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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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2
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Reddy DS, Sinha A, Kurjogi MM, Shanavaz H, Kumar A. Design, synthesis, molecular docking, and biological evaluation of coumarin-thymidine analogs as potent anti-TB agents. Arch Pharm (Weinheim) 2023; 356:e2200633. [PMID: 36634969 DOI: 10.1002/ardp.202200633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/14/2023]
Abstract
With the intent to discover new antituberculosis (TB) compounds, coumarin-thymidine analogs were synthesized using second-order nucleophilic substitution reactions of bromomethyl coumarin with thymidine. The newly synthesized coumarin-thymidine conjugates (1a-l) were characterized using IR, NMR, GC-MS, and CHN elemental analysis. The novel conjugates were found to exhibit potent anti-TB activity against the Mycobacterium tuberculosis H37 Rv strain, with minimum inhibitory concentrations (MIC) of the active compounds ranging between 0.012 and 0.482 µM. Compound 1k was established as the most active candidate with a MIC of 0.012 µM. The toxicity study on HEK cells confirmed the nontoxic nature of compounds 1e, 1h, 1i, 1j, and 1k. Also, the most active compounds (1k, 1j, and 1e) were stable in the pH range from 2.5 to 10, indicating compatibility with the biophysical environment. Based on the pKa studies, compounds 1k, 1j, and 1e are capable of crossing lipid-membrane barriers and acting on target cells. Molecular docking studies on the M. tuberculosis β-oxidation trifunctional enzyme (PDB ID: 7O4V) were conducted to investigate the mechanisms of anti-TB activity. All compounds showed excellent hydrogen binding interactions and exceptional docking scores against M. tuberculosis, which was in accordance with the results. Compounds 1a-l possessed excellent affinity to proteins, with binding energies ranging from -7.4 to -8.7 kcal/mol.
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Affiliation(s)
- Dinesh S Reddy
- Centre for Nano and Material Sciences, Jain (Deemed-to-be-University), Bangalore, Karnataka, India
| | - Anamika Sinha
- Centre for Nano and Material Sciences, Jain (Deemed-to-be-University), Bangalore, Karnataka, India
| | - Mahantesh M Kurjogi
- Multi-Disciplinary Research Unit, Karnataka Institute of Medical Sciences, Hubli, Karnataka, India
| | - H Shanavaz
- Department of Chemistry, Faculty of Engineering and Technology, Jain University, Bangalore, Karnataka, India
| | - Amit Kumar
- Centre for Nano and Material Sciences, Jain (Deemed-to-be-University), Bangalore, Karnataka, India
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3
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Alexandrova LA, Khandazhinskaya AL, Matyugina ES, Makarov DA, Kochetkov SN. Analogues of Pyrimidine Nucleosides as Mycobacteria Growth Inhibitors. Microorganisms 2022; 10:microorganisms10071299. [PMID: 35889017 PMCID: PMC9322969 DOI: 10.3390/microorganisms10071299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/25/2023] Open
Abstract
Tuberculosis (TB) is the oldest human infection disease. Mortality from TB significantly decreased in the 20th century, because of vaccination and the widespread use of antibiotics. However, about a third of the world’s population is currently infected with Mycobacterium tuberculosis (Mtb) and the death rate from TB is about 1.4–2 million people per year. In the second half of the 20th century, new extensively multidrug-resistant strains of Mtb were identified, which are steadily increasing among TB patients. Therefore, there is an urgent need to develop new anti-TB drugs, which remains one of the priorities of pharmacology and medicinal chemistry. The antimycobacterial activity of nucleoside derivatives and analogues was revealed not so long ago, and a lot of studies on their antibacterial properties have been published. Despite the fact that there are no clinically used drugs based on nucleoside analogues, some progress has been made in this area. This review summarizes current research in the field of the design and study of inhibitors of mycobacteria, primarily Mtb.
