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Padayachee T, Lamb DC, Nelson DR, Syed K. Structure-Function Analysis of the Essential Mycobacterium tuberculosis P450 Drug Target, CYP121A1. Int J Mol Sci 2024; 25:4886. [PMID: 38732102 PMCID: PMC11084333 DOI: 10.3390/ijms25094886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Cytochrome P450 CYP121A1 is a well-known drug target against Mycobacterium tuberculosis, the human pathogen that causes the deadly disease tuberculosis (TB). CYP121A1 is a unique P450 enzyme because it uses classical and non-classical P450 catalytic processes and has distinct structural features among P450s. However, a detailed investigation of CYP121A1 protein structures in terms of active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 53 CYP121A1 crystal structures were investigated in this study. Critical amino acids required for CYP121A1's overall activity were identified and highlighted this enzyme's rigid architecture and substrate selectivity. The CYP121A1-fluconazole crystal structure revealed a novel azole drug-P450 binding mode in which azole heme coordination was facilitated by a water molecule. Fragment-based inhibitor approaches revealed that CYP121A1 can be inhibited by molecules that block the substrate channel or by directly interacting with the P450 heme. This study serves as a reference for the precise understanding of CYP121A1 interactions with different ligands and the structure-function analysis of P450 enzymes in general. Our findings provide critical information for the synthesis of more specific CYP121A1 inhibitors and their development as novel anti-TB drugs.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Empangeni 3886, South Africa;
| | - David C. Lamb
- Faculty of Medicine, Health and Life Sciences, Swansea University, Swansea SA2 8PP, UK;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science, Agriculture and Engineering, University of Zululand, Empangeni 3886, South Africa;
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2
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Jasani M, Patel L. Design and synthesis of novel substituted pyrazole as small molecule inhibitor of Cytochrome P450 CYP121A1. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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3
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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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4
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Katariya KD, Reddy DV. Oxazolyl-Pyrimidines As Antibacterial And Antitubercular Agents: Synthesis, Biological Evaluation, in-silico ADMET And Molecular Docking Study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Frederickson M, Selvam IR, Evangelopoulos D, McLean KJ, Katariya MM, Tunnicliffe RB, Campbell B, Kavanagh ME, Charoensutthivarakul S, Blankley RT, Levy CW, de Carvalho LPS, Leys D, Munro AW, Coyne AG, Abell C. A new strategy for hit generation: Novel in cellulo active inhibitors of CYP121A1 from Mycobacterium tuberculosis via a combined X-ray crystallographic and phenotypic screening approach (XP screen). Eur J Med Chem 2022; 230:114105. [PMID: 35065413 PMCID: PMC8856928 DOI: 10.1016/j.ejmech.2022.114105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/27/2022]
Abstract
There is a pressing need for new drugs against tuberculosis (TB) to combat the growing resistance to current antituberculars. Herein a novel strategy is described for hit generation against promising TB targets involving X-ray crystallographic screening in combination with phenotypic screening. This combined approach (XP Screen) affords both a validation of target engagement as well as determination of in cellulo activity. The utility of this method is illustrated by way of an XP Screen against CYP121A1, a cytochrome P450 enzyme from Mycobacterium tuberculosis (Mtb) championed as a validated drug discovery target. A focused screening set was synthesized and tested by such means, with several members of the set showing promising activity against Mtb strain H37Rv. One compound was observed as an X-ray hit against CYP121A1 and showed improved activity against Mtb strain H37Rv under multiple assay conditions (pan-assay activity). Data obtained during X-ray crystallographic screening were utilized in a structure-based campaign to design a limited number of analogues (less than twenty), many of which also showed pan-assay activity against Mtb strain H37Rv. These included the benzo[b][1,4]oxazine derivative (MIC90 6.25 μM), a novel hit compound suitable as a starting point for a more involved hit to lead candidate medicinal chemistry campaign. CYP121 from M.tuberculosis has been previously shown to be a crucial target for the survival of the mycobacteria. Strategies previously employed have identified high affinity inhibitors however these have lacked activity on M.tuberculosis. The strategy reported here uses a combination of X-ray crystallography and phenotypic screening (XP Screen) to identify compounds. The XP screen approach identified a number of compounds which show good affinity (up to 3.2 μM) and MIC against M.tuberculosis (up to 6.25 μM).
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6
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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: 6] [Impact Index Per Article: 2.0] [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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7
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Lopes LGF, Carvalho EM, Sousa EHS. A bioinorganic chemistry perspective on the roles of metals as drugs and targets against Mycobacterium tuberculosis - a journey of opportunities. Dalton Trans 2021; 49:15988-16003. [PMID: 32583835 DOI: 10.1039/d0dt01365j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Medicinal inorganic chemists have provided many strategies to tackle a myriad of diseases, pushing forward the frontiers of pharmacology. As an example, the fight against tuberculosis (TB), an infectious bacterial disease, has led to the development of metal-based compounds as potential drugs. This disease remains a current health issue causing over 1.4 million of deaths per year. The emergence of multi- (MDR) and extensively-drug resistant (XDR) Mycobacterium tuberculosis (Mtb) strains along with a long dormancy process, place major challenges in developing new therapeutic compounds. Isoniazid is a front-line prodrug used against TB with appealing features for coordination chemists, which have been explored in a series of cases reported here. An isoniazid iron-based compound, called IQG-607, has caught our attention, whose in vitro and in vivo studies are advanced and thoroughly discussed, along with other metal complexes. Isoniazid is inactive against dormant Mtb, a hard to eliminate state of this bacillus, found in one-fourth of the world's population and directly implicated in the lengthy treatment of TB (ca. 6 months). Thus, our understanding of this phenomenon may lead to a rational design of new drugs. Along these lines, we describe how metals as targets can cross paths with metals used as selective therapeutics, where we mainly review heme-based sensors, DevS and DosT, as a key system in the Mtb dormancy process and a current drug target. Overall, we report new opportunities for bioinorganic chemists to tackle this longstanding and current threat.
