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Mohamed MA, Awadalla MKA, Mohamed MS, Elsaman T, Eltayib EM. Repurposing FDA-Approved Drugs for Eumycetoma Treatment: Homology Modeling and Computational Screening of CYP51 Inhibitors. Int J Mol Sci 2025; 26:315. [PMID: 39796172 PMCID: PMC11720416 DOI: 10.3390/ijms26010315] [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: 12/05/2024] [Revised: 12/28/2024] [Accepted: 12/29/2024] [Indexed: 01/13/2025] Open
Abstract
Eumycetoma, a chronic fungal infection caused by Madurella mycetomatis, is a neglected tropical disease characterized by tumor-like growths that can lead to permanent disability and deformities if untreated. Predominantly affecting regions in Africa, South America, and Asia, it imposes significant physical, social, and economic burdens. Current treatments, including antifungal drugs like itraconazole, often show variable efficacy, with severe cases necessitating surgical intervention or amputation. Drug discovery for eumycetoma faces challenges due to limited understanding of the disease's molecular mechanisms and the lack of 3D structures for key targets such as Madurella mycetomatis CYP51, a well-known target for azoles' antifungal agents. To address these challenges, this study employed computational approaches, including homology modeling, virtual screening, free energy calculations, and molecular dynamics simulations, to repurpose FDA-approved drugs as potential treatments for eumycetoma targeting Madurella mycetomatis CYP51. To this end, a library of 2619 FDA-approved drugs was screened, identifying three promising candidates: montelukast, vilanterol, and lidoflazine. These compounds demonstrated favorable binding affinities, strong interactions with critical residues of the homology model of Madurella mycetomatis CYP51, and stability in molecular dynamics simulations, offering potential for further investigation as effective therapeutic options for eumycetoma.
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Affiliation(s)
- Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | | | - Malik Suliman Mohamed
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia; (M.S.M.); (E.M.E.)
| | - Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Eyman Mohamed Eltayib
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia; (M.S.M.); (E.M.E.)
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2
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McCarty KD, Sullivan ME, Tateishi Y, Hargrove TY, Lepesheva GI, Guengerich FP. Processive kinetics in the three-step lanosterol 14α-demethylation reaction catalyzed by human cytochrome P450 51A1. J Biol Chem 2023; 299:104841. [PMID: 37209823 PMCID: PMC10285260 DOI: 10.1016/j.jbc.2023.104841] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Cytochrome P450 (P450, CYP) family 51 enzymes catalyze the 14α-demethylation of sterols, leading to critical products used for membranes and the production of steroids, as well as signaling molecules. In mammals, P450 51 catalyzes the 3-step, 6-electron oxidation of lanosterol to form (4β,5α)-4,4-dimethyl-cholestra-8,14,24-trien-3-ol (FF-MAS). P450 51A1 can also use 24,25-dihydrolanosterol (a natural substrate in the Kandutsch-Russell cholesterol pathway). 24,25-Dihydrolanosterol and the corresponding P450 51A1 reaction intermediates, the 14α-alcohol and -aldehyde derivatives of dihydrolanosterol, were synthesized to study the kinetic processivity of the overall 14α-demethylation reaction of human P450 51A1. A combination of steady-state kinetic parameters, steady-state binding constants, dissociation rates of P450-sterol complexes, and kinetic modeling of the time course of oxidation of a P450-dihydrolanosterol complex showed that the overall reaction is highly processive, with koff rates of P450 51A1-dihydrolanosterol and the 14α-alcohol and 14α-aldehyde complexes being 1 to 2 orders of magnitude less than the forward rates of competing oxidations. epi-Dihydrolanosterol (the 3α-hydroxy analog) was as efficient as the common 3β-hydroxy isomer in the binding and formation of dihydro FF-MAS. The common lanosterol contaminant dihydroagnosterol was found to be a substrate of human P450 51A1, with roughly one-half the activity of dihydrolanosterol. Steady-state experiments with 14α-methyl deuterated dihydrolanosterol showed no kinetic isotope effect, indicating that C-14α C-H bond breaking is not rate-limiting in any of the individual steps. The high processivity of this reaction generates higher efficiency and also renders the reaction less sensitive to inhibitors.
