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Finger V, Kufa M, Soukup O, Castagnolo D, Roh J, Korabecny J. Pyrimidine derivatives with antitubercular activity. Eur J Med Chem 2023; 246:114946. [PMID: 36459759 DOI: 10.1016/j.ejmech.2022.114946] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Small molecules with antitubercular activity containing the pyrimidine motif in their structure have gained more attention after three drugs, namely GSK 2556286 (GSK-286), TBA-7371 and SPR720, have entered clinical trials. This review provides an overview of recent advances in the hit-to-lead drug discovery studies of antitubercular pyrimidine-containing compounds with the aim to highlight their structural diversity. In the first part, the review discusses the pyrimidine compounds according to their targets, pinpointing the structure-activity relationships of each pyrimidine family. The second part of this review is concentrated on antitubercular pyrimidine derivatives with a yet unexplored or speculative target, dividing the compounds according to their structural types.
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Affiliation(s)
- Vladimir Finger
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Martin Kufa
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic.
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic.
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4
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Kushwaha N, Sahu A, Mishra J, Soni A, Dorwal D. An Insight on the Prospect of Quinazoline and Quinazolinone Derivatives as Anti-tubercular Agents. Curr Org Synth 2023; 20:838-869. [PMID: 36927421 DOI: 10.2174/1570179420666230316094435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 03/18/2023]
Abstract
Multiple potential drugs have been developed based on the heterocyclic molecules for the treatment of different symptoms. Among the existing heterocyclic molecules, quinazoline and quinazolinone derivatives have been found to exhibit extensive pharmacological and biological characteristics. One significant property of these molecules is their potency as anti-tubercular agents. Thus, both quinazoline and quinazolinone derivatives are modified using different functional groups as substituents for investigating their anti-tubercular activities. We present a summary of the reported anti-tubercular drugs, designed using quinazoline and quinazolinone derivatives, in this review.
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Affiliation(s)
| | - Adarsh Sahu
- Department of Pharmaceutical Sciences, Harisingh Gour Vishwavidyalaya, Sagar, MP, India
| | - Jyotika Mishra
- Department of Pharmaceutical Sciences, Harisingh Gour Vishwavidyalaya, Sagar, MP, India
| | - Ankit Soni
- Sri Aurobindo Institute of Pharmacy, Indore, MP, India
| | - Dhawal Dorwal
- Sri Aurobindo Institute of Pharmacy, Indore, MP, India
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5
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Blindheim FH, Malme AT, Dalhus B, Sundby E, Hoff BH. Synthesis and Evaluation of Fused Pyrimidines
as E. coli
Thymidylate Monophosphate Kinase Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202103796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Fredrik Heen Blindheim
- Department of Chemistry Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
| | - Ane Thoresen Malme
- Department of Chemistry Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
- BASF AS Framnesveien 41 3222 Sandefjord Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry University of Oslo and Department for Microbiology Oslo University Hospital Rikshospitalet, Postbox 4950, Nydalen 0424 Oslo Norway
| | - Eirik Sundby
- Department of Material Science Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
| | - Bård Helge Hoff
- Department of Chemistry Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
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6
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Song L, Merceron R, Hulpia F, Lucía A, Gracia B, Jian Y, Risseeuw MDP, Verstraelen T, Cos P, Aínsa JA, Boshoff HI, Munier-Lehmann H, Savvides SN, Van Calenbergh S. Structure-aided optimization of non-nucleoside M. tuberculosis thymidylate kinase inhibitors. Eur J Med Chem 2021; 225:113784. [PMID: 34450493 PMCID: PMC10500704 DOI: 10.1016/j.ejmech.2021.113784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/14/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
Mycobacterium tuberculosis thymidylate kinase (MtTMPK) has emerged as an attractive target for rational drug design. We recently investigated new families of non-nucleoside MtTMPK inhibitors in an effort to diversify MtTMPK inhibitor chemical space. We here report a new series of MtTMPK inhibitors by combining the Topliss scheme with rational drug design approaches, fueled by two co-crystal structures of MtTMPK in complex with developed inhibitors. These efforts furnished the most potent MtTMPK inhibitors in our assay, with two analogues displaying low micromolar MIC values against H37Rv Mtb. Prepared inhibitors address new sub-sites in the MtTMPK nucleotide binding pocket, thereby offering new insights into its druggability. We studied the role of efflux pumps as well as the impact of cell wall permeabilizers for selected compounds to potentially provide an explanation for the lack of correlation between potent enzyme inhibition and whole-cell activity.
