1
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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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Bukhdruker S, Varaksa T, Orekhov P, Grabovec I, Marin E, Kapranov I, Kovalev K, Astashkin R, Kaluzhskiy L, Ivanov A, Mishin A, Rogachev A, Gordeliy V, Gilep A, Strushkevich N, Borshchevskiy V. Structural insights into the effects of glycerol on ligand binding to cytochrome P450. Acta Crystallogr D Struct Biol 2023; 79:66-77. [PMID: 36601808 DOI: 10.1107/s2059798322011019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/16/2022] [Indexed: 01/06/2023] Open
Abstract
New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124-CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124-CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural-functional studies and impede rational drug-design campaigns.
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Affiliation(s)
- Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Kirill Kovalev
- EMBL Outstation Hamburg, c/o DESY, 22607 Hamburg, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Leonid Kaluzhskiy
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Alexis Ivanov
- Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk 220084, Belarus
| | | | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudnyy 141701, Russian Federation
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3
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Walter I, Adam S, Gentilini MV, Kany AM, Brengel C, Thomann A, Sparwasser T, Köhnke J, Hartmann RW. Structure-Activity Relationship and Mode-Of-Action Studies Highlight 1-(4-Biphenylylmethyl)-1H-imidazole-Derived Small Molecules as Potent CYP121 Inhibitors. ChemMedChem 2021; 16:2786-2801. [PMID: 34010508 PMCID: PMC8519103 DOI: 10.1002/cmdc.202100283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/29/2022]
Abstract
CYP121 of Mycobacterium tuberculosis (Mtb) is an essential target for the development of novel potent drugs against tuberculosis (TB). Besides known antifungal azoles, further compounds of the azole class were recently identified as CYP121 inhibitors with antimycobacterial activity. Herein, we report the screening of a similarity-oriented library based on the former hit compound, the evaluation of affinity toward CYP121, and activity against M. bovis BCG. The results enabled a comprehensive SAR study, which was extended through the synthesis of promising compounds and led to the identification of favorable features for affinity and/or activity and hit compounds with 2.7-fold improved potency. Mode of action studies show that the hit compounds inhibit substrate conversion and highlighted CYP121 as the main antimycobacterial target of our compounds. Exemplified complex crystal structures of CYP121 with three inhibitors reveal a common binding site. Engaging in both hydrophobic interactions as well as hydrogen bonding to the sixth iron ligand, our compounds block a solvent channel leading to the active site heme. Additionally, we report the first CYP inhibitors that are able to reduce the intracellular replication of M. bovis BCG in macrophages, emphasizing their potential as future drug candidates against TB.
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Affiliation(s)
- Isabell Walter
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Sebastian Adam
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Maria Virginia Gentilini
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Andreas M. Kany
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Christian Brengel
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Andreas Thomann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Tim Sparwasser
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Jesko Köhnke
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Rolf W. Hartmann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2.366123SaarbrückenGermany
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4
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Mukherjee G, Satpathy JK, Bagha UK, Mubarak MQE, Sastri CV, de Visser SP. Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Jagnyesh K. Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Umesh K. Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Fakulti Sains dan Teknologi, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Sam P. de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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5
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Ngcobo NS, Chiliza ZE, Chen W, Yu JH, Nelson DR, Tuszynski JA, Preto J, Syed K. Comparative Analysis, Structural Insights, and Substrate/Drug Interaction of CYP128A1 in Mycobacterium tuberculosis. Int J Mol Sci 2020; 21:E4816. [PMID: 32650369 PMCID: PMC7404182 DOI: 10.3390/ijms21144816] [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: 04/29/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s) are well known for their role in organisms' primary and secondary metabolism. Among 20 P450s of the tuberculosis-causing Mycobacterium tuberculosis H37Rv, CYP128A1 is particularly important owing to its involvement in synthesizing electron transport molecules such as menaquinone-9 (MK9). This study employs different in silico approaches to understand CYP128 P450 family's distribution and structural aspects. Genome data-mining of 4250 mycobacterial species has revealed the presence of 2674 CYP128 P450s in 2646 mycobacterial species belonging to six different categories. Contrast features were observed in the CYP128 gene distribution, subfamily patterns, and characteristics of the secondary metabolite biosynthetic gene cluster (BGCs) between M. tuberculosis complex (MTBC) and other mycobacterial category species. In all MTBC species (except one) CYP128 P450s belong to subfamily A, whereas subfamily B is predominant in another four mycobacterial category species. Of CYP128 P450s, 78% was a part of BGCs with CYP124A1, or together with CYP124A1 and CYP121A1. The CYP128 family ranked fifth in the conservation ranking. Unique amino acid patterns are present at the EXXR and CXG motifs. Molecular dynamic simulation studies indicate that the CYP128A1 bind to MK9 with the highest affinity compared to the azole drugs analyzed. This study provides comprehensive comparative analysis and structural insights of CYP128A1 in M. tuberculosis.