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Promising Antibacterial and Antifungal Agents Based on Thiolated Vitamin K3 Analogs: Synthesis, Bioevaluation, Molecular Docking. Pharmaceuticals (Basel) 2022; 15:ph15050586. [PMID: 35631412 PMCID: PMC9146127 DOI: 10.3390/ph15050586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 02/07/2023] Open
Abstract
In the present study, we designed and synthesized thiolated VK3 analogs (VK3a–g) along with an extensive antimicrobial study. After the evaluation of the antibacterial and antifungal activity against various bacterial and fungal strains, we presented an initial structure–activity relationship study on these VK3 analogs. In particular, four thiolated VK3 analogs exhibited superior biological potency against some Gram-positive bacterial strains, including Staphylococcus aureus (ATCC® 29213) and Enterococcus faecalis (ATCC® 29212). Next, all thiolated VK3 analogs were evaluated for their potential of cell growth inhibition on the NCI-60 cancer cell lines panel. This screening underlined that the thiolated VK3 analogs have no visible cytotoxicity on different cancer cell lines. The selected two thiolated VK3 analogs (VK3a and VK3b), having minimal hemolytic activity, which also have the lowest MIC values on S. aureus and E. faecalis, were further evaluated for their inhibition capacities on biofilm formation after evaluating their potential in vitro antimicrobial activity against each of the 20 clinically obtained resistant strains of Staphylococcus aureus. VK3b showed excellent antimicrobial activity against clinically resistant S. aureus isolates. Furthermore, the tested molecules showed nearly two log10 reduction in the viable cell count at six hours according to the time kill curve studies. Although these molecules decreased biofilm attachment about 50%, when sub-MIC concentrations were used these molecules increased the percentage of biofilm formation. The molecular docking of VK3a and VK3b in S. aureus thymidylate kinase was conducted in order to predict their molecular interactions. VK3a and VK3b exhibited excellent lead-likeness properties and pharmacokinetic profiles that qualify them for further optimization and development. In conclusion, since investigating efficient novel antimicrobial molecules is quite difficult, these studies are of high importance, especially in the present era of antimicrobial resistance.
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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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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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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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Saminathan M, Kanagarajan S, Chandrasekaran R, Sivasubramaniyan A, Raja R, Alagusundaram P. Synthesis, structural, DFT investigations and antibacterial activity assessment of pyrazoline‐thiocyanatoethanone derivatives as thymidylate kinase inhibitors. J CHIN CHEM SOC-TAIP 2019. [DOI: 10.1002/jccs.201900363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Murugavel Saminathan
- Department of PhysicsThanthai Periyar Government Institute of Technology Vellore India
| | | | | | | | - Ranganathan Raja
- Research Institute of Pharmaceutical Sciences, Seoul National University Seoul South Korea
| | - Ponnusamy Alagusundaram
- Department of Organic Chemistry, School of ChemistryMadurai Kamaraj University Madurai India
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9
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Song L, Risseeuw MDP, Froeyen M, Karalic I, Goeman J, Cappoen D, Van der Eycken J, Cos P, Munier-Lehmann H, Van Calenbergh S. Elaboration of a proprietary thymidylate kinase inhibitor motif towards anti-tuberculosis agents. Bioorg Med Chem 2016; 24:5172-5182. [PMID: 27614917 DOI: 10.1016/j.bmc.2016.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 02/02/2023]
Abstract
We report the design and synthesis of a series of non-nucleoside MtbTMPK inhibitors (1-14) based on the gram-positive bacterial TMPK inhibitor hit compound 1. A practical synthesis was developed to access these analogues. Several compounds show promising MtbTMPK inhibitory potency and allow the establishment of a structure-activity relationship, which is helpful for further optimization.
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Affiliation(s)
- Lijun Song
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Matheus Froeyen
- Medicinal Chemistry (Rega Institute), Department of Pharmaceutical and Pharmacological Sciences, KU LEUVEN, Minderbroedersstraat 10 blok x-box 1030, 3000 Leuven, Belgium
| | - Izet Karalic
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Jan Goeman
- Laboratory for Organic and Bioorganic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000 Ghent, Belgium
| | - Davie Cappoen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610 Antwerpen,. Belgium
| | - Johan Van der Eycken
- Laboratory for Organic and Bioorganic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000 Ghent, 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
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523, Paris, France
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium.