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Affiliation(s)
- Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Molly E Sullivan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yasuhiro Tateishi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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3
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Abuelizz HA, Bakheit AH, Al-Agamy MH, Rashid H, Mostafa GA, Al-Salahi R. Benzo[ g]quinazolines as antifungal against candidiasis: Screening, molecular docking, and QSAR investigations. Saudi Pharm J 2023; 31:815-823. [PMID: 37228321 PMCID: PMC10203769 DOI: 10.1016/j.jsps.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/10/2023] [Indexed: 05/27/2023] Open
Abstract
Candida albicans, an opportunistic pathogen, is the most common type of fungus and represents a substantial source of human invasive disease (nosocomial infection). This category of fungi are part of our microbiota, and given the appropriate environmental conditions, it has the potential to cause both superficial and systemic infections. There is a soaring resistance against the available anticandidal agents. The purpose of this research is to investigate the activity of certain previously synthesized benzo[g]quinazolines against C. albicans in vitro by using the cup-plate diffusion method. There was a marked difference in the effectiveness of the target compounds 1-6 against the sample of C. albicans that was tested. Benzo[g]quinazolines 1 (inhibition zone = 20 mm) and 2 (inhibition zone = 22 mm) had good effects in comparison to fluconazole (inhibition zone = 26 mm). A docking study was conducted between benzo[g]quinazolines 1-6 and Candida spp. CYP51 to establish the binding mode compared with fluconazole and VT-1161 (oteseconazole) as reference medicines, and it was determined that binding at the active site of Candida spp. CYP51 occurred in the same manner. Quantitative structure-activity relationship (QSAR) investigation was performed to further characterize the identified anticandidal agents and recognize the major regulatory components governing such activity. In future studies, the benzo[g]quinazoline scaffold could serve as a model for the design and development of novel derivatives with antifungal potential.
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Affiliation(s)
- Hatem A. Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Harunor Rashid
- National Centre for Immunisation Research and Surveillance (NCIRS), Kids Research at The Children’s Hospital, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Gamal A.E. Mostafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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4
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Permana D, Kitaoka T, Ichinose H. Conversion and synthesis of chemicals catalyzed by fungal cytochrome P450 monooxygenases: A review. Biotechnol Bioeng 2023. [PMID: 37139574 DOI: 10.1002/bit.28411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Cytochrome P450s (also called CYPs or P450s) are a superfamily of heme-containing monooxygenases. They are distributed in all biological kingdoms. Most fungi have at least two P450-encoding genes, CYP51 and CYP61, which are housekeeping genes that play important roles in the synthesis of sterols. However, the kingdom fungi is an interesting source of numerous P450s. Here, we review reports on fungal P450s and their applications in the bioconversion and biosynthesis of chemicals. We highlight their history, availability, and versatility. We describe their involvement in hydroxylation, dealkylation, oxygenation, C═C epoxidation, C-C cleavage, C-C ring formation and expansion, C-C ring contraction, and uncommon reactions in bioconversion and/or biosynthesis pathways. The ability of P450s to catalyze these reactions makes them promising enzymes for many applications. Thus, we also discuss future prospects in this field. We hope that this review will stimulate further study and exploitation of fungal P450s for specific reactions and applications.
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Research Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia (Badan Riset dan Inovasi Nasional (BRIN)), Bandung Advanced Science and Creative Engineering Space (BASICS), Kawasan Sains dan Teknologi (KST) Prof. Dr. Samaun Samadikun, Bandung, Indonesia
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Dutra JAP, Maximino SC, Gonçalves RDCR, Morais PAB, de Lima Silva WC, Rodrigues RP, Neto ÁC, Júnior VL, de Souza Borges W, Kitagawa RR. Anti-Candida, docking studies, and in vitro metabolism-mediated cytotoxicity evaluation of Eugenol derivatives. Chem Biol Drug Des 2023; 101:350-363. [PMID: 36053023 DOI: 10.1111/cbdd.14131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/14/2022] [Indexed: 01/14/2023]
Abstract
The high morbidity and mortality rates of Candida infections, especially among immunocompromised patients, are related to the increased resistance rate of these species and the limited therapeutic arsenal. In this context, we evaluated the anti-Candida potential and the cytotoxic profile of eugenol derivatives. Anti-Candida activity was evaluated on C. albicans and C. parapsilosis strains by minimum inhibitory concentration (MIC), scanning electron microscopy (SEM), and molecular docking calculations at the site of the enzyme lanosterol-14-α-demethylase active site, responsible for ergosterol formation. The cytotoxic profile was evaluated in HepG2 cells, in the presence and absence of the metabolizing system (S9 system). The results indicated compounds 1b and 1d as the most active ones. The compounds have anti-Candida activity against both strains with MIC ranging from 50 to 100 μg ml-1 . SEM analyses of 1b and 1d indicated changes in the envelope architecture of both C. albicans and C. parapsilosis like the ones of eugenol and fluconazole, respectively. Docking results of the evaluated compounds indicated a similar binding pattern of fluconazole and posaconazole at the lanosterol-14-α-demethylase binding site. In the presence of the S9 system, compound 1b showed the same cytotoxicity profile as fluconazole (1.08 times) and compound 1d had 1.23 times increase in cytotoxicity. Eugenol and other evaluated compounds showed a significant increase in cytotoxicity. Our results suggest compound 1b as a promising starting point candidate to be used in the design of new anti-Candida agent prototypes.