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Affiliation(s)
- Nokwanda Samantha Ngcobo
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.S.N.); (Z.E.C.)
| | - Zinhle Edith Chiliza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.S.N.); (Z.E.C.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Jack A. Tuszynski
- Department of Physics and Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino TO, Italy
| | - Jordane Preto
- Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69622 Lyon, France
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.S.N.); (Z.E.C.)
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6
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Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Nat Commun 2020; 11:2676. [PMID: 32472090 PMCID: PMC7260179 DOI: 10.1038/s41467-020-16500-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/07/2020] [Indexed: 01/12/2023] Open
Abstract
Cytochrome P450 monooxygenases are versatile heme-thiolate enzymes that catalyze a wide range of reactions. Self-sufficient cytochrome P450 enzymes contain the redox partners in a single polypeptide chain. Here, we present the crystal structure of full-length CYP116B46, a self-sufficient P450. The continuous polypeptide chain comprises three functional domains, which align well with the direction of electrons traveling from FMN to the heme through the [2Fe-2S] cluster. FMN and the [2Fe-2S] cluster are positioned closely, which facilitates efficient electron shuttling. The edge-to-edge straight-line distance between the [2Fe-2S] cluster and heme is approx. 25.3 Å. The role of several residues located between the [2Fe-2S] cluster and heme in the catalytic reaction is probed in mutagenesis experiments. These findings not only provide insights into the intramolecular electron transfer of self-sufficient P450s, but are also of interest for biotechnological applications of self-sufficient P450s. Self-sufficient cytochrome P450 monooxygenases, which contain all redox partners in a single polypeptide chain, are of interest for biotechnological applications. Here, the authors present the crystal structure of full-length Thermobispora bispora CYP116B46 and discuss the potential electron transfer pathway.
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7
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Wright WC, Chenge J, Wang J, Girvan HM, Yang L, Chai SC, Huber AD, Wu J, Oladimeji PO, Munro AW, Chen T. Clobetasol Propionate Is a Heme-Mediated Selective Inhibitor of Human Cytochrome P450 3A5. J Med Chem 2020; 63:1415-1433. [PMID: 31965799 PMCID: PMC7087482 DOI: 10.1021/acs.jmedchem.9b02067] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human cytochrome P450 (CYP) enzymes CYP3A4 and CYP3A5 metabolize most drugs and have high similarities in their structure and substrate preference. Whereas CYP3A4 is predominantly expressed in the liver, CYP3A5 is upregulated in cancer, contributing to drug resistance. Selective inhibitors of CYP3A5 are, therefore, critical to validating it as a therapeutic target. Here we report clobetasol propionate (clobetasol) as a potent and selective CYP3A5 inhibitor identified by high-throughput screening using enzymatic and cell-based assays. Molecular dynamics simulations suggest a close proximity of clobetasol to the heme in CYP3A5 but not in CYP3A4. UV-visible spectroscopy and electron paramagnetic resonance analyses confirmed the formation of an inhibitory type I heme-clobetasol complex in CYP3A5 but not in CYP3A4, thus explaining the CYP3A5 selectivity of clobetasol. Our results provide a structural basis for selective CYP3A5 inhibition, along with mechanistic insights, and highlight clobetasol as an important chemical tool for target validation.