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Adamska A, Rumijowska-Galewicz A, Ruszczynska A, Studzińska M, Jabłońska A, Paradowska E, Bulska E, Munier-Lehmann H, Dziadek J, Leśnikowski ZJ, Olejniczak AB. Anti-mycobacterial activity of thymine derivatives bearing boron clusters. Eur J Med Chem 2016; 121:71-81. [DOI: 10.1016/j.ejmech.2016.05.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
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Abstract
Purine and pyrimidine nucleoside and nucleotide analogs have been extensively studied as anticancer and antiviral agents. In addition to this, they have recently shown great potential against Mycobacterium Tuberculosis, the causative agent of TB. TB ranks as the tenth most common cause of death in the world. The current treatment for TB infection is limited by side effects and cost of the drugs and most importantly by the development of resistance to the therapy. Therefore the development of novel drugs, capable of overcoming the drawbacks of the existing treatments, has become the focus of many research programs. In parallel to that, a tremendous effort has been made to elucidate the unique metabolism of this pathogen with the aim to identify new possible targets. This review presents the state of the art in nucleoside and nucleotide analogs in the treatment of TB. In particular, we report on the inhibitory activity of this class of compounds, both in enzymatic and whole-cell assays, providing a brief insight to which reported target these novel compounds are hitting.
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Doharey PK, Suthar MK, Verma A, Kumar V, Yadav S, Balaramnavar VM, Rathaur S, Saxena AK, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Brugia malayi thymidylate kinase. Acta Trop 2014; 133:83-92. [PMID: 24556140 DOI: 10.1016/j.actatropica.2014.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 02/03/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of deoxythymidine triphosphate, which is an essential component for DNA synthesis. The gene encoding thymidylate kinase of Brugia malayi was amplified by PCR and expressed in Escherichia coli. The native molecular weight of recombinant B. malayi thymidylate kinase (rBmTMK) was estimated to be ∼52kDa by gel filtration chromatography, suggesting a homodimeric structure. rBmTMK activity required divalent cation and Mg(2+) was found to be the most effective cation. The enzyme was sensitive to pH and temperature, it showed maximum activity at pH 7.4 and 37°C. The Km values for dTMP and ATP were 17 and 66μM, respectively. The turnover number kcat was found to be 38.09s(-1), a value indicating the higher catalytic efficiency of the filarial enzyme. The nucleoside analogues 5-bromo-2'-deoxyuridine (5-BrdU), 5-chloro-2'-deoxyuridine (5-CldU) and 3'-azido-3'-deoxythymidine (AZT) showed specific inhibitory effect on the enzyme activity and these effects were in good association with binding interactions and the scoring functions as compared to human TMK. Differences in kinetic properties and structural differences in the substrate binding site of BmTMK model with respect to human TMK can serve as basis for designing specific inhibitors against parasitic enzyme.
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13
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Kumar M, Makhal B, Gupta VK, Sharma A. In silico investigation of medicinal spectrum of imidazo-azines from the perspective of multitarget screening against malaria, tuberculosis and Chagas disease. J Mol Graph Model 2014; 50:1-9. [DOI: 10.1016/j.jmgm.2014.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 02/14/2014] [Accepted: 02/21/2014] [Indexed: 11/29/2022]
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14
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Tomioka H, Tatano Y, Yasumoto K, Shimizu T. Recent advances in antituberculous drug development and novel drug targets. Expert Rev Respir Med 2014; 2:455-71. [DOI: 10.1586/17476348.2.4.455] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Shmalenyuk ER, Kochetkov SN, Alexandrova LA. Novel inhibitors ofMycobacterium tuberculosisgrowth based on modified pyrimidine nucleosides and their analogues. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n09abeh004404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Keating TA, Newman JV, Olivier NB, Otterson LG, Andrews B, Boriack-Sjodin PA, Breen JN, Doig P, Dumas J, Gangl E, Green OM, Guler SY, Hentemann MF, Joseph-McCarthy D, Kawatkar S, Kutschke A, Loch JT, McKenzie AR, Pradeepan S, Prasad S, Martínez-Botella G. In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound. ACS Chem Biol 2012; 7:1866-72. [PMID: 22908966 DOI: 10.1021/cb300316n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is an urgent need for new antibacterials that pinpoint novel targets and thereby avoid existing resistance mechanisms. We have created novel synthetic antibacterials through structure-based drug design that specifically target bacterial thymidylate kinase (TMK), a nucleotide kinase essential in the DNA synthesis pathway. A high-resolution structure shows compound TK-666 binding partly in the thymidine monophosphate substrate site, but also forming new induced-fit interactions that give picomolar affinity. TK-666 has potent, broad-spectrum Gram-positive microbiological activity (including activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus), bactericidal action with rapid killing kinetics, excellent target selectivity over the human ortholog, and low resistance rates. We demonstrate in vivo efficacy against S. aureus in a murine infected-thigh model. This work presents the first validation of TMK as a compelling antibacterial target and provides a rationale for pursuing novel clinical candidates for treating Gram-positive infections through TMK.
