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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:ijms231810669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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Acebrón-García-de-Eulate M, Mayol-Llinàs J, Holland MTO, Kim SY, Brown KP, Marchetti C, Hess J, Di Pietro O, Mendes V, Abell C, Floto RA, Coyne AG, Blundell TL. Discovery of Novel Inhibitors of Uridine Diphosphate- N-Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa, an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients. J Med Chem 2022; 65:2149-2173. [PMID: 35080396 PMCID: PMC7614804 DOI: 10.1021/acs.jmedchem.1c01684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is of major concern for cystic fibrosis patients where this infection can be fatal. With the emergence of drug-resistant strains, there is an urgent need to develop novel antibiotics against P. aeruginosa. MurB is a promising target for novel antibiotic development as it is involved in the cell wall biosynthesis. MurB has been shown to be essential in P. aeruginosa, and importantly, no MurB homologue exists in eukaryotic cells. A fragment-based drug discovery approach was used to target Pa MurB. This led to the identification of a number of fragments, which were shown to bind to MurB. One fragment, a phenylpyrazole scaffold, was shown by ITC to bind with an affinity of Kd = 2.88 mM (LE 0.23). Using a structure guided approach, different substitutions were synthesized and the initial fragment was optimized to obtain a small molecule with Kd = 3.57 μM (LE 0.35).
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Affiliation(s)
| | - Joan Mayol-Llinàs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Matthew T O Holland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Chiara Marchetti
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeannine Hess
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Ornella Di Pietro
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
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Walter I, Adam S, Gentilini MV, Kany AM, Brengel C, Thomann A, Sparwasser T, Köhnke J, Hartmann RW. Structure-Activity Relationship and Mode-Of-Action Studies Highlight 1-(4-Biphenylylmethyl)-1H-imidazole-Derived Small Molecules as Potent CYP121 Inhibitors. ChemMedChem 2021; 16:2786-2801. [PMID: 34010508 PMCID: PMC8519103 DOI: 10.1002/cmdc.202100283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/29/2022]
Abstract
CYP121 of Mycobacterium tuberculosis (Mtb) is an essential target for the development of novel potent drugs against tuberculosis (TB). Besides known antifungal azoles, further compounds of the azole class were recently identified as CYP121 inhibitors with antimycobacterial activity. Herein, we report the screening of a similarity-oriented library based on the former hit compound, the evaluation of affinity toward CYP121, and activity against M. bovis BCG. The results enabled a comprehensive SAR study, which was extended through the synthesis of promising compounds and led to the identification of favorable features for affinity and/or activity and hit compounds with 2.7-fold improved potency. Mode of action studies show that the hit compounds inhibit substrate conversion and highlighted CYP121 as the main antimycobacterial target of our compounds. Exemplified complex crystal structures of CYP121 with three inhibitors reveal a common binding site. Engaging in both hydrophobic interactions as well as hydrogen bonding to the sixth iron ligand, our compounds block a solvent channel leading to the active site heme. Additionally, we report the first CYP inhibitors that are able to reduce the intracellular replication of M. bovis BCG in macrophages, emphasizing their potential as future drug candidates against TB.
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Affiliation(s)
- Isabell Walter
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Sebastian Adam
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Maria Virginia Gentilini
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Andreas M. Kany
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Christian Brengel
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Andreas Thomann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Tim Sparwasser
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Jesko Köhnke
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Rolf W. Hartmann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2.366123SaarbrückenGermany
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Roles for Structural Biology in the Discovery of Drugs and Agrochemicals Targeting Sterol 14α-Demethylases. J Fungi (Basel) 2021; 7:jof7020067. [PMID: 33498194 PMCID: PMC7908997 DOI: 10.3390/jof7020067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/08/2021] [Accepted: 01/17/2021] [Indexed: 02/06/2023] Open
Abstract
Antifungal drugs and antifungal agrochemicals have significant limitations. These include several unintended consequences of their use including the growing importance of intrinsic and acquired resistance. These problems underpin an increasingly urgent need to improve the existing classes of antifungals and to discover novel antifungals. Structural insights into drug targets and their complexes with both substrates and inhibitory ligands increase opportunity for the discovery of more effective antifungals. Implementation of this promise, which requires multiple skill sets, is beginning to yield candidates from discovery programs that could more quickly find their place in the clinic. This review will describe how structural biology is providing information for the improvement and discovery of inhibitors targeting the essential fungal enzyme sterol 14α-demethylase.