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Affiliation(s)
- Luiz G F Lopes
- Group of Bioinorganic, Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil.
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8
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Hoarau M, Vanichtanankul J, Srimongkolpithak N, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S. Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening. J Enzyme Inhib Med Chem 2021; 36:198-206. [PMID: 33530764 PMCID: PMC8759724 DOI: 10.1080/14756366.2020.1854244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In various malaria-endemic regions, the appearance of resistance has precluded the use of pyrimidine-based antifolate drugs. Here, a three-step fragment screening was used to identify new non-pyrimidine Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors. Starting from a 1163-fragment commercial library, a two-step differential scanning fluorimetry screen identified 75 primary fragment hits. Subsequent enzyme inhibition assay identified 11 fragments displaying IC50 in the 28-695 μM range and selectivity for PfDHFR. In addition to the known pyrimidine, three new anti-PfDHFR chemotypes were identified. Fragments from each chemotype were successfully co-crystallized with PfDHFR, revealing a binding in the active site, in the vicinity of catalytic residues, which was confirmed by molecular docking on all fragment hits. Finally, comparison with similar non-hit fragments provides preliminary input on available growth vectors for future drug development.
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Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
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9
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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10
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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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Surface hydrophobics mediate functional dimerization of CYP121A1 of Mycobacterium tuberculosis. Sci Rep 2021; 11:394. [PMID: 33431984 PMCID: PMC7801616 DOI: 10.1038/s41598-020-79545-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022] Open
Abstract
Tuberculosis is caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb) and remains the leading cause of death by infection world-wide. The Mtb genome encodes a disproportionate number of twenty cytochrome P450 enzymes, of which the essential enzyme cytochrome P450 121A1 (CYP121A1) remains a target of drug design efforts. CYP121A1 mediates a phenol coupling reaction of the tyrosine dipeptide cyclo-L-Tyr-L-Tyr (cYY). In this work, a structure and function investigation of dimerization was performed as an overlooked feature of CYP121A1 function. This investigation showed that CYP121A1 dimers form via intermolecular contacts on the distal surface and are mediated by a network of solvent-exposed hydrophobic residues. Disruption of CYP121A1 dimers by site-directed mutagenesis leads to a partial loss of specificity for cYY, resulting in an approximate 75% decrease in catalysis. 19F labeling and nuclear magnetic resonance of the enzyme FG-loop was also combined with protein docking to develop a working model of a functional CYP121A1 dimer. The results obtained suggest that participation of a homodimer interface in substrate selectivity represents a novel paradigm of substrate binding in CYPs, while also providing important mechanistic insight regarding a relevant drug target in the development of novel anti-tuberculosis agents.
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12
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Discovery of a chemical compound that suppresses expression of BEX2, a dormant cancer stem cell-related protein. Biochem Biophys Res Commun 2021; 537:132-139. [PMID: 33412384 DOI: 10.1016/j.bbrc.2020.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
Abstract
Cancer stem cells (CSCs) are believed to cause cancer metastasis and recurrence. BEX2 (brain expressed X-linked gene 2) is a CSC-related gene that is expressed in dormant CSCs in cholangiocarcinoma and induces resistance against chemotherapy. The aim of the present study was to identify small compounds that have activity to inhibit BEX2 expression and result in the attenuation of CSC-related phenotypes. We screened 9600 small chemical compounds in high-throughput screening using cholangiocarcinoma cell line HuCCT1 expressing BEX2 protein fused with NanoLuc, and identified a compound, BMPP (1, 3-Benzenediol, [4-(4-methoxyphenyl)-1H-pyrazol-3-yl]). BMPP was found to exert decreasing effects on BEX2 protein expression and G0 phase population of the tumor cells, and increasing effects on ATP levels and chemotherapeutic sensitivity of the cells. These findings indicate that BMPP is a valuable chemical compound for reducing dormant CSC-related phenotypes. Thus, the identification of BMPP as a potential CSC suppressor provides scope for the development of novel therapeutic modalities for the treatment of cancers with BEX2 overexpressing CSCs.