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Affiliation(s)
- Thomas A. Keating
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Joseph V. Newman
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nelson B. Olivier
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Linda G. Otterson
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Beth Andrews
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - P. Ann Boriack-Sjodin
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - John N. Breen
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Peter Doig
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Jacques Dumas
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Eric Gangl
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Oluyinka M. Green
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Satenig Y. Guler
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Martin F. Hentemann
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Diane Joseph-McCarthy
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Sameer Kawatkar
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Amy Kutschke
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - James T. Loch
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Andrew R. McKenzie
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Selvi Pradeepan
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Swati Prasad
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Gabriel Martínez-Botella
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
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17
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Bueno RV, Toledo NR, Neves BJ, Braga RC, Andrade CH. Structural and chemical basis for enhanced affinity to a series of mycobacterial thymidine monophosphate kinase inhibitors: fragment-based QSAR and QM/MM docking studies. J Mol Model 2012; 19:179-92. [DOI: 10.1007/s00894-012-1527-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
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18
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Shakya N, Garg G, Agrawal B, Kumar R. Chemotherapeutic interventions against tuberculosis. Pharmaceuticals (Basel) 2012; 5:690-718. [PMID: 24281707 PMCID: PMC3763665 DOI: 10.3390/ph5070690] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/12/2012] [Accepted: 06/21/2012] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis is the second leading cause of infectious deaths globally. Many effective conventional antimycobacterial drugs have been available, however, emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) has overshadowed the effectiveness of the current first and second line drugs. Further, currently available agents are complicated by serious side effects, drug interactions and long-term administration. This has prompted urgent research efforts in the discovery and development of new anti-tuberculosis agent(s). Several families of compounds are currently being explored for the treatment of tuberculosis. This review article presents an account of the existing chemotherapeutics and highlights the therapeutic potential of emerging molecules that are at different stages of development for the management of tuberculosis disease.
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Affiliation(s)
- Neeraj Shakya
- Department of Laboratory Medicine and Pathology, 728-Heritage Medical Research Center, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada.
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19
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Choi JY, Plummer MS, Starr J, Desbonnet CR, Soutter H, Chang J, Miller JR, Dillman K, Miller AA, Roush WR. Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation. J Med Chem 2012; 55:852-70. [PMID: 22243413 DOI: 10.1021/jm201349f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of an essential component, thymidine triphosphate, in DNA replication. All reported TMK inhibitors are thymidine analogues, which might retard their development as potent therapeutics due to cell permeability and off-target activity against human TMK. A small molecule hit (1, IC(50) = 58 μM), which has reasonable inhibition potency against Pseudomonas aeruginosa TMK (PaTMK), was identified by the analysis of the binding mode of thymidine or TP(5)A in a PaTMK homology model. This hit (1) was cocrystallized with PaTMK, and several potent PaTMK inhibitors (leads, 46, 47, 48, and 56, IC(50) = 100-200 nM) were synthesized using computer-aided design approaches including virtual synthesis/screening, which was used to guide the design of inhibitors. The binding mode of the optimized leads in PaTMK overlaps with that of other bacterial TMKs but not with human TMK, which shares few common features with the bacterial enzymes. Therefore, the optimized TMK inhibitors described here should be useful for the development of antibacterial agents targeting TMK without undesired off-target effects. In addition, an inhibition mechanism associated with the LID loop, which mimics the process of phosphate transfer from ATP to dTMP, was proposed based on X-ray cocrystal structures, homology models, and structure-activity relationship results.