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Affiliation(s)
- Lijun Song
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Tergestensis 460, B-9000, Gent, Belgium; 3M, Zwijndrecht, Belgium
| | - Romain Merceron
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium; Eurofins Group, Poitiers, France
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Tergestensis 460, B-9000, Gent, Belgium; Janssen Pharmaceutica, Beerse, Belgium
| | - Ainhoa Lucía
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, and BIFI, Universidad de Zaragoza, Zaragoza, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Begoña Gracia
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, and BIFI, Universidad de Zaragoza, Zaragoza, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Yanlin Jian
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Tergestensis 460, B-9000, Gent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Tergestensis 460, B-9000, Gent, Belgium
| | - Toon Verstraelen
- Center for Melecular Modeling, Ghent University, Zwijnaarde, Ghent, 9052, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610, Antwerpen, Belgium
| | - José A Aínsa
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, and BIFI, Universidad de Zaragoza, Zaragoza, Spain; CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Hélène Munier-Lehmann
- CNRS UMR3523, Department of Structural Biology and Chemistry, Institut Pasteur, 75724, Paris Cedex 15, France
| | - Savvas N Savvides
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Tergestensis 460, B-9000, Gent, Belgium.
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7
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An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis. Molecules 2021; 26:molecules26237082. [PMID: 34885662 PMCID: PMC8659263 DOI: 10.3390/molecules26237082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/04/2022] Open
Abstract
The elucidation of the structure of enzymes and their complexes with ligands continues to provide invaluable insights for the development of drugs against many diseases, including bacterial infections. After nearly three decades since the World Health Organization’s (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. The structural elucidation of enzyme-ligand complexes is fundamental to identify hot-spots, define possible interaction sites, and elaborate strategies to develop optimized molecules with high affinity. This review offers a critical and comprehensive overview of the most recent structural information on traditional and emerging mycobacterial enzymatic targets. A selection of more than twenty enzymes is here discussed, with a special emphasis on the analysis of their binding sites, the definition of the structure–activity relationships (SARs) of their inhibitors, and the study of their main intermolecular interactions. This work corroborates the potential of structural studies, substantiating their relevance in future anti-mycobacterial drug discovery and development efforts.
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8
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Abstract
A radical mediated C-H direct formylation of N-heteroarenes with methanol is reported. The reaction features a novel iron-catalyzed Minisci oxidative coupling process using commercially available methanol as a formylating reagent. It effectively solved the long-standing problems associated with using methanol as a formylating reagent in these types of reactions. Compared to the traditional Minisci C-H formylation methods, this protocol is highly atom-economical, simple to operate, and environmentally friendly and shows good functional group tolerance. This Minisci formylation strategy is a straightforward approach for the late-stage functionalization of N-heteroarenes.