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Karczmarzyk Z, Swatko-Ossor M, Wysocki W, Drozd M, Ginalska G, Pachuta-Stec A, Pitucha M. New Application of 1,2,4-Triazole Derivatives as Antitubercular Agents. Structure, In Vitro Screening and Docking Studies. Molecules 2020; 25:E6033. [PMID: 33352814 PMCID: PMC7767103 DOI: 10.3390/molecules25246033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 01/02/2023] Open
Abstract
A series of 1,2,4-triazole derivatives were synthesized and assigned as potential anti-tuberculosis substances. The molecular and crystal structures for the model compounds C1, C12, and C13 were determined using X-ray analysis. The X-ray investigation confirmed the synthesis pathway and the assumed molecular structures for analyzed 1,2,4-triazol-5-thione derivatives. The conformational preferences resulting from rotational degrees of freedom of the 1,2,4-triazole ring substituents were characterized. The lipophilicity (logP) and electronic parameters as the energy of frontier orbitals, dipole moments, NBO net charge distribution on the atoms, and electrostatic potential distribution for all structures were calculated at AM1 and DFT/B3LYP/6-311++G(d,p) level. The in vitro test was done against M. tuberculosis H37Ra, M. phlei, M. smegmatis, and M. timereck. The obtained results clearly confirmed the antituberculosis potential of compound C4, which turned out to be the most active against Mycobacterium H37Ra (MIC = 0.976 μg/mL), Mycobaterium pheli (MIC = 7.81 μg/mL) and Mycobacerium timereck (62.6 μg/mL). Satisfactory results were obtained with compounds C8, C11, C14 versus Myc. H37Ra, Myc. pheli, Myc. timereck (MIC = 31.25-62.5 μg/mL). The molecular docking studies were carried out for all investigated compounds using the Mycobacterium tuberculosis cytochrome P450 CYP121 enzyme as molecular a target connected with antimycobacterial activity.
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Affiliation(s)
- Zbigniew Karczmarzyk
- Faculty of Science, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland;
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland; (M.S.-O.); (W.W.); (G.G.)
| | - Waldemar Wysocki
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland; (M.S.-O.); (W.W.); (G.G.)
| | - Monika Drozd
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland; (M.D.); (A.P.-S.)
| | - Grazyna Ginalska
- Department of Biochemistry and Biotechnology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland; (M.S.-O.); (W.W.); (G.G.)
| | - Anna Pachuta-Stec
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland; (M.D.); (A.P.-S.)
| | - Monika Pitucha
- Independent Radiopharmacy Unit, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland; (M.D.); (A.P.-S.)
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14
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Campaniço A, Harjivan SG, Warner DF, Moreira R, Lopes F. Addressing Latent Tuberculosis: New Advances in Mimicking the Disease, Discovering Key Targets, and Designing Hit Compounds. Int J Mol Sci 2020; 21:ijms21228854. [PMID: 33238468 PMCID: PMC7700174 DOI: 10.3390/ijms21228854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Despite being discovered and isolated more than one hundred years ago, tuberculosis (TB) remains a global public health concern arch. Our inability to eradicate this bacillus is strongly related with the growing resistance, low compliance to current drugs, and the capacity of the bacteria to coexist in a state of asymptomatic latency. This last state can be sustained for years or even decades, waiting for a breach in the immune system to become active again. Furthermore, most current therapies are not efficacious against this state, failing to completely clear the infection. Over the years, a series of experimental methods have been developed to mimic the latent state, currently used in drug discovery, both in vitro and in vivo. Most of these methods focus in one specific latency inducing factor, with only a few taking into consideration the complexity of the granuloma and the genomic and proteomic consequences of each physiological factor. A series of targets specifically involved in latency have been studied over the years with promising scaffolds being discovered and explored. Taking in account that solving the latency problem is one of the keys to eradicate the disease, herein we compile current therapies and diagnosis techniques, methods to mimic latency and new targets and compounds in the pipeline of drug discovery.
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Affiliation(s)
- André Campaniço
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (A.C.); (S.G.H.); (R.M.)
| | - Shrika G. Harjivan
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (A.C.); (S.G.H.); (R.M.)
| | - Digby F. Warner
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa;
- Department of Pathology, SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, University of Cape Town, Rondebosch 7701, South Africa
- Welcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Rondebosch 7701, South Africa
| | - Rui Moreira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (A.C.); (S.G.H.); (R.M.)
| | - Francisca Lopes
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (A.C.); (S.G.H.); (R.M.)
- Correspondence:
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15
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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16
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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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17
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Anti-Tubercular Activity of Substituted 7-Methyl and 7-Formylindolizines and In Silico Study for Prospective Molecular Target Identification. Antibiotics (Basel) 2019; 8:antibiotics8040247. [PMID: 31816928 PMCID: PMC6963442 DOI: 10.3390/antibiotics8040247] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 11/17/2022] Open
Abstract
Novel series of diversely substituted indolizines were designed, synthesized, and evaluated for their in vitro anti-mycobacterial activity against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB). Many compounds exhibited significant inhibitory activity against MTB H37Rv strains. Indolizines 2d, 2e, and 4 were also found to be active against MTB clinical isolates with multi-resistance to rifampicin and isoniazid. Indolizine 4 was identified as the most promising anti-mycobacterial agent, displaying minimum inhibitory concentration (MIC) values of 4 and 32 μg/mL against H37Rv and MDR strains, respectively. Furthermore, an in silico study was carried out for prospective molecular target identification and revealed favorable interactions with the target enzymes CYP 121, malate synthase, and DNA GyrB ATPase. None of the potent molecules presented toxicity against peripheral blood mononuclear (PBM) cell lines, demonstrating their potentiality to be used for drug-sensitive and drug-resistant tuberculosis therapy.