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Affiliation(s)
- Jun Yong Choi
- Department of Chemistry, Scripps Florida, Jupiter, Florida 33458, United States
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20
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Chitre TS, Kathiravan MK, Bothara KG, Bhandari SV, Jalnapurkar RR. Pharmacophore Optimization and Design of Competitive Inhibitors of Thymidine Monophosphate Kinase Through Molecular Modeling Studies. Chem Biol Drug Des 2011; 78:826-34. [DOI: 10.1111/j.1747-0285.2011.01200.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Labesse G, Benkali K, Salard-Arnaud I, Gilles AM, Munier-Lehmann H. Structural and functional characterization of the Mycobacterium tuberculosis uridine monophosphate kinase: insights into the allosteric regulation. Nucleic Acids Res 2010; 39:3458-72. [PMID: 21149268 PMCID: PMC3082897 DOI: 10.1093/nar/gkq1250] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nucleoside Monophosphate Kinases (NMPKs) family are key enzymes in nucleotide metabolism. Bacterial UMPKs depart from the main superfamily of NMPKs. Having no eukaryotic counterparts they represent attractive therapeutic targets. They are regulated by GTP and UTP, while showing different mechanisms in Gram(+), Gram(–) and archaeal bacteria. In this work, we have characterized the mycobacterial UMPK (UMPKmt) combining enzymatic and structural investigations with site-directed mutagenesis. UMPKmt exhibits cooperativity toward ATP and an allosteric regulation by GTP and UTP. The crystal structure of the complex of UMPKmt with GTP solved at 2.5 Å, was merely identical to the modelled apo-form, in agreement with SAXS experiments. Only a small stretch of residues was affected upon nucleotide binding, pointing out the role of macromolecular dynamics rather than major structural changes in the allosteric regulation of bacterial UMPKs. We further probe allosteric regulation by site-directed mutagenesis. In particular, a key residue involved in the allosteric regulation of this enzyme was identified.
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Affiliation(s)
- Gilles Labesse
- Atelier de Bio- et Chimie Informatique Structurale, CNRS, UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, F-34090 Montpellier, France
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22
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Design, synthesis and inhibitory activity against Mycobacterium tuberculosis thymidine monophosphate kinase of acyclic nucleoside analogues with a distal imidazoquinolinone. Eur J Med Chem 2010; 45:5910-8. [DOI: 10.1016/j.ejmech.2010.09.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/23/2010] [Accepted: 09/27/2010] [Indexed: 11/23/2022]
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23
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Frecer V, Seneci P, Miertus S. Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase. J Comput Aided Mol Des 2010; 25:31-49. [PMID: 21082329 DOI: 10.1007/s10822-010-9399-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 10/28/2010] [Indexed: 11/28/2022]
Abstract
Thymidine monophosphate kinase (TMPK(mt)) is an essential enzyme for nucleotide metabolism in Mycobacterium tuberculosis, and thus an attractive target for novel antituberculosis agents. In this work, we have explored the chemical space around the 2',3'-bicyclic thymidine nucleus by designing and in silico screening of a virtual focused library selected via structure based methods to identify more potent analogs endowed with favorable ADME-related properties. In all the library members we have exchanged the ribose ring of the template with a cyclopentane moiety that is less prone to enzymatic degradation. In addition, we have replaced the six-membered 2',3'-ring by a number of five-membered and six-membered heterocyclic rings containing alternative proton donor and acceptor groups, to exploit the interaction with the carboxylate groups of Asp9 and Asp163 as well as with several cationic residues present in the vicinity of the TMPK(mt) binding site. The three-dimensional structure of the TMPK(mt) complexed with 5-hydroxymethyl-dUMP, an analog of dTMP, was employed to develop a QSAR model, to parameterize a scoring function specific for the TMPK(mt) target and to select analogues which display the highest predicted binding to the target. As a result, we identified a small highly focused combinatorial subset of bicyclic thymidine analogues as virtual hits that are predicted to inhibit the mycobacterial TMPK in the submicromolar concentration range and to display favorable ADME-related properties.