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Affiliation(s)
- Jessyca Aparecida Paes Dutra
- Graduate Program of Pharmaceutical Sciences, Health Sciences Center, Federal University of Espírito Santo, Bonfim, Brazil
| | - Sarah Canal Maximino
- Graduate Program of Pharmaceutical Sciences, Health Sciences Center, Federal University of Espírito Santo, Bonfim, Brazil
| | | | - Pedro Alves Bezerra Morais
- Department of Chemistry and Physics, Exact, Natural and Health Sciences Center, Federal University of Espírito Santo, Guararema, Brazil
| | | | - Ricardo Pereira Rodrigues
- Graduate Program of Pharmaceutical Sciences, Health Sciences Center, Federal University of Espírito Santo, Bonfim, Brazil
| | - Álvaro Cunha Neto
- Department of Chemistry, Exact Sciences Center, Federal University of Espírito Santo, Goiabeiras, Brazil
| | - Valdemar Lacerda Júnior
- Department of Chemistry, Exact Sciences Center, Federal University of Espírito Santo, Goiabeiras, Brazil
| | - Warley de Souza Borges
- Department of Chemistry, Exact Sciences Center, Federal University of Espírito Santo, Goiabeiras, Brazil
| | - Rodrigo Rezende Kitagawa
- Graduate Program of Pharmaceutical Sciences, Health Sciences Center, Federal University of Espírito Santo, Bonfim, Brazil
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6
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Churchman LR, Salisbury LJ, De Voss JJ. Synthesis of obtusifoliol and analogues as CYP51 substrates. Org Biomol Chem 2022; 20:7316-7324. [PMID: 36069327 DOI: 10.1039/d2ob01307j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sterol 14α-demethylases (CYP51s) are a ubiquitous superfamily of cytochrome P450 enzymes that play an essential role in sterol biosynthesis. As fungal CYP51s are the target of azole-based antifungal agents, which are facing the problem of increasing resistance, the substrate specificity of this enzyme subclass has recently garnered significant attention. Herein we report the first chemical synthesis of the final endogenous substrate of this enzyme class, obtusifoliol, in 1.3% yield across ten steps from a commercially available lanosterol mixture. Intermediates along this pathway provide a basis for further derivatisation of the sterol skeleton and future investigation into CYP51 inhibition to overcome pathogens' azole resistance.
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Affiliation(s)
- Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Lauren J Salisbury
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4072, Australia.
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Foudah AI, Alqarni MH, Alam A, Salkini MA, Ross SA, Yusufoglu HS. Phytochemical Screening, In Vitro and In Silico Studies of Volatile Compounds from Petroselinum crispum (Mill) Leaves Grown in Saudi Arabia. Molecules 2022; 27:molecules27030934. [PMID: 35164196 PMCID: PMC8840193 DOI: 10.3390/molecules27030934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
The herbal plant Petroselinum crispum (P. crispum) (Mill) is commonly available around the world. In this study, the leaves of the herbal plant P. crispum were collected from the central region of Al-Kharj, Saudi Arabia, to explore their in vitro pharmacological activity. Essential oil from the leaves of P. crispum was isolated using the hydrodistillation method. The composition of P. crispum essential oil (PCEO) was determined using Gas chromatography-mass spectrometry (GC-MS). A total of 67 components were identified, representing approximately 96.02% of the total volatile composition. Myristicin was identified as the principal constituent (41.45%). The in vitro biological activity was assessed to evaluate the antioxidant, antimicrobial, and anti-inflammatory potential of PCEO. PCEO showed the highest antimicrobial activity against Candida albicans and Staphylococcus aureus among all the evaluated microbial species. In vitro anti-inflammatory evaluation using albumin and trypsin assays showed the excellent anti-inflammatory potential of PCEO compared to the standard drugs. An in silico study of the primary PCEO compound was conducted using online tools such as PASS, Swiss ADME, and Molecular docking. In silico PASS prediction results supported our in vitro findings. Swiss ADME revealed the drug likeness and safety properties of the major metabolites present in PCEO. Molecular docking results were obtained by studying the interaction of Myristicin with an antifungal (PDB: 1IYL and 3LD6), antibacterial (PDB: 1AJ6 and 1JIJ), antioxidant (PDB: 3NM8 and 1HD2), and anti-inflammatory (3N8Y and 3LN1) receptors supported the in vitro results. Therefore, PCEO or Myristicin might be valuable for developing anti-inflammatory and antimicrobial drugs.