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18
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Rajput S, McLean KJ, Poddar H, Selvam IR, Nagalingam G, Triccas JA, Levy CW, Munro AW, Hutton CA. Structure-Activity Relationships of cyclo(l-Tyrosyl-l-tyrosine) Derivatives Binding to Mycobacterium tuberculosis CYP121: Iodinated Analogues Promote Shift to High-Spin Adduct. J Med Chem 2019; 62:9792-9805. [PMID: 31618032 DOI: 10.1021/acs.jmedchem.9b01199] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A series of analogues of cyclo(l-tyrosyl-l-tyrosine), the substrate of the Mycobacterium tuberculosis enzyme CYP121, have been synthesized and analyzed by UV-vis and electron paramagnetic resonance spectroscopy and by X-ray crystallography. The introduction of iodine substituents onto cyclo(l-tyrosyl-l-tyrosine) results in sub-μM binding affinity for the CYP121 enzyme and a complete shift to the high-spin state of the heme FeIII. The introduction of halogens that are able to interact with heme groups is thus a feasible approach to the development of next-generation, tight binding inhibitors of the CYP121 enzyme, in the search for novel antitubercular compounds.
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Affiliation(s)
- Sunnia Rajput
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry , University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Harshwardhan Poddar
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry , University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Irwin R Selvam
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry , University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Gayathri Nagalingam
- Department of Infectious Diseases and Immunology, Sydney Medical School , The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - James A Triccas
- Department of Infectious Diseases and Immunology, Sydney Medical School , The University of Sydney , Sydney , New South Wales 2006 , Australia
| | - Colin W Levy
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry , 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, School of Chemistry , University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Craig A Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute , University of Melbourne , 30 Flemington Road , Parkville , Victoria 3010 , Australia
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19
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Kishk SM, McLean KJ, Sood S, Smith D, Evans JW, Helal MA, Gomaa MS, Salama I, Mostafa SM, de Carvalho LPS, Levy CW, Munro AW, Simons C. Design and Synthesis of Imidazole and Triazole Pyrazoles as Mycobacterium Tuberculosis CYP121A1 Inhibitors. ChemistryOpen 2019; 8:995-1011. [PMID: 31367508 PMCID: PMC6646865 DOI: 10.1002/open.201900227] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
The emergence of untreatable drug-resistant strains of Mycobacterium tuberculosis is a major public health problem worldwide, and the identification of new efficient treatments is urgently needed. Mycobacterium tuberculosis cytochrome P450 CYP121A1 is a promising drug target for the treatment of tuberculosis owing to its essential role in mycobacterial growth. Using a rational approach, which includes molecular modelling studies, three series of azole pyrazole derivatives were designed through two synthetic pathways. The synthesized compounds were biologically evaluated for their inhibitory activity towards M. tuberculosis and their protein binding affinity (K D). Series 3 biarylpyrazole imidazole derivatives were the most effective with the isobutyl (10 f) and tert-butyl (10 g) compounds displaying optimal activity (MIC 1.562 μg/mL, K D 0.22 μM (10 f) and 4.81 μM (10 g)). The spectroscopic data showed that all the synthesised compounds produced a type II red shift of the heme Soret band indicating either direct binding to heme iron or (where less extensive Soret shifts are observed) putative indirect binding via an interstitial water molecule. Evaluation of biological and physicochemical properties identified the following as requirements for activity: LogP >4, H-bond acceptors/H-bond donors 4/0, number of rotatable bonds 5-6, molecular volume >340 Å3, topological polar surface area <40 Å2.
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Affiliation(s)
- Safaa M. Kishk
- School of Pharmacy & Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBU.K.
- Medicinal Chemistry Department, Faculty of PharmacySuez Canal UniversityIsmailiaEgypt
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, School of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNU.K.
| | - Sakshi Sood
- Mycobacterial Metabolism and Antibiotic Research LaboratoryThe Francis Crick Institute1 Midland RoadLondonNW1 1ATU.K.
| | - Darren Smith
- School of Pharmacy & Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBU.K.
| | - Jack W.D. Evans
- School of Pharmacy & Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBU.K.
| | - Mohamed A. Helal
- Medicinal Chemistry Department, Faculty of PharmacySuez Canal UniversityIsmailiaEgypt
- Biomedical Sciences ProgramUniversity of Science and Technology Zewail City of Science and TechnologyGiza12588Egypt
| | - Mohamed S. Gomaa
- Medicinal Chemistry Department, Faculty of PharmacySuez Canal UniversityIsmailiaEgypt
- Department of Chemistry College of Clinical PharmacyImam Abdulrahman Bin Faisal UniversityDammamKingdom of Saudi Arabia
| | - Ismail Salama
- Medicinal Chemistry Department, Faculty of PharmacySuez Canal UniversityIsmailiaEgypt
| | - Samia M. Mostafa
- Medicinal Chemistry Department, Faculty of PharmacySuez Canal UniversityIsmailiaEgypt
| | - Luiz Pedro S. de Carvalho
- Mycobacterial Metabolism and Antibiotic Research LaboratoryThe Francis Crick Institute1 Midland RoadLondonNW1 1ATU.K.
| | - Colin W. Levy
- Manchester Institute of Biotechnology, School of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNU.K.
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNU.K.
| | - Claire Simons
- School of Pharmacy & Pharmaceutical SciencesCardiff UniversityKing Edward VII AvenueCardiffCF10 3NBU.K.