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Affiliation(s)
- Vladimir Frecer
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, 34012, Trieste, Italy
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24
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Kumar M, Sharma S, Srinivasan A, Singh TP, Kaur P. Structure-based in-silico rational design of a selective peptide inhibitor for thymidine monophosphate kinase of mycobacterium tuberculosis. J Mol Model 2010; 17:1173-82. [PMID: 20697760 DOI: 10.1007/s00894-010-0821-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 07/22/2010] [Indexed: 11/28/2022]
Abstract
Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide synthesis. TMPK in M.tb has emerged as an attractive drug target since blocking it will affect both the pathways involved in the thymidine triphosphate synthesis. Moreover, the unique differences at the active site of TMPK enzyme in M.tb and humans can be exploited for the development of ideal drug candidates. Based on a detailed evaluation of known inhibitors and available three-dimensional structures of TMPK, several peptidic inhibitors were designed. In silico docking and selectivity analysis of these inhibitors with TMPK from M.tb and human was carried out to examine their differential binding at the active site. The designed tripeptide, Trp-Pro-Asp, was found to be most selective for M.tb. The ADMET analysis of this peptide indicated that it is likely to be a drug candidate. The tripeptide so designed is a suitable lead molecule for the development of novel TMPK inhibitors as anti-tubercular drugs.
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Affiliation(s)
- Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India
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25
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Synthesis and anti-HCV activity of 3′,4′-oxetane nucleosides. Bioorg Med Chem Lett 2010; 20:4539-43. [DOI: 10.1016/j.bmcl.2010.06.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 06/02/2010] [Accepted: 06/04/2010] [Indexed: 12/25/2022]
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26
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Lou Z, Zhang X. Protein targets for structure-based anti-Mycobacterium tuberculosis drug discovery. Protein Cell 2010; 1:435-42. [PMID: 21203958 DOI: 10.1007/s13238-010-0057-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 05/01/2010] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis, which belongs to the genus Mycobacterium, is the pathogenic agent for most tuberculosis (TB). As TB remains one of the most rampant infectious diseases, causing morbidity and death with emergence of multi-drug-resistant and extensively-drug-resistant forms, it is urgent to identify new drugs with novel targets to ensure future therapeutic success. In this regards, the structural genomics of M. tuberculosis provides important information to identify potential targets, perform biochemical assays, determine crystal structures in complex with potential inhibitor(s), reveal the key sites/residues for biological activity, and thus validate drug targets and discover novel drugs. In this review, we will discuss the recent progress on novel targets for structure-based anti-M. tuberculosis drug discovery.
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Affiliation(s)
- Zhiyong Lou
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
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27
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Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ. 3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents. J Comput Aided Mol Des 2010; 24:157-72. [PMID: 20217185 DOI: 10.1007/s10822-010-9323-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
Abstract
Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r(2) ranging from 0.83 to 0.92 and q(2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.
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Affiliation(s)
- Carolina Horta Andrade
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Bloco 13, Sao Paulo, SP, 05586-900, Brazil.
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28
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29
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Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ. Rational design and 3D-pharmacophore mapping of 5'-thiourea-substituted alpha-thymidine analogues as mycobacterial TMPK inhibitors. J Chem Inf Model 2009; 49:1070-8. [PMID: 19296716 DOI: 10.1021/ci8004622] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5'-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5'-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.
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Affiliation(s)
- Carolina H Andrade
- Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes, 580, University of Sao Paulo, Sao Paulo, 05508-900, Brazil.