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Ortega Ugalde S, Wallraven K, Speer A, Bitter W, Grossmann TN, Commandeur JNM. Acetylene containing cyclo(L-Tyr-L-Tyr)-analogs as mechanism-based inhibitors of CYP121A1 from Mycobacterium tuberculosis. Biochem Pharmacol 2020; 177:113938. [PMID: 32224137 DOI: 10.1016/j.bcp.2020.113938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/24/2020] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is a globally significant infective disease that is caused by a single infectious agent, Mycobacterium tuberculosis (Mtb). Because of the rise in the number of multidrug-resistant (MDR) TB strains, identification of alternative drug targets for the development of drugs with different mechanism of actions is desired. CYP121A1, one of the twenty cytochrome P450 enzymes encoded in the Mtb genome, was previously shown to be essential for bacterial growth. This enzyme catalyzes the intramolecular C-C crosslinking reaction of the cyclopeptide cyclo(L-tyr-L-tyr) (cYY) yielding the metabolite mycocyclosin. In the present study, acetylene-substituted cYY-analogs were synthesized and evaluated as potential mechanism-based inhibitors of CYP121A1. The acetylene-substituted cYY-analogs were capable of binding to CYP121A1 with affinities comparable with cYY, and exhibited a Type I binding mode, indicative of a substrate-like binding, mandatory for metabolism. Only the cYY-analogs which contain an acetylene-substitution at one (2a) or both (3) para-positions of cYY showed mechanism-based inhibition of CYP121A1 activity. The values of KI and kinact were 236 µM and 0.045 min-1, respectively, for compound 2a, and 145 µM and 0.015 min-1, repectively, for compound 3 The inactivation could neither be reversed by dialysis nor be prevented by including glutathione. LC-MS analysis demonstrated that the inactivation results from covalent binding to the apoprotein, whereas the heme was unmodified. Interestingly, the mass increment of the CYP121A1 apoprotein was significantly smaller than was expected from the ketene formed by oxidation of the acetylene-group, indicative for a secondary cleavage reaction in the active site of CYP121A1. Although the two acetylene-containing cYY-analogs showed significant mechanism-based inhibition, growth inhibition of the Mtb strains was only observed at millimolar concentrations. This low efficacy may be due to insufficient irreversible inactivation of CYP121A1 and/or insufficient cellular uptake. Although the identified mechanism-based inhibitors have no perspective for Mtb-treatment, this study is the first proof-of-principle that mechanism-based inhibition of CYP121A1 is feasible and may provide the basis for new strategies in the design and development of compounds against this promising therapeutic target.
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Affiliation(s)
- Sandra Ortega Ugalde
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Kerstin Wallraven
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
| | - Jan N M Commandeur
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
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6
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Abstract
Abstract
Natural product (NP)-derived drugs can be extracts, biological macromolecules, or purified small molecule substances. Small molecule drugs can be originally purified from NPs, can represent semisynthetic molecules, natural fragments containing small molecules, or are fully synthetic molecules that mimic natural compounds. New semisynthetic NP-like drugs are entering the pharmaceutical market almost every year and reveal growing interests in the application of fragment-based approaches for NPs. Thus, several NP databases were constructed to be implemented in the fragment-based drug design (FBDD) workflows. FBDD has been established previously as an approach for hit identification and lead generation. Several biophysical and computational methods are used for fragment screening to identify potential hits. Once the fragments within the binding pocket of the protein are identified, they can be grown, linked, or merged to design more active compounds. This work discusses applications of NPs and NP scaffolds to FBDD. Moreover, it briefly reviews NP databases containing fragments and reports on case studies where the approach has been successfully applied for the design of antimalarial and anticancer drug candidates.