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20
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Wang F, Zhang Y, Liu Z, Du Z, Zhang L, Ren J, Qu X. A Biocompatible Heterogeneous MOF-Cu Catalyst for In Vivo Drug Synthesis in Targeted Subcellular Organelles. Angew Chem Int Ed Engl 2019; 58:6987-6992. [PMID: 30888728 DOI: 10.1002/anie.201901760] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Indexed: 01/05/2023]
Abstract
As a typical bioorthogonal reaction, the copper-catalyzed azide-alkyne cycloaddition (CuAAC) has been used for drug design and synthesis. However, for localized drug synthesis, it is important to be able to determine where the CuAAC reaction occurs in living cells. In this study, we constructed a heterogeneous copper catalyst on a metal-organic framework that could preferentially accumulate in the mitochondria of living cells. Our system enabled the localized synthesis of drugs through a site-specific CuAAC reaction in mitochondria with good biocompatibility. Importantly, the subcellular catalytic process for localized drug synthesis avoided the problems of the delivery and distribution of toxic molecules. In vivo tumor therapy experiments indicated that the localized synthesis of resveratrol-derived drugs led to greater antitumor efficacy and minimized side effects usually associated with drug delivery and distribution.
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Affiliation(s)
- Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yan Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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21
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Wang F, Zhang Y, Liu Z, Du Z, Zhang L, Ren J, Qu X. A Biocompatible Heterogeneous MOF–Cu Catalyst for In Vivo Drug Synthesis in Targeted Subcellular Organelles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901760] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Yan Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Lu Zhang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
- University of Chinese Academy of Sciences Beijing 100039 China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun Jilin 130022 China
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22
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Child SA, Flint KL, Bruning JB, Bell SG. The characterisation of two members of the cytochrome P450 CYP150 family: CYP150A5 and CYP150A6 from Mycobacterium marinum. Biochim Biophys Acta Gen Subj 2019; 1863:925-934. [PMID: 30826435 DOI: 10.1016/j.bbagen.2019.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Actinobacteria, including the Mycobacteria, have a large component of cytochrome P450 family monooxygenases. This includes Mycobacterium tuberculosis, M. ulcerans and M. marinum, and M. vanbaalenii. These enzymes can abstract CH bonds and have important roles in natural product biosynthesis. METHODS Two members of the bacterial CYP150 family, CYP150A5 and CYP150A6 from M. marinum, were produced, purified and characterised. The potential substrate ranges of both enzymes were analysed and the monooxygenase activity of CYP150A5 was reconstituted using a physiological electron transfer partner system. CYP150A6 was structurally characterised by X-ray crystallography. RESULTS CYP150A5 was shown to bind various norisoprenoids and terpenoids. It could regioselectively hydroxylate β-ionol. The X-ray crystal structure of substrate-free CYP150A6 was solved to 1.5 Å. This displayed an open conformation with short F and G helices, an unresolved F-G loop region and exposed active site pocket. The active site residues could be identified and important variations were found among the CYP150A enzymes. Haem-binding azole inhibitors were identified for both enzymes. CONCLUSIONS The structure of CYP150A6 will facilitate the identification of physiological substrates and the design of better inhibitors for members of this P450 family. Based on the observed differences in substrate binding preference and sequence variations among the active site residues, their roles are predicted to be different. GENERAL SIGNIFICANCE Multiple CYP150 family members were found in many bacteria and are prevalent in the Mycobacteria including several human pathogens. Inhibition and structural data are reported here for these enzymes for the first time.
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Affiliation(s)
- Stella A Child
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - Kate L Flint
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
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23
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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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24
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Moreau RJ, Skepper CK, Appleton BA, Blechschmidt A, Balibar CJ, Benton BM, Drumm JE, Feng BY, Geng M, Li C, Lindvall MK, Lingel A, Lu Y, Mamo M, Mergo W, Polyakov V, Smith TM, Takeoka K, Uehara K, Wang L, Wei JR, Weiss AH, Xie L, Xu W, Zhang Q, de Vicente J. Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria. J Med Chem 2018; 61:3309-3324. [DOI: 10.1021/acs.jmedchem.7b01691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert J. Moreau
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Colin K. Skepper
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brent A. Appleton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Anke Blechschmidt
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Carl J. Balibar
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Bret M. Benton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Joseph E. Drumm
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian Y. Feng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mei Geng
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika K. Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yipin Lu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mulugeta Mamo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Valery Polyakov
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Thomas M. Smith
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kenneth Takeoka
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kyoko Uehara
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lisha Wang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Andrew H. Weiss
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Lili Xie
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wenjian Xu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Qiong Zhang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Javier de Vicente
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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25
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NMR-Fragment Based Virtual Screening: A Brief Overview. Molecules 2018; 23:molecules23020233. [PMID: 29370102 PMCID: PMC6017141 DOI: 10.3390/molecules23020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 01/23/2023] Open
Abstract
Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.