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30
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Familiar O, Munier‐Lehmann H, Negri A, Gago F, Douguet D, Rigouts L, Hernández A, Camarasa M, Pérez‐Pérez M. Exploring Acyclic Nucleoside Analogues as Inhibitors ofMycobacterium tuberculosisThymidylate Kinase. ChemMedChem 2008; 3:1083-93. [DOI: 10.1002/cmdc.200800060] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Gasse C, Douguet D, Huteau V, Marchal G, Munier-Lehmann H, Pochet S. Substituted benzyl-pyrimidines targeting thymidine monophosphate kinase of Mycobacterium tuberculosis: Synthesis and in vitro anti-mycobacterial activity. Bioorg Med Chem 2008; 16:6075-85. [DOI: 10.1016/j.bmc.2008.04.045] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 04/11/2008] [Accepted: 04/18/2008] [Indexed: 10/22/2022]
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32
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Tomioka H. Development of new antituberculous agents based on new drug targets and structure–activity relationship. Expert Opin Drug Discov 2007; 3:21-49. [DOI: 10.1517/17460441.3.1.21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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33
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Van Daele I, Munier-Lehmann H, Froeyen M, Balzarini J, Van Calenbergh S. Rational Design of 5‘-Thiourea-Substituted α-Thymidine Analogues as Thymidine Monophosphate Kinase Inhibitors Capable of Inhibiting Mycobacterial Growth. J Med Chem 2007; 50:5281-92. [PMID: 17910427 DOI: 10.1021/jm0706158] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, thymidine monophosphate kinase (TMPK) emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. The elucidation of the X-ray structure of TMPK of M. tuberculosis (TMPKmt), as well as the structure of an earlier serendipitously discovered dimeric thymidine inhibitor, laid the foundation for the design of potent and selective TMPKmt inhibitors reported here. Several hits identified within a series of 3'-C-branched thiourea-substituted beta-thymidine derivatives inspired us to construct a set of 5'-thiourea-substituted alpha-thymidine derivatives characterized by a similar relative orientation of the thymine and arylthiourea moieties. alpha-Thymidine derivative 15, featuring a (3-trifluoromethyl-4-chlorophenyl)thiourea moiety, has a Ki of 0.6 microM and a selectivity index of 600 versus human TMPK. Moreover, it represents the first TMPK inhibitor showing good inhibitory activity on growing M. bovis (MIC99 = 20 microg/mL) and M. tuberculosis (MIC50 = 6.25 microg/mL) strains.
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Affiliation(s)
- Ineke Van Daele
- Laboratory for Medicinal Chemistry (FFW), University of Gent, Harelbekestraat 72, 9000 Ghent, Belgium
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34
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Sun J, Wu J, Yang H. Synthesis, Structure, and Conformation of 2′,3′-Fused Oxathiane and Thiomorpholine Uridines. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Janin YL. Antituberculosis drugs: ten years of research. Bioorg Med Chem 2007; 15:2479-513. [PMID: 17291770 DOI: 10.1016/j.bmc.2007.01.030] [Citation(s) in RCA: 360] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 12/26/2006] [Accepted: 01/17/2007] [Indexed: 02/03/2023]
Abstract
Tuberculosis is today amongst the worldwide health threats. As resistant strains of Mycobacterium tuberculosis have slowly emerged, treatment failure is too often a fact, especially in countries lacking the necessary health care organisation to provide the long and costly treatment adapted to patients. Because of lack of treatment or lack of adapted treatment, at least two million people will die of tuberculosis this year. Due to this concern, this infectious disease was the focus of renewed scientific interest in the last decade. Regimens were optimized and much was learnt on the mechanisms of action of the antituberculosis drugs used. Moreover, the quest for original drugs overcoming some of the problems of current regimens also became the focus of research programmes and many new series of M. tuberculosis growth inhibitors were reported. This review presents the drugs currently used in antituberculosis treatments and the most advanced compounds undergoing clinical trials. We then provide a description of their mechanism of action along with other series of inhibitors known to act on related biochemical targets. This is followed by other inhibitors of M. tuberculosis growth, including recently reported compounds devoid of a reported mechanism of action.