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7
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Ortega Ugalde S, Boot M, Commandeur JNM, Jennings P, Bitter W, Vos JC. Function, essentiality, and expression of cytochrome P450 enzymes and their cognate redox partners in Mycobacterium tuberculosis: are they drug targets? Appl Microbiol Biotechnol 2019; 103:3597-3614. [PMID: 30810776 PMCID: PMC6469627 DOI: 10.1007/s00253-019-09697-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 11/26/2022]
Abstract
This review covers the current knowledge of the cytochrome P450 enzymes (CYPs) of the human pathogen Mycobacterium tuberculosis (Mtb) and their endogenous redox partners, focusing on their biological function, expression, regulation, involvement in antibiotic resistance, and suitability for exploitation as antitubercular targets. The Mtb genome encodes twenty CYPs and nine associated redox partners required for CYP catalytic activity. Transposon insertion mutagenesis studies have established the (conditional) essentiality of several of these enzymes for in vitro growth and host infection. Biochemical characterization of a handful of Mtb CYPs has revealed that they have specific physiological functions in bacterial virulence and persistence in the host. Analysis of the transcriptional response of Mtb CYPs and redox partners to external insults and to first-line antibiotics used to treat tuberculosis showed a diverse expression landscape, suggesting for some enzymes a potential role in drug resistance. Combining the knowledge about the physiological roles and expression profiles indicates that, at least five Mtb CYPs, CYP121A1, CYP125A1, CYP139A1, CYP142A1, and CYP143A1, as well as two ferredoxins, FdxA and FdxC, can be considered promising novel therapeutic targets.
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Affiliation(s)
- Sandra Ortega Ugalde
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Maikel Boot
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jan N M Commandeur
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Paul Jennings
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section of Molecular Microbiology, AIMMS, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - J Chris Vos
- Division of Molecular Toxicology, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), Faculty of Sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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8
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Sommer K, Flachsenberg F, Rarey M. NAOMInext – Synthetically feasible fragment growing in a structure-based design context. Eur J Med Chem 2019; 163:747-762. [DOI: 10.1016/j.ejmech.2018.11.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022]
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9
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Vekariya MK, Vekariya RH, Patel KD, Raval NP, Shah PU, Rajani DP, Shah NK. Pyrimidine-Pyrazole Hybrids as Morpholinopyrimidine-Based Pyrazole Carboxamides: Synthesis, Characterisation, Docking, ADMET Study and Biological Evaluation. ChemistrySelect 2018. [DOI: 10.1002/slct.201801011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mayur K. Vekariya
- Department of Chemistry; Gujarat University, Ahmedabad; Gujarat 380009 India
| | - Rajesh H. Vekariya
- BlueORB Solution LLC; 1100 Corporate Square Drive Suite 123, Creve Coeur, Saint Louis MO 63132 USA
| | - Kinjal D. Patel
- Department of Chemistry; Gujarat University, Ahmedabad; Gujarat 380009 India
| | - Nirav P. Raval
- Department of Environmental Science; Gujarat University, Ahmedabad; Gujarat 380009 India
| | - Prapti U. Shah
- Department of Environmental Science; Gujarat University, Ahmedabad; Gujarat 380009 India
| | | | - Nisha K. Shah
- Department of Chemistry; Gujarat University, Ahmedabad; Gujarat 380009 India
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Potential drug targets in the Mycobacterium tuberculosis cytochrome P450 system. J Inorg Biochem 2018; 180:235-245. [PMID: 29352597 DOI: 10.1016/j.jinorgbio.2018.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 01/30/2023]
Abstract
The Mycobacterium tuberculosis genome encodes twenty cytochrome P450 enzymes, most or all of which appear to have specific physiological functions rather than being devoted to the removal of xenobiotics. However, in many cases their specific functions remain obscure. Considerable spectroscopic, biophysical, crystallographic, and catalytic information is available on nine of these cytochrome P450 enzymes, although gaps exist in our knowledge of even these enzymes. The available evidence indicates that at least three of the better-characterized enzymes are promising targets for antituberculosis drug discovery. This review summarizes the information on the nine relatively well-characterized cytochrome P450 enzymes, with a particular emphasis on CYP121, CYP125, and CYP142 from Mycobacterium tuberculosis and Mycobacterium smegmatis.
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Thomas SE, Mendes V, Kim SY, Malhotra S, Ochoa-Montaño B, Blaszczyk M, Blundell TL. Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew. J Mol Biol 2017; 429:2677-2693. [PMID: 28648615 DOI: 10.1016/j.jmb.2017.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.