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Affiliation(s)
- Zhengbao Xu
- Institute of Biomedical Research, Shandong University of Technology, Zibo, 255000, Shandong, P. R. China. .,Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, Shandong, P. R. China
| | - Lizhi Zhang
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo, 255000, Shandong, P. R. China
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9
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Blindheim FH, Olsen CE, Krogh Søgaard C, Otterlei M, Sundby E, Hoff BH. Synthetic Strategies towards Imidazopyridinones and 7‐Azaoxindoles and their Evaluation as Antibacterial Agents. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fredrik Heen Blindheim
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Cecilie Elisabeth Olsen
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) 7489 Trondheim Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) 7489 Trondheim Norway
| | - Eirik Sundby
- Department of Material Science Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Bård Helge Hoff
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
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10
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Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
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Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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11
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Jian Y, Forbes HE, Hulpia F, Risseeuw MDP, Caljon G, Munier-Lehmann H, Boshoff HIM, Van Calenbergh S. 2-((3,5-Dinitrobenzyl)thio)quinazolinones: Potent Antimycobacterial Agents Activated by Deazaflavin (F 420)-Dependent Nitroreductase (Ddn). J Med Chem 2021; 64:440-457. [PMID: 33347317 PMCID: PMC10629625 DOI: 10.1021/acs.jmedchem.0c01374] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Swapping the substituents in positions 2 and 4 of the previously synthesized but yet undisclosed 5-cyano-4-(methylthio)-2-arylpyrimidin-6-ones 4, ring closure, and further optimization led to the identification of the potent antitubercular 2-thio-substituted quinazolinone 26. Structure-activity relationship (SAR) studies indicated a crucial role for both meta-nitro substituents for antitubercular activity, while the introduction of polar substituents on the quinazolinone core allowed reduction of bovine serum albumin (BSA) binding (63c, 63d). While most of the tested quinazolinones exhibited no cytotoxicity against MRC-5, the most potent compound 26 was found to be mutagenic via the Ames test. This analogue exhibited moderate inhibitory potency against Mycobacterium tuberculosis thymidylate kinase, the target of the 3-cyanopyridones that lies at the basis of the current analogues, indicating that the whole-cell antimycobacterial activity of the present S-substituted thioquinazolinones is likely due to modulation of alternative or additional targets. Diminished antimycobacterial activity was observed against mutants affected in cofactor F420 biosynthesis (fbiC), cofactor reduction (fgd), or deazaflavin-dependent nitroreductase activity (rv3547), indicating that reductive activation of the 3,5-dinitrobenzyl analogues is key to antimycobacterial activity.
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Affiliation(s)
- Yanlin Jian
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Martijn D. P. Risseeuw
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1 (S7), B-2610 Wilrijk, Belgium
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28 Rue du Dr. Roux, Cedex 15 75724 Paris, France
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
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12
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Jian Y, Merceron R, De Munck S, Forbes HE, Hulpia F, Risseeuw MDP, Van Hecke K, Savvides SN, Munier-Lehmann H, Boshoff HIM, Van Calenbergh S. Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents. Eur J Med Chem 2020; 206:112659. [PMID: 32823003 PMCID: PMC11000207 DOI: 10.1016/j.ejmech.2020.112659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 01/30/2023]
Abstract
As the last enzyme in nucleotide synthesis as precursors for DNA replication, thymidylate kinase of M. tuberculosis (MtbTMPK) attracts significant interest as a target in the discovery of new anti-tuberculosis agents. Earlier, we discovered potent MtbTMPK inhibitors, but these generally suffered from poor antimycobacterial activity, which we hypothesize is due to poor bacterial uptake. To address this, we herein describe our efforts to equip previously reported MtbTMPK inhibitors with targeting moieties to increase the whole cell activity of the hybrid analogues. Introduction of a simplified Fe-chelating siderophore motif gave rise to analogue 17 that combined favorable enzyme inhibitory activity with significant activity against M. tuberculosis (MIC of 12.5 μM). Conjugation of MtbTMPK inhibitors with an imidazo[1,2-a]pyridine or 3,5-dinitrobenzamide scaffold afforded analogues 26, 27 and 28, with moderate MtbTMPK enzyme inhibitory potency, but sub-micromolar activity against mycobacteria without significant cytotoxicity. These results indicate that conjugation with structural motifs known to favor mycobacterial uptake may be a valid approach for discovering new antimycobacterial agents.
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Affiliation(s)
- Yanlin Jian
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Romain Merceron
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, 9052, Belgium
| | - Steven De Munck
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, 9052, Belgium
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281 S3, Gent, B-9000, Belgium
| | - Savvas N Savvides
- VIB Center for Inflammation Research, Zwijnaarde, Ghent, 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent, 9052, Belgium
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28 Rue du Dr. Roux, Cedex, 15 75724, Paris, France
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.