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Affiliation(s)
- Yves L Janin
- URA 2128 CNRS-Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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36
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Van Daele I, Munier-Lehmann H, Hendrickx PMS, Marchal G, Chavarot P, Froeyen M, Qing L, Martins JC, Van Calenbergh S. Synthesis and biological evaluation of bicyclic nucleosides as inhibitors of M. tuberculosis thymidylate kinase. ChemMedChem 2007; 1:1081-90. [PMID: 16921580 DOI: 10.1002/cmdc.200600028] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herein we describe the synthesis and conformational analysis of a series of bicyclic thymidine derivatives and their evaluation as inhibitors of thymidine monophosphate kinase from Mycobacterium tuberculosis (TMPKmt), based on previously discovered bicyclic sugar nucleosides. With a K(i) value of 2.3 microm, 1-[3-aminomethyl-3,5-dideoxy-2-O,6-N-(thiocarbonyl)-beta-D-ribofuranosyl]thymine emerged as the most potent TMPK inhibitor of this series. Moreover, this promising compound displays inhibitory potency against Mycobacteria cultures with an IC(99) value of 100 microg mL(-1), thus promoting TMPKmt for the first time as a validated target for further inhibitory design. Attempts to rationalise the observed structure-activity relationship (SAR) involving molecular modelling and conformational analysis are described.
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Affiliation(s)
- Ineke Van Daele
- Laboratory for Medicinal Chemistry (FFW), Gent University Harelbekestraat 72, Gent, Belgium
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37
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Barker JJ. Antibacterial drug discovery and structure-based design. Drug Discov Today 2006; 11:391-404. [PMID: 16635801 DOI: 10.1016/j.drudis.2006.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
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Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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38
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Hible G, Christova P, Renault L, Seclaman E, Thompson A, Girard E, Munier-Lehmann H, Cherfils J. Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase. Proteins 2006; 62:489-500. [PMID: 16288457 DOI: 10.1002/prot.20662] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Bacterial nucleoside monophosphate (NMP) kinases, which convert NMPs to nucleoside diphosphates (NDP), are investigated as potential antibacterial targets against pathogenic bacteria. Herein, we report the biochemical and structural characterization of GMP kinase from Mycobacterium tuberculosis (GMPKMt). GMPKMt is a monomer with an unusual specificity for ATP as a phosphate donor, a lower catalytic efficiency compared with eukaryotic GMPKs, and it carries two redox-sensitive cysteines in the central CORE domain. These properties were analyzed in the light of the high-resolution crystal structures of unbound, GMP-bound, and GDP-bound GMPKMt. The latter structure was obtained in both an oxidized form, in which the cysteines form a disulfide bridge, and a reduced form which is expected to correspond to the physiological enzyme. GMPKMt has a modular domain structure as most NMP kinases. However, it departs from eukaryotic GMPKs by the unusual conformation of its CORE domain, and by its partially open LID and GMP-binding domains which are the same in the apo-, GMP-bound, and GDP-bound forms. GMPKMt also features a unique GMP binding site which is less close-packed than that of mammalian GMPKs, and in which the replacement of a critical tyrosine by a serine removes a catalytic interaction. In contrast, the specificity of GMPKMt for ATP may be a general feature of GMPKs because of an invariant structural motif that recognizes the adenine base. Altogether, differences in domain dynamics and GMP binding between GMPKMt and mammalian GMPKs should reveal clues for the design of GMPKMt-specific inhibitors.
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Affiliation(s)
- Guillaume Hible
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
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39
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40
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Seifert MHJ. ProPose: Steered Virtual Screening by Simultaneous Protein−Ligand Docking and Ligand−Ligand Alignment. J Chem Inf Model 2005; 45:449-60. [PMID: 15807511 DOI: 10.1021/ci0496393] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 'model-free' screening engine ProPose implements a general method for performing simultaneous protein-ligand docking, ligand-ligand alignment, pharmacophore queries-and combinations thereof-in order to incorporate a priori information into screening protocols. In this manuscript we describe a case study on herpes simplex virus thymidine kinase, an important antiviral drug target, where we evaluate different approaches for handling a specific type of a priori information, i.e., multiple target structures. We demonstrate that a simultaneous alignment on two target structures--in conjunction with logic operations on interactions and docking constraints derived from protein structure--is an effective means of (i) improving the enrichment of chemical substructures that are compatible with the a priori known ligands, (ii) ensuring the steric fit into the target protein, and (iii) handling target flexibility. The combination of ligand- and receptor-based methods steers the virtual screening by ranking molecules according to the similarity of their interaction pattern with known ligands, thereby--to some extent--outweighing the deficiencies of simple scoring functions often used in initial virtual screening.
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