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Affiliation(s)
- Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Bernardo Ochoa-Montaño
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK.
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Dornevil K, Davis I, Fielding AJ, Terrell JR, Ma L, Liu A. Cross-linking of dicyclotyrosine by the cytochrome P450 enzyme CYP121 from Mycobacterium tuberculosis proceeds through a catalytic shunt pathway. J Biol Chem 2017; 292:13645-13657. [PMID: 28667013 DOI: 10.1074/jbc.m117.794099] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
CYP121, the cytochrome P450 enzyme in Mycobacterium tuberculosis that catalyzes a single intramolecular C-C cross-linking reaction in the biosynthesis of mycocyclosin, is crucial for the viability of this pathogen. This C-C coupling reaction represents an expansion of the activities carried out by P450 enzymes distinct from oxygen insertion. Although the traditional mechanism for P450 enzymes has been well studied, it is unclear whether CYP121 follows the general P450 mechanism or uses a different catalytic strategy for generating an iron-bound oxidant. To gain mechanistic insight into the CYP121-catalyzed reaction, we tested the peroxide shunt pathway by using rapid kinetic techniques to monitor the enzyme activity with its substrate dicyclotyrosine (cYY) and observed the formation of the cross-linked product mycocyclosin by LC-MS. In stopped-flow experiments, we observed that cYY binding to CYP121 proceeds in a two-step process, and EPR spectroscopy indicates that the binding induces active site reorganization and uniformity. Using rapid freeze-quenching EPR, we observed the formation of a high-spin intermediate upon the addition of peracetic acid to the enzyme-substrate complex. This intermediate exhibits a high-spin (S = 5/2) signal with g values of 2.00, 5.77, and 6.87. Likewise, iodosylbenzene could also produce mycocyclosin, implicating compound I as the initial oxidizing species. Moreover, we also demonstrated that CYP121 performs a standard peroxidase type of reaction by observing substrate-based radicals. On the basis of these results, we propose plausible free radical-based mechanisms for the C-C bond coupling reaction.
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Affiliation(s)
- Kednerlin Dornevil
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Ian Davis
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Andrew J Fielding
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - James R Terrell
- the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Li Ma
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - Aimin Liu
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
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13
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Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1. Biochemistry 2017; 56:1559-1572. [PMID: 28169518 DOI: 10.1021/acs.biochem.6b00954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Similarity between the ligand binding profiles of enzymes may aid functional characterization and be of greater relevance to inhibitor development than sequence similarity or structural homology. Fragment screening is an efficient approach for characterization of the ligand binding profile of an enzyme and has been applied here to study the family of cytochrome P450 enzymes (P450s) expressed by Mycobacterium tuberculosis (Mtb). The Mtb P450s have important roles in bacterial virulence, survival, and pathogenicity. Comparing the fragment profiles of seven of these enzymes revealed that P450s which share a similar biological function have significantly similar fragment profiles, whereas functionally unrelated or orphan P450s exhibit distinct ligand binding properties, despite overall high structural homology. Chemical structures that exhibit promiscuous binding between enzymes have been identified, as have selective fragments that could provide leads for inhibitor development. The similarity between the fragment binding profiles of the orphan enzyme CYP144A1 and CYP121A1, a characterized enzyme that is important for Mtb viability, provides a case study illustrating the subsequent identification of novel CYP144A1 ligands. The different binding modes of these compounds to CYP144A1 provide insight into structural and dynamic aspects of the enzyme, possible biological function, and provide the opportunity to develop inhibitors. Expanding this fragment profiling approach to include a greater number of functionally characterized and orphan proteins may provide a valuable resource for understanding enzyme-ligand interactions.