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Affiliation(s)
- Ahmed I. Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
- Correspondence:
| | - Mohammad H. Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
| | - Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
| | - Mohammad Ayman Salkini
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia; (M.H.A.); (A.A.); (M.A.S.)
| | - Samir A. Ross
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, University, MS 38677, USA;
- Department of Biomolecular Sciences, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Hasan S. Yusufoglu
- Department of Pharmacognosy & Pharmaceutical Chemistry, College of Dentistry & Pharmacy, Buraydah Private College, Buraydah 81418, Saudi Arabia;
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8
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Madan B, Virshup DM, Nes WD, Leaver DJ. Unearthing the Janus-face cholesterogenesis pathways in cancer. Biochem Pharmacol 2021; 196:114611. [PMID: 34010597 DOI: 10.1016/j.bcp.2021.114611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022]
Abstract
Cholesterol biosynthesis, primarily associated with eukaryotes, occurs as an essential component of human metabolism with biosynthetic deregulation a factor in cancer viability. The segment that partitions between squalene and the C27-end cholesterol yields the main cholesterogenesis branch subdivided into the Bloch and Kandutsch-Russell pathways. Their importance in cell viability, in normal growth and development originates primarily from the amphipathic property and shape of the cholesterol molecule which makes it suitable as a membrane insert. Cholesterol can also convert to variant oxygenated product metabolites of distinct function producing a complex interplay between cholesterol synthesis and overall steroidogenesis. In this review, we disassociate the two sides of cholesterogenesisis affecting the type and amounts of systemic sterols-one which is beneficial to human welfare while the other dysfunctional leading to misery and disease that could result in premature death. Our focus here is first to examine the cholesterol biosynthetic genes, enzymes, and order of biosynthetic intermediates in human cholesterogenesis pathways, then compare the effect of proximal and distal inhibitors of cholesterol biosynthesis against normal and cancer cell growth and metabolism. Collectively, the inhibitor studies of druggable enzymes and specific biosynthetic steps, suggest a potential role of disrupted cholesterol biosynthesis, in coordination with imported cholesterol, as a factor in cancer development and as discussed some of these inhibitors have chemotherapeutic implications.
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Affiliation(s)
- Babita Madan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore; Department of Pediatrics, Duke University, Durham, NC, USA
| | - W David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
| | - David J Leaver
- Department of Biology, Geology, and Physical Sciences, Sul Ross State University, Alpine, TX, USA.
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9
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Dorababu A. Pharmacology Profile of Recently Developed Multi‐Functional Azoles; SAR‐Based Predictive Structural Modification. ChemistrySelect 2020. [DOI: 10.1002/slct.202000294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Atukuri Dorababu
- Department of Studies in ChemistrySRMPP Govt. First Grade College Huvinahadagali 583219, Karnataka India
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10
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Jović O, Šmuc T. Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides. Molecules 2020; 25:molecules25092198. [PMID: 32397151 PMCID: PMC7249108 DOI: 10.3390/molecules25092198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
Novel machine learning and molecular modelling filtering procedures for drug repurposing have been carried out for the recognition of the novel fungicide targets of Cyp51 and Erg2. Classification and regression approaches on molecular descriptors have been performed using stepwise multilinear regression (FS-MLR), uninformative-variable elimination partial-least square regression, and a non-linear method called Forward Stepwise Limited Correlation Random Forest (FS-LM-RF). Altogether, 112 prediction models from two different approaches have been built for the descriptor recognition of fungicide hit compounds. Aiming at the fungal targets of sterol biosynthesis in membranes, antifungal hit compounds have been selected for docking experiments from the Drugbank database using the Autodock4 molecular docking program. The results were verified by Gold Protein-Ligand Docking Software. The best-docked conformation, for each high-scored ligand considered, was submitted to quantum mechanics/molecular mechanics (QM/MM) gradient optimization with final single point calculations taking into account both the basis set superposition error and thermal corrections (with frequency calculations). Finally, seven Drugbank lead compounds were selected based on their high QM/MM scores for the Cyp51 target, and three were selected for the Erg2 target. These lead compounds could be recommended for further in vitro studies.
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Scotti MT, Monteiro AFM, de Oliveira Viana J, Bezerra Mendonça Junior FJ, Ishiki HM, Tchouboun EN, De Araújo RSA, Scotti L. Recent Theoretical Studies Concerning Important Tropical Infections. Curr Med Chem 2020; 27:795-834. [DOI: 10.2174/0929867326666190711121418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated
with poverty, flourish in impoverished environments, and thrive best in tropical areas,
where they tend to present overlap. They comprise several diseases, and the symptoms
vary dramatically from disease to disease, often causing from extreme pain, and untold misery
that anchors populations to poverty, permanent disability, and death. They affect more than 1
billion people worldwide; mostly in poor populations living in tropical and subtropical climates.
In this review, several complementary in silico approaches are presented; including
identification of new therapeutic targets, novel mechanisms of activity, high-throughput
screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship
and recent molecular docking studies. Current and active research against Sleeping
Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully
lead to safer, more effective, less costly and more widely available treatments against
these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.