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13
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Chen T, Xiong H, Yang JF, Zhu XL, Qu RY, Yang GF. Diaryl Ether: A Privileged Scaffold for Drug and Agrochemical Discovery. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9839-9877. [PMID: 32786826 DOI: 10.1021/acs.jafc.0c03369] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diaryl ether (DE) is a functional scaffold existing widely both in natural products (NPs) and synthetic organic compounds. Statistically, DE is the second most popular and enduring scaffold within the numerous medicinal chemistry and agrochemical reports. Given its unique physicochemical properties and potential biological activities, DE nucleus is recognized as a fundamental element of medicinal and agrochemical agents aimed at different biological targets. Its drug-like derivatives have been extensively synthesized with interesting biological features including anticancer, anti-inflammatory, antiviral, antibacterial, antimalarial, herbicidal, fungicidal, insecticidal, and so on. In this review, we highlight the medicinal and agrochemical versatility of the DE motif according to the published information in the past decade and comprehensively give a summary of the target recognition, structure-activity relationship (SAR), and mechanism of action of its analogues. It is expected that this profile may provide valuable guidance for the discovery of new active ingredients both in drug and pesticide research.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hao Xiong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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14
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Jian Y, Hulpia F, Risseeuw MDP, Forbes HE, Munier-Lehmann H, Caljon G, Boshoff HIM, Van Calenbergh S. Synthesis and structure activity relationships of cyanopyridone based anti-tuberculosis agents. Eur J Med Chem 2020; 201:112450. [PMID: 32623208 DOI: 10.1016/j.ejmech.2020.112450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 11/15/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, relies on thymidylate kinase (MtbTMPK) for the synthesis of thymidine triphosphates and thus also DNA synthesis. Therefore, this enzyme constitutes a potential Achilles heel of the pathogen. Based on a previously reported MtbTMPK 6-aryl-substituted pyridone inhibitor and guided by two co-crystal structures of MtbTMPK with pyridone- and thymine-based inhibitors, we report the synthesis of a series of aryl-shifted cyanopyridone analogues. These compounds generally lacked significant MtbTMPK inhibitory potency, but some analogues did exhibit promising antitubercular activity. Analogue 11i demonstrated a 10-fold increased antitubercular activity (MIC H37Rv, 1.2 μM) compared to literature compound 5. Many analogues with whole-cell antimycobacterial activity were devoid of significant cytotoxicity.
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Affiliation(s)
- Yanlin Jian
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B9000, Gent, Belgium
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B9000, Gent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B9000, Gent, Belgium
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28 Rue du Dr. Roux, Cedex 15, 75724, Paris, France
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1(S7), B2610, Wilrijk, Belgium
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, United States
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Ottergemsesteenweg 460, B9000, Gent, Belgium.
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15
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1-(1-Arylethylpiperidin-4-yl)thymine Analogs as Antimycobacterial TMPK Inhibitors. Molecules 2020; 25:molecules25122805. [PMID: 32560578 PMCID: PMC7356956 DOI: 10.3390/molecules25122805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/09/2020] [Accepted: 06/14/2020] [Indexed: 11/17/2022] Open
Abstract
A series of Mycobacterium tuberculosis TMPK (MtbTMPK) inhibitors based on a reported compound 3 were synthesized and evaluated for their capacity to inhibit MtbTMPK catalytic activity and the growth of a virulent M. tuberculosis strain (H37Rv). Modifications of the scaffold of 3 failed to afford substantial improvements in MtbTMPK inhibitory activity and antimycobacterial activity. Optimization of the substitution pattern of the D ring of 3 resulted in compound 21j with improved MtbTMPK inhibitory potency (three-fold) and H37Rv growth inhibitory activity (two-fold). Moving the 3-chloro substituent of 21j to the para-position afforded isomer 21h, which, despite a 10-fold increase in IC50-value, displayed promising whole cell activity (minimum inhibitory concentration (MIC) = 12.5 μM).