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26
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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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El-wahab HAA, Accietto M, Marino LB, McLean KJ, Levy CW, Abdel-Rahman HM, El-Gendy MA, Munro AW, Aboraia AS, Simons C. Design, synthesis and evaluation against Mycobacterium tuberculosis of azole piperazine derivatives as dicyclotyrosine (cYY) mimics. Bioorg Med Chem 2018; 26:161-176. [DOI: 10.1016/j.bmc.2017.11.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/14/2017] [Accepted: 11/18/2017] [Indexed: 11/29/2022]
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28
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Taban IM, Elshihawy HEAE, Torun B, Zucchini B, Williamson CJ, Altuwairigi D, Ngu AST, McLean KJ, Levy CW, Sood S, Marino LB, Munro AW, de Carvalho LPS, Simons C. Novel Aryl Substituted Pyrazoles as Small Molecule Inhibitors of Cytochrome P450 CYP121A1: Synthesis and Antimycobacterial Evaluation. J Med Chem 2017; 60:10257-10267. [PMID: 29185746 PMCID: PMC5748275 DOI: 10.1021/acs.jmedchem.7b01562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Three series of biarylpyrazole imidazole and triazoles are described, which vary in the linker between the biaryl pyrazole and imidazole/triazole group. The imidazole and triazole series with the short -CH2- linker displayed promising antimycobacterial activity, with the imidazole-CH2- series (7) showing low MIC values (6.25-25 μg/mL), which was also influenced by lipophilicity. Extending the linker to -C(O)NH(CH2)2- resulted in a loss of antimycobacterial activity. The binding affinity of the compounds with CYP121A1 was determined by UV-visible optical titrations with KD values of 2.63, 35.6, and 290 μM, respectively, for the tightest binding compounds 7e, 8b, and 13d from their respective series. Both binding affinity assays and docking studies of the CYP121A1 inhibitors suggest type II indirect binding through interstitial water molecules, with key binding residues Thr77, Val78, Val82, Val83, Met86, Ser237, Gln385, and Arg386, comparable with the binding interactions observed with fluconazole and the natural substrate dicyclotyrosine.
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Affiliation(s)
- Ismail M Taban
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Hosam E A E Elshihawy
- Department of Organic Chemistry, Faculty of Pharmacy, Suez Canal University , Ismalia, Egypt
| | - Beyza Torun
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K.,Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University , 06100 Tandogan, Ankara, Turkey
| | - Benedetta Zucchini
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K.,Department of Pharmaceutical Sciences, University of Perugia , Via del Liceo, 1-06123 Perugia, Italy
| | - Clare J Williamson
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Dania Altuwairigi
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Adeline S T Ngu
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K
| | - Kirsty J McLean
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Colin W Levy
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Sakshi Sood
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute , 1 Midland Road, London NW1 1AT, U.K
| | - Leonardo B Marino
- Faculty of Pharmaceutical Sciences, UNESP-Univ Estadual Paulista , Araraquara, São Paulo14801-902, Brazil
| | - Andrew W Munro
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , 131 Princess Street, Manchester M1 7DN, U.K
| | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute , 1 Midland Road, London NW1 1AT, U.K
| | - Claire Simons
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University , King Edward VII Avenue, Cardiff CF10 3NB, U.K
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29
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Johnson CN, Erlanson DA, Jahnke W, Mortenson PN, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2016. J Med Chem 2017; 61:1774-1784. [PMID: 29087197 DOI: 10.1021/acs.jmedchem.7b01298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The popularity of fragment-based drug discovery (FBDD) is demonstrated by the number of recent successful fragment-to-lead (F2L) publications. This Miniperspective provides a tabulated summary of the F2L literature published in the year 2016, along with discussion of general trends. It uses the same format as our summary of the 2015 literature and is intended to be a resource for both FBDD practitioners and medicinal chemists in general.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics , 4002 Basel , Switzerland
| | - Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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30
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Brengel C, Thomann A, Schifrin A, Allegretta G, Kamal AAM, Haupenthal J, Schnorr I, Cho SH, Franzblau SG, Empting M, Eberhard J, Hartmann RW. Biophysical Screening of a Focused Library for the Discovery of CYP121 Inhibitors as Novel Antimycobacterials. ChemMedChem 2017; 12:1616-1626. [DOI: 10.1002/cmdc.201700363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Giuseppe Allegretta
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Ahmed A. M. Kamal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Isabell Schnorr
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Sang Hyun Cho
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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31
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Solution NMR Studies of Mycobacterium tuberculosis Proteins for Antibiotic Target Discovery. Molecules 2017; 22:molecules22091447. [PMID: 28858250 PMCID: PMC6151718 DOI: 10.3390/molecules22091447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/27/2017] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is an infectious disease caused by Mycobacteriumtuberculosis, which triggers severe pulmonary diseases. Recently, multidrug/extensively drug-resistant tuberculosis strains have emerged and continue to threaten global health. Because of the development of drug-resistant tuberculosis, there is an urgent need for novel antibiotics to treat these drug-resistant bacteria. In light of the clinical importance of M. tuberculosis, 2067 structures of M. tuberculsosis proteins have been determined. Among them, 52 structures have been solved and studied using solution nuclear magnetic resonance (NMR). The functional details based on structural analysis of M. tuberculosis using NMR can provide essential biochemical data for the development of novel antibiotic drugs. In this review, we introduce diverse structural and biochemical studies on M. tuberculosis proteins determined using NMR spectroscopy.