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Affiliation(s)
- Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | | | - Hamilton M. Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos A. De Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
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12
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Ramdass AC, Villafana RT, Rampersad SN. Comparative Sequence Analysis of TRI1 of Fusarium. Toxins (Basel) 2019; 11:E689. [PMID: 31771208 PMCID: PMC6950058 DOI: 10.3390/toxins11120689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Trichothecene mycotoxins are a class of secondary metabolites produced by multiple genera of fungi, including certain plant pathogenic Fusarium species. Functional variation in the TRI1 gene produces a novel Type A trichothecene called NX-2 in strains of F. graminearum. Using a bioinformatics approach, a systematic analysis of 52 translated TRI1 sequences of Fusarium species, including five F. graminearum NX-2 producers and four F. graminearum non-NX-2 producers, was conducted to explain the functional difference of TRI1p of FGNX-2. An assessment of several signature motifs of fungal P450s revealed amino acid substitutions in addition to the post-translational N-X-S/T sequons motif, which is indicative of N-linked glycosylation of this TRI1-encoded protein characteristic of NX-2 producers. There was evidence of selection bias, where TRI1 gene sequences were found to be under positive selection and, therefore, under functional constraints. The cumulative amino acid changes in the TRI1p sequences were reflected in the phylogenetic analyses which revealed species-specific clustering with a distinct separation of FGNX-2 from FG-non-NX-2 producers with high bootstrap support. Together, our findings provide insight into the amino acid sequence features responsible for the functional diversification of this TRI1p.
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13
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Villalta F, Rachakonda G. Advances in preclinical approaches to Chagas disease drug discovery. Expert Opin Drug Discov 2019; 14:1161-1174. [PMID: 31411084 PMCID: PMC6779130 DOI: 10.1080/17460441.2019.1652593] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 12/21/2022]
Abstract
Introduction: Chagas disease affects 8-10 million people worldwide, mainly in Latin America. The current therapy for Chagas disease is limited to nifurtimox and benznidazole, which are effective in treating only the acute phase of the disease but with severe side effects. Therefore, there is an unmet need for new drugs and for the exploration of innovative approaches which may lead to the discovery of new effective and safe drugs for its treatment. Areas covered: The authors report and discuss recent approaches including structure-based design that have led to the discovery of new promising small molecule candidates for Chagas disease which affect prime targets that intervene in the sterol pathway of T. cruzi. Other trypanosome targets, phenotypic screening, the use of artificial intelligence and the challenges with Chagas disease drug discovery are also discussed. Expert opinion: The application of recent scientific innovations to the field of Chagas disease have led to the discovery of new promising drug candidates for Chagas disease. Phenotypic screening brought new hits and opportunities for drug discovery. Artificial intelligence also has the potential to accelerate drug discovery in Chagas disease and further research into this is warranted.
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Affiliation(s)
- Fernando Villalta
- Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College , Nashville , TN , USA
| | - Girish Rachakonda
- Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College , Nashville , TN , USA
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14
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Khare SP, Deshmukh TR, Akolkar SV, Sangshetti JN, Khedkar VM, Shingate BB. New 1,2,3-triazole-linked tetrahydrobenzo[b]pyran derivatives: Facile synthesis, biological evaluation and molecular docking study. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-019-03906-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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15
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Rendic SP, Peter Guengerich F. Human cytochrome P450 enzymes 5-51 as targets of drugs and natural and environmental compounds: mechanisms, induction, and inhibition - toxic effects and benefits. Drug Metab Rev 2019; 50:256-342. [PMID: 30717606 DOI: 10.1080/03602532.2018.1483401] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytochrome P450 (P450, CYP) enzymes have long been of interest due to their roles in the metabolism of drugs, pesticides, pro-carcinogens, and other xenobiotic chemicals. They have also been of interest due to their very critical roles in the biosynthesis and metabolism of steroids, vitamins, and certain eicosanoids. This review covers the 22 (of the total of 57) human P450s in Families 5-51 and their substrate selectivity. Furthermore, included is information and references regarding inducibility, inhibition, and (in some cases) stimulation by chemicals. We update and discuss important aspects of each of these 22 P450s and questions that remain open.