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16
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Makarov V, Salina E, Reynolds RC, Kyaw Zin PP, Ekins S. Molecule Property Analyses of Active Compounds for Mycobacterium tuberculosis. J Med Chem 2020; 63:8917-8955. [PMID: 32259446 DOI: 10.1021/acs.jmedchem.9b02075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) continues to claim the lives of around 1.7 million people per year. Most concerning are the reports of multidrug drug resistance. Paradoxically, this global health pandemic is demanding new therapies when resources and interest are waning. However, continued tuberculosis drug discovery is critical to address the global health need and burgeoning multidrug resistance. Many diverse classes of antitubercular compounds have been identified with activity in vitro and in vivo. Our analyses of over 100 active leads are representative of thousands of active compounds generated over the past decade, suggests that they come from few chemical classes or natural product sources. We are therefore repeatedly identifying compounds that are similar to those that preceded them. Our molecule-centered cheminformatics analyses point to the need to dramatically increase the diversity of chemical libraries tested and get outside of the historic Mtb property space if we are to generate novel improved antitubercular leads.
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Affiliation(s)
- Vadim Makarov
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Elena Salina
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Robert C Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Phyo Phyo Kyaw Zin
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, North Carolina 27606, United States
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17
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Gul S, Khalil R, Zaheer Ul-Haq, Mubarak MS. Computational Overview of Mycobacterial Thymidine Monophosphate Kinase. Curr Pharm Des 2020; 26:1676-1681. [PMID: 32242781 DOI: 10.2174/1381612826666200403114152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/30/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) ranks among the diseases with the highest morbidity rate with significantly high prevalence in developing countries. Globally, tuberculosis poses the most substantial burden of mortality. Further, a partially treated tuberculosis patient is worse than untreated; they may lead to standing out as a critical obstacle to global tuberculosis control. The emergence of multi-drug resistant (MDR) and extremely drug-resistant (XDR) strains, and co-infection of HIV further worsen the situation. The present review article discusses validated targets of the bacterial enzyme thymidine monophosphate kinase (TMPK). TMPKMTB enzyme belongs to the nucleoside monophosphate kinases (NMPKs) family. It is involved in phosphorylation of TMP to TDP, and TDP is phosphorylated to TTP. This review highlights structure elucidation of TMP enzymes and their inhibitors study on TMP scaffold, and it also discusses different techniques; including molecular docking, virtual screening, 3DPharmacophore, QSAR for finding anti-tubercular agents.
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Affiliation(s)
- Sana Gul
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
| | - Ruqaiya Khalil
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
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18
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Weng WZ, Guo JS, Liu KX, Shao TQ, Song LQ, Zhu YP, Sun YY, Meng QG. Metal-free oxidative C(sp3)–H functionalization: a facile route to quinoline formaldehydes from methyl-azaheteroarenes. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A facile protocol for the synthesis of quinoline formaldehydes via direct oxidative C–H bonds functionalization of methyl-azaheteroarenes in the presence of I2–DMSO has been described. This method is metal-free and easy to operate. This reaction provided a convenient route for the preparation of a range of important quinoline formaldehydes.