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Affiliation(s)
- William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
- Integrated Biomedical Sciences Program, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jude Chenge
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jingheng Wang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Hazel M. Girvan
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Sergio C. Chai
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Peter O. Oladimeji
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
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8
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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: 12] [Impact Index Per Article: 2.4] [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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9
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Qiao B, Lopez L, Olvera de la Cruz M. “Mirror”-like Protein Dimers Stabilized by Local Heterogeneity at Protein Surfaces. J Phys Chem B 2019; 123:3907-3915. [DOI: 10.1021/acs.jpcb.9b01394] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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10
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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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11
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Di Nardo G, Cimicata G, Baravalle R, Dell'Angelo V, Ciaramella A, Catucci G, Ugliengo P, Gilardi G. Working at the membrane interface: Ligand-induced changes in dynamic conformation and oligomeric structure in human aromatase. Biotechnol Appl Biochem 2017; 65:46-53. [DOI: 10.1002/bab.1613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/14/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology; University of Torino; Torino Italy
- CrisDi; Interdepartmental Center for Crystallography; Torino Italy
| | - Giuseppe Cimicata
- Department of Life Sciences and Systems Biology; University of Torino; Torino Italy
| | - Roberta Baravalle
- Department of Life Sciences and Systems Biology; University of Torino; Torino Italy
| | | | - Alberto Ciaramella
- Department of Life Sciences and Systems Biology; University of Torino; Torino Italy
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology; University of Torino; Torino Italy
| | - Piero Ugliengo
- Department of Chemistry; University of Torino; Torino Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology; University of Torino; Torino Italy
- CrisDi; Interdepartmental Center for Crystallography; Torino Italy
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12
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Lampe JN. Advances in the Understanding of Protein-Protein Interactions in Drug Metabolizing Enzymes through the Use of Biophysical Techniques. Front Pharmacol 2017; 8:521. [PMID: 28848438 PMCID: PMC5550701 DOI: 10.3389/fphar.2017.00521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
In recent years, a growing appreciation has developed for the importance of protein-protein interactions to modulate the function of drug metabolizing enzymes. Accompanied with this appreciation, new methods and technologies have been designed for analyzing protein-protein interactions both in vitro and in vivo. These technologies have been applied to several classes of drug metabolizing enzymes, including: cytochrome P450's (CYPs), monoamine oxidases (MAOs), UDP-glucuronosyltransferases (UGTs), glutathione S-transferases (GSTs), and sulfotransferases (SULTs). In this review, we offer a brief description and assessment of the impact of many of these technologies to the study of protein-protein interactions in drug disposition. The still expanding list of these techniques and assays has the potential to revolutionize our understanding of how these enzymes carry out their important functions in vivo.
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Affiliation(s)
- Jed N Lampe
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical CenterKansas City, MO, United States
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13
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Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1. Biochemistry 2017; 56:1559-1572. [PMID: 28169518 DOI: 10.1021/acs.biochem.6b00954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Similarity between the ligand binding profiles of enzymes may aid functional characterization and be of greater relevance to inhibitor development than sequence similarity or structural homology. Fragment screening is an efficient approach for characterization of the ligand binding profile of an enzyme and has been applied here to study the family of cytochrome P450 enzymes (P450s) expressed by Mycobacterium tuberculosis (Mtb). The Mtb P450s have important roles in bacterial virulence, survival, and pathogenicity. Comparing the fragment profiles of seven of these enzymes revealed that P450s which share a similar biological function have significantly similar fragment profiles, whereas functionally unrelated or orphan P450s exhibit distinct ligand binding properties, despite overall high structural homology. Chemical structures that exhibit promiscuous binding between enzymes have been identified, as have selective fragments that could provide leads for inhibitor development. The similarity between the fragment binding profiles of the orphan enzyme CYP144A1 and CYP121A1, a characterized enzyme that is important for Mtb viability, provides a case study illustrating the subsequent identification of novel CYP144A1 ligands. The different binding modes of these compounds to CYP144A1 provide insight into structural and dynamic aspects of the enzyme, possible biological function, and provide the opportunity to develop inhibitors. Expanding this fragment profiling approach to include a greater number of functionally characterized and orphan proteins may provide a valuable resource for understanding enzyme-ligand interactions.
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Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jude Chenge
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Azedine Zoufir
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andreas Bender
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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