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Affiliation(s)
| | - F Peter Guengerich
- b Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , TN , USA
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16
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Zhou W, Ramos E, Zhu X, Fisher PM, Kidane ME, Vanderloop BH, Thomas CD, Yan J, Singha U, Chaudhuri M, Nagel MT, Nes WD. Steroidal antibiotics are antimetabolites of Acanthamoeba steroidogenesis with phylogenetic implications. J Lipid Res 2019; 60:981-994. [PMID: 30709898 PMCID: PMC6495176 DOI: 10.1194/jlr.m091587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/22/2019] [Indexed: 12/28/2022] Open
Abstract
Pathogenic organisms may be sensitive to inhibitors of sterol biosynthesis, which carry antimetabolite properties, through manipulation of the key enzyme, sterol methyltransferase (SMT). Here, we isolated natural suicide substrates of the ergosterol biosynthesis pathway, cholesta-5,7,22,24-tetraenol (CHT) and ergosta-5,7,22,24(28)-tetraenol (ERGT), and demonstrated their interference in Acanthamoeba castellanii steroidogenesis: CHT and ERGT inhibit trophozoite growth (EC50 of 51 nM) without affecting cultured human cell growth. Washout experiments confirmed that the target for vulnerability was SMT. Chemical, kinetic, and protein-binding studies of inhibitors assayed with 24-AcSMT [catalyzing C28-sterol via Δ24(28)-olefin production] and 28-AcSMT [catalyzing C29-sterol via Δ25(27)-olefin production] revealed interrupted partitioning and irreversible complex formation from the conjugated double bond system in the side chain of either analog, particularly with 28-AcSMT. Replacement of active site Tyr62 with Phe or Leu residues involved in cation-π interactions that model product specificity prevented protein inactivation. The alkylating properties and high selective index of 103 for CHT and ERGT against 28-AcSMT are indicative of a new class of steroidal antibiotic that, as an antimetabolite, can limit sterol expansion across phylogeny and provide a novel scaffold in the design of amoebicidal drugs. Animal studies of these suicide substrates can further explore the potential of their antibiotic properties.
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Affiliation(s)
- Wenxu Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Emilio Ramos
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Xunlu Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Paxtyn M Fisher
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Medhanie E Kidane
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Boden H Vanderloop
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Crista D Thomas
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Juqiang Yan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Ujjal Singha
- Department of Microbiology and Immunology Meharry Medical College, Nashville, TN 37208
| | - Minu Chaudhuri
- Department of Microbiology and Immunology Meharry Medical College, Nashville, TN 37208
| | - Michael T Nagel
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - W David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409.
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Duschak VG. Major Kinds of Drug Targets in Chagas Disease or American Trypanosomiasis. Curr Drug Targets 2019; 20:1203-1216. [PMID: 31020939 DOI: 10.2174/1389450120666190423160804] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 11/22/2022]
Abstract
American Trypanosomiasis, a parasitic infection commonly named Chagas disease, affects millions of people all over Latin American countries. Presently, the World Health Organization (WHO) predicts that the number of international infected individuals extends to 7 to 8 million, assuming that more than 10,000 deaths occur annually. The transmission of the etiologic agent, Trypanosoma cruzi, through people migrating to non-endemic world nations makes it an emergent disease. The best promising targets for trypanocidal drugs may be classified into three main groups: Group I includes the main molecular targets that are considered among specific enzymes involved in the essential processes for parasite survival, principally Cruzipain, the major antigenic parasite cysteine proteinase. Group II involves biological pathways and their key specific enzymes, such as Sterol biosynthesis pathway, among others, specific antioxidant defense mechanisms, and bioenergetics ones. Group III includes the atypical organelles /structures present in the parasite relevant clinical forms, which are absent or considerably different from those present in mammals and biological processes related to them. These can be considered potential targets to develop drugs with extra effectiveness and fewer secondary effects than the currently used therapeutics. An improved distinction between the host and the parasite targets will help fight against this neglected disease.
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Affiliation(s)
- Vilma G Duschak
- National Council of Scientific and Technical Reasearch (CONICET) Researcher, Area of Protein Biochemistry and Parasite Glycobiology, Research Department, National Institute of Parasitology (INP), "Dr. Mario Fatala Chaben", ANLIS-Malbran, National Health Secretary, Av. Paseo Colon 568, Lab 506, Ciudad Autonoma de Buenos Aires (1063), Buenos Aires, Argentina
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18
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Elevated cellular cholesterol in Familial Alzheimer's presenilin 1 mutation is associated with lipid raft localization of β-amyloid precursor protein. PLoS One 2019; 14:e0210535. [PMID: 30682043 PMCID: PMC6347419 DOI: 10.1371/journal.pone.0210535] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/26/2018] [Indexed: 11/30/2022] Open
Abstract
Familial Alzheimer’s disease (FAD)-associated presenilin 1 (PS1) serves as a catalytic subunit of γ-secretase complex, which mediates the proteolytic liberation of β-amyloid (Aβ) from β-amyloid precursor protein (APP). In addition to its proteolytic role, PS1 is involved in non-proteolytic functions such as protein trafficking and ion channel regulation. Furthermore, postmortem AD brains as well as AD patients showed dysregulation of cholesterol metabolism. Since cholesterol has been implicated in regulating Aβ production, we investigated whether the FAD PS1-associated cholesterol elevation could influence APP processing. We found that in CHO cells stably expressing FAD-associated PS1 ΔE9, total cholesterol levels are elevated compared to cells expressing wild-type PS1. We also found that localization of APP in cholesterol-enriched lipid rafts is substantially increased in the mutant cells. Reducing the cholesterol levels by either methyl-β-cyclodextrin or an inhibitor of CYP51, an enzyme mediating the elevated cholesterol in PS1 ΔE9-expressing cells, significantly reduced lipid raft-associated APP. In contrast, exogenous cholesterol increased lipid raft-associated APP. These data suggest that in the FAD PS1 ΔE9 cells, the elevated cellular cholesterol level contributes to the altered APP processing by increasing APP localized in lipid rafts.