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Affiliation(s)
- Wei-Zhao Weng
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Jiang-Shan Guo
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Kai-Xuan Liu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Tian-Qi Shao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Li-Qun Song
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Yan-Ping Zhu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Yuan-Yuan Sun
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
| | - Qing-Guo Meng
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Shandong, Yantai 264005, P.R. China
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19
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Venugopala KN, Tratrat C, Pillay M, Chandrashekharappa S, Al-Attraqchi OHA, Aldhubiab BE, Attimarad M, Alwassil OI, Nair AB, Sreeharsha N, Venugopala R, Morsy MA, Haroun M, Kumalo HM, Odhav B, Mlisana K. In silico Design and Synthesis of Tetrahydropyrimidinones and Tetrahydropyrimidinethiones as Potential Thymidylate Kinase Inhibitors Exerting Anti-TB Activity Against Mycobacterium tuberculosis. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:1027-1039. [PMID: 32214795 PMCID: PMC7082623 DOI: 10.2147/dddt.s228381] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/20/2020] [Indexed: 01/03/2023]
Abstract
Background and Purpose Tuberculosis has been reported to be the worldwide leading cause of death resulting from a sole infectious agent. The emergence of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis has made the battle against the infection more difficult since most currently available therapeutic options are ineffective against these resistant strains. Therefore, novel molecules need to be developed to effectively treat tuberculosis disease. Preliminary docking studies revealed that tetrahydropyrimidinone derivatives have favorable interactions with the thymidylate kinase receptor. In the present investigation, we report the synthesis and the mycobacterial activity of several pyrimidinones and pyrimidinethiones as potential thymidylate kinase inhibitors. Methods The title compounds (1a-d) and (2a-b) were synthesized by a one-pot three-component Biginelli reaction. They were subsequently characterized and used for whole-cell anti-TB screening against H37Rv and multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by the resazurin microplate assay (REMA) plate method. Molecular modeling was conducted using the Accelry's Discovery Studio 4.0 client program to explain the observed bioactivity of the compounds. The pharmacokinetic properties of the synthesized compounds were predicted and analyzed. Results Of the compounds tested for anti-TB activity, pyrimidinone 1a and pyrimidinethione 2a displayed moderate activity against susceptible MTB H37Rv strains at 16 and 32 µg/mL, respectively. Only compound 2a was observed to exert modest activity at 128 µg/mL against MTB strains with cross-resistance to rifampicin and isoniazid. The presence of the trifluoromethyl group was essential to retain the inhibitory activity of compounds 1a and 2a. Molecular modeling studies of these compounds against thymidylate kinase targets demonstrated a positive correlation between the bioactivity and structure of the compounds. The in-silico ADME (absorption, distribution, metabolism, and excretion) prediction indicated favorable pharmacokinetic and drug-like properties for most compounds. Conclusion Pyrimidinone 1a and pyrimidinethione 2a were identified as the leading compounds and can serve as a starting point to develop novel anti-TB therapeutic agents.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | | | | | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Osama I Alwassil
- Department of Pharmaceutical Sciences, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Rashmi Venugopala
- Department of Public Health Medicine, University of KwaZulu-Natal, Howard College Campus, Durban 4001, South Africa
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.,Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia 61511, Egypt
| | - Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Hezekiel M Kumalo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Medical School, Durban 4001, South Africa
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
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20
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Jian Y, Risseeuw MDP, Froeyen M, Song L, Cappoen D, Cos P, Munier-Lehmann H, van Calenbergh S. 1-(Piperidin-3-yl)thymine amides as inhibitors of M. tuberculosis thymidylate kinase. J Enzyme Inhib Med Chem 2019; 34:1730-1739. [PMID: 31822127 PMCID: PMC6920704 DOI: 10.1080/14756366.2019.1662790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A series of readily accessible 1-(piperidin-3-yl)thymine amides was designed, synthesised and evaluated as Mycobacterium tuberculosis TMPK (MtbTMPK) inhibitors. In line with the modelling results, most inhibitors showed reasonable MtbTMPK inhibitory activity. Compounds 4b and 4i were slightly more potent than the parent compound 3. Moreover, contrary to the latter, amide analogue 4g was active against the avirulent M. tuberculosis H37Ra strain (MIC50=35 µM). This finding opens avenues for future modifications.