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Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jude Chenge
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Azedine Zoufir
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andreas Bender
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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15
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Chenge JT, Duyet LV, Swami S, McLean KJ, Kavanagh ME, Coyne AG, Rigby SEJ, Cheesman MR, Girvan HM, Levy CW, Rupp B, von Kries JP, Abell C, Leys D, Munro AW. Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1. J Biol Chem 2016; 292:1310-1329. [PMID: 27932461 PMCID: PMC5270475 DOI: 10.1074/jbc.m116.748822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/02/2016] [Indexed: 12/12/2022] Open
Abstract
The Mycobacterium tuberculosis H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many M. tuberculosis P450s remain uncharacterized, suggesting that their further analysis may provide new insights into M. tuberculosis metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands. A survey of azole antifungal drugs showed that CYP126A1 is inhibited strongly by azoles containing an imidazole ring but not by those tested containing a triazole ring. To further explore the molecular preferences of CYP126A1 and search for probes of enzyme function, we conducted a high throughput screen. Compounds containing three or more ring structures dominated the screening hits, including nitroaromatic compounds that induce substrate-like shifts in the heme spectrum of CYP126A1. Spectroelectrochemical measurements revealed a 155-mV increase in heme iron potential when bound to one of the newly identified nitroaromatic drugs. CYP126A1 dimers were observed in crystal structures of ligand-free CYP126A1 and for CYP126A1 bound to compounds discovered in the screen. However, ketoconazole binds in an orientation that disrupts the BC-loop regions at the P450 dimer interface and results in a CYP126A1 monomeric crystal form. Structural data also reveal that nitroaromatic ligands "moonlight" as substrates by displacing the CYP126A1 distal water but inhibit enzyme activity. The relatively polar active site of CYP126A1 distinguishes it from its most closely related sterol-binding P450s in M. tuberculosis, suggesting that further investigations will reveal its diverse substrate selectivity.
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Affiliation(s)
- Jude T Chenge
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Le Van Duyet
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Shalini Swami
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kirsty J McLean
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Madeline E Kavanagh
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Anthony G Coyne
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Myles R Cheesman
- the School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom, and
| | - Hazel M Girvan
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin W Levy
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bernd Rupp
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jens P von Kries
- the Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Chris Abell
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew W Munro
- From the Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom,
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16
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Abstract
Tuberculosis is an infectious disease associated with significant mortality and morbidity worldwide, particularly in developing countries. The rise of antibiotic resistance in Mycobacterium tuberculosis (Mtb) urgently demands the development of new drug leads to tackle resistant strains. Fragment-based methods have recently emerged at the forefront of pharmaceutical development as a means to generate more effective lead structures, via the identification of fragment molecules that form weak but high quality interactions with the target biomolecule and subsequent fragment optimization. This review highlights a number of novel inhibitors of Mtb targets that have been developed through fragment-based approaches in recent years.
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17
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Mendes V, Blundell TL. Targeting tuberculosis using structure-guided fragment-based drug design. Drug Discov Today 2016; 22:546-554. [PMID: 27742535 DOI: 10.1016/j.drudis.2016.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/20/2023]
Abstract
Fragment-based drug discovery is now widely used in academia and industry to obtain small molecule inhibitors for a given target and is established for many fields of research including antimicrobials and oncology. Many molecules derived from fragment-based approaches are already in clinical trials and two - vemurafenib and venetoclax - are on the market, but the approach has been used sparsely in the tuberculosis field. Here, we describe the progress of our group and others, and examine the most recent successes and challenges in developing compounds with antimycobacterial activity.
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Affiliation(s)
- Vitor Mendes
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK.
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18
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Snow Setzer M, Sharifi-Rad J, Setzer WN. The Search for Herbal Antibiotics: An In-Silico Investigation of Antibacterial Phytochemicals. Antibiotics (Basel) 2016; 5:E30. [PMID: 27626453 PMCID: PMC5039526 DOI: 10.3390/antibiotics5030030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/14/2016] [Accepted: 08/26/2016] [Indexed: 01/12/2023] Open
Abstract
Recently, the emergence and spread of pathogenic bacterial resistance to many antibiotics (multidrug-resistant strains) have been increasing throughout the world. This phenomenon is of great concern and there is a need to find alternative chemotherapeutic agents to combat these antibiotic-resistant microorganisms. Higher plants may serve as a resource for new antimicrobials to replace or augment current therapeutic options. In this work, we have carried out a molecular docking study of a total of 561 antibacterial phytochemicals listed in the Dictionary of Natural Products, including 77 alkaloids (17 indole alkaloids, 27 isoquinoline alkaloids, 4 steroidal alkaloids, and 28 miscellaneous alkaloids), 99 terpenoids (5 monoterpenoids, 31 sesquiterpenoids, 52 diterpenoids, and 11 triterpenoids), 309 polyphenolics (87 flavonoids, 25 chalcones, 41 isoflavonoids, 5 neoflavonoids, 12 pterocarpans, 10 chromones, 7 condensed tannins, 11 coumarins, 30 stilbenoids, 2 lignans, 5 phenylpropanoids, 13 xanthones, 5 hydrolyzable tannins, and 56 miscellaneous phenolics), 30 quinones, and 46 miscellaneous phytochemicals, with six bacterial protein targets (peptide deformylase, DNA gyrase/topoisomerase IV, UDP-galactose mutase, protein tyrosine phosphatase, cytochrome P450 CYP121, and NAD⁺-dependent DNA ligase). In addition, 35 known inhibitors were docked with their respective targets for comparison purposes. Prenylated polyphenolics showed the best docking profiles, while terpenoids had the poorest. The most susceptible protein targets were peptide deformylases and NAD⁺-dependent DNA ligases.