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Lepesheva GI, Friggeri L, Waterman MR. CYP51 as drug targets for fungi and protozoan parasites: past, present and future. Parasitology 2018; 145:1820-1836. [PMID: 29642960 PMCID: PMC6185833 DOI: 10.1017/s0031182018000562] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The efficiency of treatment of human infections with the unicellular eukaryotic pathogens such as fungi and protozoa remains deeply unsatisfactory. For example, the mortality rates from nosocomial fungemia in critically ill, immunosuppressed or post-cancer patients often exceed 50%. A set of six systemic clinical azoles [sterol 14α-demethylase (CYP51) inhibitors] represents the first-line antifungal treatment. All these drugs were discovered empirically, by monitoring their effects on fungal cell growth, though it had been proven that they kill fungal cells by blocking the biosynthesis of ergosterol in fungi at the stage of 14α-demethylation of the sterol nucleus. This review briefs the history of antifungal azoles, outlines the situation with the current clinical azole-based drugs, describes the attempts of their repurposing for treatment of human infections with the protozoan parasites that, similar to fungi, also produce endogenous sterols, and discusses the most recently acquired knowledge on the CYP51 structure/function and inhibition. It is our belief that this information should be helpful in shifting from the traditional phenotypic screening to the actual target-driven drug discovery paradigm, which will rationalize and substantially accelerate the development of new, more efficient and pathogen-oriented CYP51 inhibitors.
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Affiliation(s)
- Galina I. Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Laura Friggeri
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Michael R. Waterman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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20
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Hargrove TY, Wawrzak Z, Fisher PM, Child SA, Nes WD, Guengerich FP, Waterman MR, Lepesheva GI. Binding of a physiological substrate causes large-scale conformational reorganization in cytochrome P450 51. J Biol Chem 2018; 293:19344-19353. [PMID: 30327430 DOI: 10.1074/jbc.ra118.005850] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/15/2018] [Indexed: 11/06/2022] Open
Abstract
Sterol 14α-demethylases (CYP51s) are phylogenetically the most conserved cytochromes P450, and their three-step reaction is crucial for biosynthesis of sterols and serves as a leading target for clinical and agricultural antifungal agents. The structures of several (bacterial, protozoan, fungal, and human) CYP51 orthologs, in both the ligand-free and inhibitor-bound forms, have been determined and have revealed striking similarity at the secondary and tertiary structural levels, despite having low sequence identity. Moreover, in contrast to many of the substrate-promiscuous, drug-metabolizing P450s, CYP51 structures do not display substantial rearrangements in their backbones upon binding of various inhibitory ligands, essentially representing a snapshot of the ligand-free sterol 14α-demethylase. Here, using the obtusifoliol-bound I105F variant of Trypanosoma cruzi CYP51, we report that formation of the catalytically competent complex with the physiological substrate triggers a large-scale conformational switch, dramatically reshaping the enzyme active site (3.5-6.0 Å movements in the FG arm, HI arm, and helix C) in the direction of catalysis. Notably, our X-ray structural analyses revealed that the substrate channel closes, the proton delivery route opens, and the topology and electrostatic potential of the proximal surface reorganize to favor interaction with the electron-donating flavoprotein partner, NADPH-cytochrome P450 reductase. Site-directed mutagenesis of the amino acid residues involved in these events revealed a key role of active-site salt bridges in contributing to the structural dynamics that accompanies CYP51 function. Comparative analysis of apo-CYP51 and its sterol-bound complex provided key conceptual insights into the molecular mechanisms of CYP51 catalysis, functional conservation, lineage-specific substrate complementarity, and druggability differences.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439
| | - Paxtyn M Fisher
- the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, and
| | - Stella A Child
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - W David Nes
- the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, and
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Michael R Waterman
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Galina I Lepesheva
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, .,the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
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21
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Synthesis and Biological Activity of Sterol 14α-Demethylase and Sterol C24-Methyltransferase Inhibitors. Molecules 2018; 23:molecules23071753. [PMID: 30018257 PMCID: PMC6099924 DOI: 10.3390/molecules23071753] [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: 06/20/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 11/17/2022] Open
Abstract
Sterol 14α-demethylase (SDM) is essential for sterol biosynthesis and is the primary molecular target for clinical and agricultural antifungals. SDM has been demonstrated to be a valid drug target for antiprotozoal therapies, and much research has been focused on using SDM inhibitors to treat neglected tropical diseases such as human African trypanosomiasis (HAT), Chagas disease, and leishmaniasis. Sterol C24-methyltransferase (24-SMT) introduces the C24-methyl group of ergosterol and is an enzyme found in pathogenic fungi and protozoa but is absent from animals. This difference in sterol metabolism has the potential to be exploited in the development of selective drugs that specifically target 24-SMT of invasive fungi or protozoa without adversely affecting the human or animal host. The synthesis and biological activity of SDM and 24-SMT inhibitors are reviewed herein.