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Affiliation(s)
- Yanlin Jian
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Mathy Froeyen
- Department of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Lijun Song
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Davie Cappoen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, Paris, France
| | - Serge van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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21
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Wang DW, Zhang RB, Ismail I, Xue ZY, Liang L, Yu SY, Wen X, Xi Z. Design, Herbicidal Activity, and QSAR Analysis of Cycloalka[ d]quinazoline-2,4-dione-Benzoxazinones as Protoporphyrinogen IX Oxidase Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9254-9264. [PMID: 31356740 DOI: 10.1021/acs.jafc.9b02996] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In continuation of our search for potent protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) inhibitors, we designed and synthesized a series of novel herbicidal cycloalka[d]quinazoline-2,4-dione-benzoxazinones. The bioassay results of these synthesized compounds indicated that most of the compounds exhibited very strong Nicotiana tabacum PPO (NtPPO) inhibition activity. More than half of the 37 synthesized compounds displayed over 80% control of all three tested broadleaf weeds at 37.5-150 g ai/ha by postemergent application, and a majority of them showed no phytotoxicity toward at least one kind of crop at 150 g ai/ha. Promisingly, 17i (Ki = 6.7 nM) was 6 and 4 times more potent than flumioxazin (Ki = 46 nM) and trifludimoxazin (Ki = 31 nM), respectively. Moreover, 17i displayed excellent, broad-spectrum herbicidal activity, even at levels as low as 37.5 g ai/ha, and it was determined to be safe for wheat at 150 g ai/ha in postemergent application, indicating the great potential for 17i development as a herbicide for weed control in wheat fields.
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Affiliation(s)
- Da-Wei Wang
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Rui-Bo Zhang
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Ismail Ismail
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Zhi-Yuan Xue
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Lu Liang
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Shu-Yi Yu
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , PR China
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22
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Ivanenkov YA, Yamidanov RS, Osterman IA, Sergiev PV, Aladinskiy VA, Aladinskaya AV, Terentiev VA, Veselov MS, Ayginin AA, Skvortsov DA, Komarova KS, Chemeris AV, Baimiev AK, Sofronova AA, Malyshev AS, Machulkin AE, Petrov RA, Bezrukov DS, Filkov GI, Puchinina MM, Zainullina LF, Maximova MA, Zileeva ZR, Vakhitova YV, Dontsova OA. Identification of N-Substituted Triazolo-azetidines as Novel Antibacterials using pDualrep2 HTS Platform. Comb Chem High Throughput Screen 2019; 22:346-354. [DOI: 10.2174/1386207322666190412165316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/17/2022]
Abstract
Aim and Objective:
Antibiotic resistance is a serious constraint to the development of new
effective antibacterials. Therefore, the discovery of the new antibacterials remains one of the main
challenges in modern medicinal chemistry. This study was undertaken to identify novel molecules with
antibacterial activity.
Materials and Methods:
Using our unique double-reporter system, in-house large-scale HTS campaign
was conducted for the identification of antibacterial potency of small-molecule compounds. The
construction allows us to visually assess the underlying mechanism of action. After the initial HTS and
rescreen procedure, luciferase assay, C14-test, determination of MIC value and PrestoBlue test were
carried out.
Results:
HTS rounds and rescreen campaign have revealed the antibacterial activity of a series of Nsubstituted
triazolo-azetidines and their isosteric derivatives that has not been reported previously. Primary
hit-molecule demonstrated a MIC value of 12.5 µg/mL against E. coli Δ tolC with signs of translation
blockage and no SOS-response. Translation inhibition (26%, luciferase assay) was achieved at high
concentrations up to 160 µg/mL, while no activity was found using C14-test. The compound did not
demonstrate cytotoxicity in the PrestoBlue assay against a panel of eukaryotic cells. Within a series of
direct structural analogues bearing the same or bioisosteric scaffold, compound 2 was found to have an
improved antibacterial potency (MIC=6.25 µg/mL) close to Erythromycin (MIC=2.5-5 µg/mL) against the
same strain. In contrast to the parent hit, this compound was more active and selective, and provided a
robust IP position.
Conclusion:
N-substituted triazolo-azetidine scaffold may be used as a versatile starting point for the
development of novel active and selective antibacterial compounds.