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Affiliation(s)
- Mary Snow Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
- Department of Pharmacognosy, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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19
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Spirooxindoles as novel 3D-fragment scaffolds: Synthesis and screening against CYP121 from M. tuberculosis. Bioorg Med Chem Lett 2016; 26:3735-40. [DOI: 10.1016/j.bmcl.2016.05.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 01/17/2023]
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20
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Kavanagh ME, Coyne AG, McLean KJ, James GG, Levy CW, Marino LB, de Carvalho LPS, Chan DSH, Hudson SA, Surade S, Leys D, Munro AW, Abell C. Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. J Med Chem 2016; 59:3272-302. [PMID: 27002486 PMCID: PMC4835159 DOI: 10.1021/acs.jmedchem.6b00007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV-vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.
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Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Guy G James
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Colin W Levy
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Leonardo B Marino
- Laboratory of Mycobacterial Metabolism and Antibiotic Research, Francis Crick Institute, The Mill Hill Laboratory , London NW7 1AA, U.K.,School of Pharmaceutical Sciences, São Paulo State University (UNESP) , 4801-902 Araraquara, SP, Brazil
| | - Luiz Pedro S de Carvalho
- Laboratory of Mycobacterial Metabolism and Antibiotic Research, Francis Crick Institute, The Mill Hill Laboratory , London NW7 1AA, U.K
| | - Daniel S H Chan
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Sean A Hudson
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Sachin Surade
- Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA U.K
| | - David Leys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
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21
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Kim BR, Sung GH, Ryu KE, Lee SG, Yoon HJ, Shin DS, Yoon YJ. Direct synthesis of pyrazoles from esters using tert-butoxide-assisted C-(C=O) coupling. Chem Commun (Camb) 2016; 51:9201-4. [PMID: 25952163 DOI: 10.1039/c5cc02020d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the direct synthesis of pyrazoles from esters that comprises two sequential reactions: tert-butoxide-assisted C-C(=O) coupling reaction to yield β-ketonitrile or α,β-alkynone intermediates, and condensation by hydrazine addition. The method reported allows for easy control of the regioselectivity and structure of substituents at N-1, C-3, C-4 and/or C-5 positions.
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Affiliation(s)
- Bo Ram Kim
- Department of Chemistry & Research Institute of Natural Science, Gyeongsang National University, Jinju 660-701, Korea.
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22
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Scott DE, Spry C, Abell C. Differential Scanning Fluorimetry as Part of a Biophysical Screening Cascade. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch07] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Villemagne B, Flipo M, Blondiaux N, Crauste C, Malaquin S, Leroux F, Piveteau C, Villeret V, Brodin P, Villoutreix BO, Sperandio O, Soror SH, Wohlkönig A, Wintjens R, Deprez B, Baulard AR, Willand N. Ligand efficiency driven design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging, and linking approaches. J Med Chem 2014; 57:4876-88. [PMID: 24818704 DOI: 10.1021/jm500422b] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tuberculosis remains a major cause of mortality and morbidity, killing each year more than one million people. Although the combined use of first line antibiotics (isoniazid, rifampicin, pyrazinamide, and ethambutol) is efficient to treat most patients, the rapid emergence of multidrug resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. Mycobacterial transcriptional repressor EthR is a key player in the control of second-line drugs bioactivation such as ethionamide and has been shown to impair the sensitivity of the human pathogen Mycobacterium tuberculosis to this antibiotic. As a way to identify new potent ligands of this protein, we have developed fragment-based approaches. In the current study, we combined surface plasmon resonance assay, X-ray crystallography, and ligand efficiency driven design for the rapid discovery and optimization of new chemotypes of EthR ligands starting from a fragment. The design, synthesis, and in vitro and ex vivo activities of these compounds will be discussed.