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32
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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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33
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Ge SJ, Zhao TP, Wang M, Deng LL, Lin BP, Zhang XQ, Sun Y, Yang H, Chen EQ. A homeotropic main-chain tolane-type liquid crystal elastomer film exhibiting high anisotropic thermal conductivity. SOFT MATTER 2017; 13:5463-5468. [PMID: 28726970 DOI: 10.1039/c7sm01154g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The development of pure polymeric films with anisotropic thermal conductivities for electronic device packaging applications has attracted intense scientific attention. In order to enhance the polymeric film's normal-direction thermal conductivity, homeotropic alignment of macromolecular chains is the primary concern. One of the promising preparation strategies is to perform in situ photopolymerization of homeotropic-oriented liquid crystal monomers. In this work, we design and synthesize a novel tolane-core thiol-ene-tailed liquid crystal monomer. Benefitting from the conjugated and extended tolane π-system of the mesogenic core and length extension of the terminal aliphatic tails, the normal-to-plane thermal conductivity value and the thermal conductivity anisotropy value of the corresponding cross-linked main-chain end-on liquid crystal polymer (xMELCP) film reach 3.56 W m-1 K-1 and 15.0, respectively. Compared with the data of a previously reported ester-type thiol-ene xMELCP film, the two primary values of this novel tolane-type thiol-ene xMELCP material are increased dramatically by 46% and 29%, respectively.
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Affiliation(s)
- Si-Jia Ge
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory for Science and Application of Molecular Ferroelectrics, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Jiangsu Optoelectronic Functional Materials and Engineering Laboratory, Southeast University, Nanjing, 211189, P. R. China.
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34
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Rode ND, Sonawane AD, Nawale L, Khedkar VM, Joshi RA, Likhite AP, Sarkar D, Joshi RR. Synthesis, biological evaluation, and molecular docking studies of novel 3-aryl-5-(alkyl-thio)-1H-1,2,4-triazoles derivatives targeting Mycobacterium tuberculosis. Chem Biol Drug Des 2017; 90:1206-1214. [PMID: 28609019 DOI: 10.1111/cbdd.13040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/08/2017] [Accepted: 05/30/2017] [Indexed: 02/01/2023]
Abstract
A small library of new 3-aryl-5-(alkyl-thio)-1H-1,2,4-triazoles was synthesized and screened for the antimycobacterial potency against Mycobacterium tuberculosis H37 Ra strain and Mycobacterium bovis BCG both in active and dormant stage. Among the synthesized library, 25 compounds exhibited promising anti-TB activity in the range of IC50 0.03-5.88 μg/ml for dormant stage and 20 compounds in the range of 0.03-6.96 μg/ml for active stage. Their lower toxicity (>100 μg/ml) and higher selectivity (SI = >10) against all cancer cell lines screened make them interesting compounds with potential antimycobacterial effects. Furthermore, to rationalize the observed biological activity data and to establish a structural basis for inhibition of M. tuberculosis, the molecular docking study was carried out against a potential target MTB CYP121 which revealed a significant correlation between the binding score and biological activity for these compounds. Cytotoxicity and in vivo pharmacokinetic studies suggested that 1,2,4-triazole analogues have an acceptable safety index, in vivo stability and bio-availability.
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Affiliation(s)
- Navnath D Rode
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India
| | - Amol D Sonawane
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India
| | - Laxman Nawale
- Combi-Chem Resource Centre, CSIR-National Chemical Laboratory, Pune, India
| | - Vijay M Khedkar
- Combi-Chem Resource Centre, CSIR-National Chemical Laboratory, Pune, India
| | - Ramesh A Joshi
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India
| | - Anjali P Likhite
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India
| | - Dhiman Sarkar
- Combi-Chem Resource Centre, CSIR-National Chemical Laboratory, Pune, India
| | - Rohini R Joshi
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India
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35
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Ryan A, Polycarpou E, Lack NA, Evangelopoulos D, Sieg C, Halman A, Bhakta S, Eleftheriadou O, McHugh TD, Keany S, Lowe ED, Ballet R, Abuhammad A, Jacobs WR, Ciulli A, Sim E. Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach. Br J Pharmacol 2017; 174:2209-2224. [PMID: 28380256 PMCID: PMC5481647 DOI: 10.1111/bph.13810] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 03/22/2017] [Accepted: 03/24/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND PURPOSE With the emergence of extensively drug-resistant tuberculosis, there is a need for new anti-tubercular drugs that work through novel mechanisms of action. The meta cleavage product hydrolase, HsaD, has been demonstrated to be critical for the survival of Mycobacterium tuberculosis in macrophages and is encoded in an operon involved in cholesterol catabolism, which is identical in M. tuberculosis and M. bovis BCG. EXPERIMENTAL APPROACH We generated a mutant strain of M. bovis BCG with a deletion of hsaD and tested its growth on cholesterol. Using a fragment based approach, over 1000 compounds were screened by a combination of differential scanning fluorimetry, NMR spectroscopy and enzymatic assay with pure recombinant HsaD to identify potential inhibitors. We used enzymological and structural studies to investigate derivatives of the inhibitors identified and to test their effects on growth of M. bovis BCG and M. tuberculosis. KEY RESULTS The hsaD deleted strain was unable to grow on cholesterol as sole carbon source but did grow on glucose. Of seven chemically distinct 'hits' from the library, two chemical classes of fragments were found to bind in the vicinity of the active site of HsaD by X-ray crystallography. The compounds also inhibited growth of M. tuberculosis on cholesterol. The most potent inhibitor of HsaD was also found to be the best inhibitor of mycobacterial growth on cholesterol-supplemented minimal medium. CONCLUSIONS AND IMPLICATIONS We propose that HsaD is a novel therapeutic target, which should be fully exploited in order to design and discover new anti-tubercular drugs. LINKED ARTICLES This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.