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Affiliation(s)
- Yan A. Ivanenkov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Renat S. Yamidanov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Ilya A. Osterman
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Petr V. Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | | | | | - Victor A. Terentiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Mark S. Veselov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Andrey A. Ayginin
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Dmitry A. Skvortsov
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Katerina S. Komarova
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Alexey V. Chemeris
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Alexey Kh. Baimiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Alina A. Sofronova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russian Federation
| | | | - Alexey E. Machulkin
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Rostislav A. Petrov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Dmitry S. Bezrukov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Gleb I. Filkov
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Maria M. Puchinina
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Liana F. Zainullina
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Marina A. Maximova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Zulfiya R. Zileeva
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Yulia V. Vakhitova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Olga A. Dontsova
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
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23
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Gao X, Han S, Zheng M, Liang A, Li J, Zou D, Wu Y, Wu Y. Transition-Metal-Free Oxidation of Benzylic C-H Bonds of Six-Membered N-Heteroaromatic Compounds. J Org Chem 2019; 84:4040-4049. [PMID: 30854850 DOI: 10.1021/acs.joc.9b00035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel oxidation of benzylic C-H bonds for the synthesis of diverse six-membered N-heteroaromatic aldehydes and ketones has been developed. The obvious advantages of this approach are the simple operation, mild reaction conditions, and without use of toxic reagent and transition metal. The present method should provide a useful access for the synthesis and modification of N-heterocycles.
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Affiliation(s)
- Xianying Gao
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China
| | - Shuaijun Han
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China
| | - Maolin Zheng
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China
| | - Apeng Liang
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China
| | - Jingya Li
- Tetranov Biopharm LLC and Collaborative Innovation Center of New Drug Research and Safety Evaluation , Zhengzhou 450052 , People's Republic of China
| | - Dapeng Zou
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China
| | - Yusheng Wu
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China.,Tetranov Biopharm LLC and Collaborative Innovation Center of New Drug Research and Safety Evaluation , Zhengzhou 450052 , People's Republic of China.,Tetranov International, Inc. , 100 Jersey Avenue, Suite A340 , New Brunswick , New Jersey 08901 , United States
| | - Yangjie Wu
- The College of Chemistry and Molecular Engineering, Henan Key Laboratory of Chemical Biology and Organic Chemistry , Zhengzhou University , Zhengzhou 450052 , People's Republic of China
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24
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Kandeel M, Kitade Y, Al-Taher A, Al-Nazawi M. The structural basis of unique substrate recognition by Plasmodium thymidylate kinase: Molecular dynamics simulation and inhibitory studies. PLoS One 2019; 14:e0212065. [PMID: 30730992 PMCID: PMC6366710 DOI: 10.1371/journal.pone.0212065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) showed structural and catalytic distinctions from the host enzyme rendering it a hopeful antiprotozoal drug target. Despite the comprehensive enzymologic, structural, inhibitory and chemical synthesis approaches targeting this enzyme, the elucidation of the exact mechanism underlying the recognition of the atypical purine substrates remains to be determined. In this study, molecular dynamics (MD) simulation of a broad range of substrates and inhibitors as well as the inhibitory properties of deoxyguanosine (dG) derivatives were used to assess the PfTMK substructure molecular rearrangements. The estimated changes during the favourable binding of high affinity substrate (TMP) include lower interaction with P-loop, free residue fluctuations of the lid domain and the average RMSD value. The RMSD of TMP complex was higher and more rapidly stabilized than the dGMP complex. The lid domain flexibility is severely affected by dGMP and β-thymidine derivatives, while being partially fluctuating with other thymidine derivatives. The TMK-purine (dGMP) complex was slowly and gradually stabilized with lower over all structure flexibility and residue fluctuations especially at the lid domain, which closes the active site during its catalytic state. Thymidine derivatives allow structure flexibility of the lid domain being highly fluctuating in α- and β-thymidine derivatives and TMP. dG derivatives remains less efficient than thymidine derivatives in inhibiting TMK. The variations in the structural dynamics of the P-loop and lid domain in response to TMP or dGMP might favour thymidine-based compounds. The provided MD simulation strategy can be used for predicating structural changes in PfTMK during lead optimization.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Hofuf, Alahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Kafrelsheikh, Egypt
- * E-mail: ,
| | - Yukio Kitade
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Yachigusa, Yakuza, Toyota, Japan
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu, Japan
| | - Abdulla Al-Taher
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Hofuf, Alahsa, Saudi Arabia
| | - Mohammed Al-Nazawi
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Hofuf, Alahsa, Saudi Arabia
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