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24
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Hudson SA, Mashalidis EH, Bender A, McLean KJ, Munro AW, Abell C. Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. Chembiochem 2014; 15:549-55. [PMID: 24677424 PMCID: PMC4159592 DOI: 10.1002/cbic.201300697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Indexed: 11/21/2022]
Abstract
We present a novel fragment-based approach that tackles some of the challenges for chemical biology of predicting protein function. The general approach, which we have termed biofragments, comprises two key stages. First, a biologically relevant fragment library (biofragment library) can be designed and constructed from known sets of substrate-like ligands for a protein class of interest. Second, the library can be screened for binding to a novel putative ligand-binding protein from the same or similar class, and the characterization of hits provides insight into the basis of ligand recognition, selectivity, and function at the substrate level. As a proof-of-concept, we applied the biofragments approach to the functionally uncharacterized Mycobacterium tuberculosis (Mtb) cytochrome P450 isoform, CYP126. This led to the development of a tailored CYP biofragment library with notable 3D characteristics and a significantly higher screening hit rate (14%) than standard drug-like fragment libraries screened previously against Mtb CYP121 and 125 (4% and 1%, respectively). Biofragment hits were identified that make both substrate-like type-I and inhibitor-like type-II interactions with CYP126. A chemical-fingerprint-based substrate model was built from the hits and used to search a virtual TB metabolome, which led to the discovery that CYP126 has a strong preference for the recognition of aromatics and substrate-like type-I binding of chlorophenol moieties within the active site near the heme. Future catalytic analyses will be focused on assessing CYP126 for potential substrate oxidative dehalogenation.
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Affiliation(s)
- Sean A Hudson
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK) E-mail: Homepage: http://www-abell.ch.cam.ac.uk/
| | - Ellene H Mashalidis
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK) E-mail: Homepage: http://www-abell.ch.cam.ac.uk/
| | - Andreas Bender
- Unilever Centre for Molecular Informatics Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Kirsty J McLean
- Manchester Institute of Biotechnology, University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Andrew W Munro
- Manchester Institute of Biotechnology, University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Chris Abell
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK) E-mail: Homepage: http://www-abell.ch.cam.ac.uk/
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25
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Murray J, Giannetti AM, Steffek M, Gibbons P, Hearn BR, Cohen F, Tam C, Pozniak C, Bravo B, Lewcock J, Jaishankar P, Ly CQ, Zhao X, Tang Y, Chugha P, Arkin MR, Flygare J, Renslo AR. Tailoring small molecules for an allosteric site on procaspase-6. ChemMedChem 2013; 9:73-7, 2. [PMID: 24259468 DOI: 10.1002/cmdc.201300424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 12/20/2022]
Abstract
Although they represent attractive therapeutic targets, caspases have so far proven recalcitrant to the development of drugs targeting the active site. Allosteric modulation of caspase activity is an alternate strategy that potentially avoids the need for anionic and electrophilic functionality present in most active-site inhibitors. Caspase-6 has been implicated in neurodegenerative disease, including Huntington's and Alzheimer's diseases. Herein we describe a fragment-based lead discovery effort focused on caspase-6 in its active and zymogen forms. Fragments were identified for procaspase-6 using surface plasmon resonance methods and subsequently shown by X-ray crystallography to bind a putative allosteric site at the dimer interface. A fragment-merging strategy was employed to produce nanomolar-affinity ligands that contact residues in the L2 loop at the dimer interface, significantly stabilizing procaspase-6. Because rearrangement of the L2 loop is required for caspase-6 activation, our results suggest a strategy for the allosteric control of caspase activation with drug-like small molecules.
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Affiliation(s)
- Jeremy Murray
- Departments of Structural Biology, Biochemical Pharmacology, Neuroscience, and Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (USA).
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