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Affiliation(s)
- Ali Ryan
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Elena Polycarpou
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Nathan A Lack
- Department of PharmacologyUniversity of OxfordOxfordUK
- School of MedicineKoç UniversityIstanbulTurkey
| | - Dimitrios Evangelopoulos
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological SciencesBirkbeck, University of LondonLondonUK
- Centre for Clinical MicrobiologyUniversity College London, Royal Free CampusLondonUK
- Mycobacterial Metabolism and Antibiotic Research LaboratoryThe Francis Crick Institute, Mill Hill LaboratoryLondonUK
| | - Christian Sieg
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Alice Halman
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological SciencesBirkbeck, University of LondonLondonUK
| | - Olga Eleftheriadou
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
| | - Timothy D McHugh
- Centre for Clinical MicrobiologyUniversity College London, Royal Free CampusLondonUK
| | | | - Edward D Lowe
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Romain Ballet
- Department of PharmacologyUniversity of OxfordOxfordUK
| | | | - William R Jacobs
- Department of Microbiology and ImmunologyHoward Hughes Medical Institute, Albert Einstein College of MedicineBronxNew YorkUSA
| | - Alessio Ciulli
- Department of ChemistryUniversity of CambridgeCambridgeUK
- Division of Biological Chemistry & Drug Discovery, School of Life SciencesUniversity of Dundee, James Black CentreDundeeUK
| | - Edith Sim
- Faculty of Science, Engineering and ComputingKingston University LondonKingston upon ThamesUK
- Department of PharmacologyUniversity of OxfordOxfordUK
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36
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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: 32] [Impact Index Per Article: 4.6] [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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37
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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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38
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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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39
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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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40
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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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41
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Kavanagh ME, Gray JL, Gilbert SH, Coyne AG, McLean KJ, Davis HJ, Munro AW, Abell C. Substrate Fragmentation for the Design of M. tuberculosis CYP121 Inhibitors. ChemMedChem 2016; 11:1924-35. [PMID: 27432475 PMCID: PMC5026067 DOI: 10.1002/cmdc.201600248] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/24/2016] [Indexed: 11/11/2022]
Abstract
The cyclo-dipeptide substrates of the essential M. tuberculosis (Mtb) enzyme CYP121 were deconstructed into their component fragments and screened against the enzyme. A number of hits were identified, one of which exhibited an unexpected inhibitor-like binding mode. The inhibitory pharmacophore was elucidated, and fragment binding affinity was rapidly improved by synthetic elaboration guided by the structures of CYP121 substrates. The resulting inhibitors have low micromolar affinity, good predicted physicochemical properties and selectivity for CYP121 over other Mtb P450s. Spectroscopic characterisation of the inhibitors' binding mode provides insight into the effect of weak nitrogen-donor ligands on the P450 heme, an improved understanding of factors governing CYP121-ligand recognition and speculation into the biological role of the enzyme for Mtb.
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Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Janine L Gray
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sophie H Gilbert
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Anthony G Coyne
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of LifeSciences, The University of Manchester, Manchester, M1 7DN, UK
| | - Holly J Davis
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of LifeSciences, The University of Manchester, Manchester, M1 7DN, UK
| | - Chris Abell
- Department of Chemistry, The University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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42
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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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43
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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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44
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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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45
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Quesne MG, Borowski T, de Visser SP. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs. Chemistry 2015; 22:2562-81. [PMID: 26696271 DOI: 10.1002/chem.201503802] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Indexed: 11/08/2022]
Abstract
Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
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Affiliation(s)
- Matthew G Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland. .,Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry of the, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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46
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Gajbhiye JM, More NA, Patil MD, Ummanni R, Kotapalli SS, Yogeeswari P, Sriram D, Masand VH. Discovery of Rimonabant and its potential analogues as anti-TB drug candidates. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1346-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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48
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Chukwu JU, López C, González A, Font-Bardía M, Calvet MT, Messeguer R, Calvis C. Pd(II) complexes with N-substituted pyrazoles as ligands. The influence of the R group [OMe versus NMe2] of [1-{R–(CH2)2–}-3,5-Ph2–(C3HN2)] on their cytotoxic activity on breast cancer cell lines. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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49
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Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol 2014; 9:1528-35. [PMID: 24807704 PMCID: PMC4215856 DOI: 10.1021/cb5001636] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.
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Affiliation(s)
- Sarah Barelier
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
| | - Oliv Eidam
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
| | - Inbar Fish
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Department
of Biochemistry and Molecular Biology, George S. Wise Faculty of Life
SciencesTel-Aviv University, Ramat Aviv, Israel
| | | | | | - Ruta Nachane
- ZoBio, Eisteinweg 55, 2300-RA Leiden, The Netherlands
| | - John J. Irwin
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada M5S 3E1
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada M5S 3E1
| | - Gregg Siegal
- ZoBio, Eisteinweg 55, 2300-RA Leiden, The Netherlands
- Leiden University, Eisteinweg 55, 2300-RA Leiden, The Netherlands
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50
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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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