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22
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Vijayakumar S, Das P. Structural, molecular motions, and free-energy landscape of Leishmania sterol-14α-demethylase wild type and drug resistant mutant: a comparative molecular dynamics study. J Biomol Struct Dyn 2018; 37:1477-1493. [PMID: 29620481 DOI: 10.1080/07391102.2018.1461135] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sterol-14α-demethylase (CYP51) is an ergosterol pathway enzyme crucial for the survival of infectious Leishmania parasite. Recent high-throughput metabolomics and whole genome sequencing study revealed amphotericin B resistance in Leishmania is indeed due to mutation in CYP51. The residue of mutation (asparagine 176) is conserved across the kinetoplastidae and not in yeast or humans, portraying its functional significance. In order to understand the possible cause for the resistance, knowledge of structural changes due to mutation is of high importance. To shed light on the structural changes of wild and mutant CYP51, we conducted comparative molecular dynamics simulation study. The active site, substrate biding cavity, substrate channel entrance (SCE), and cavity involving the mutated site were studied based on basic parameters and large concerted molecular motions derived from essential dynamics analyses of 100 ns simulation. Results indicated that mutant CYP51 is stable and less compact than the wild type. Correspondingly, the solvent accessible surface area (SASA) of the mutant was found to be increased, especially in active site and cavities not involving the mutation site. Free-energy landscape analysis disclosed mutant to have a rich conformational diversity than wild type, with various free-energy conformations of mutant having SASA greater than wild type with SCE open. More residues were found to interact with the mutant CYP51 upon docking of substrate to both the wild and mutant CYP51. These results indicate that, relative to wild type, the N176I mutation of CYP51 in Leishmania mexicana could possibly favor increased substrate binding efficiency.
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Affiliation(s)
- Saravanan Vijayakumar
- a Department of Statistics/Bioinformatics , Rajendra Memorial Research Institute of Medical Science, Indian Council for Medical Research , Agamkuan, Patna 800007 , Bihar , India
| | - Pradeep Das
- b Department of Molecular Biology/Bioinformatics Centre , Rajendra Memorial Research Institute of Medical Science, Indian Council for Medical Research , Agamkuan, Patna 800007 , Bihar , India
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23
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Keighobadi M, Emami S, Lagzian M, Fakhar M, Rafiei A, Valadan R. Molecular Modeling and Structural Stability of Wild-Type and Mutant CYP51 from Leishmania major: In Vitro and In Silico Analysis of a Laboratory Strain. Molecules 2018; 23:molecules23030696. [PMID: 29562710 PMCID: PMC6017637 DOI: 10.3390/molecules23030696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 02/22/2018] [Accepted: 03/14/2018] [Indexed: 11/16/2022] Open
Abstract
Cutaneous leishmaniasis is a neglected tropical disease and a major public health in the most countries. Leishmania major is the most common cause of cutaneous leishmaniasis. In the Leishmania parasites, sterol 14α-demethylase (CYP51), which is involved in the biosynthesis of sterols, has been identified as an attractive target for development of new therapeutic agents. In this study, the sequence and structure of CYP51 in a laboratory strain (MRHO/IR/75/ER) of L. major were determined and compared to the wild-type strain. The results showed 19 mutations including seven non-synonymous and 12 synonymous ones in the CYP51 sequence of strain MRHO/IR/75/ER. Importantly, an arginine to lysine substitution at position of 474 resulted in destabilization of CYP51 (ΔΔG = 1.17 kcal/mol) in the laboratory strain; however, when the overall effects of all substitutions were evaluated by 100 ns molecular dynamics simulation, the final structure did not show any significant changes (p-value < 0.05) in stability parameter of the strain MRHO/IR/75/ER compared to the wild-type protein. The energy level for the CYP51 of wild-type and MRHO/IR/75/ER strain were −40,027.1 and −39,706.48 Kcal/mol respectively. The overall Root-mean-square deviation (RMSD) deviation between two proteins was less than 1 Å throughout the simulation and Root-mean-square fluctuation (RMSF) plot also showed no substantial differences between amino acids fluctuation of the both protein. The results also showed that, these mutations were located on the protein periphery that neither interferes with protein folding nor with substrate/inhibitor binding. Therefore, L. major strain MRHO/IR/75/ER is suggested as a suitable laboratory model for studying biological role of CYP51 and inhibitory effects of sterol 14α-demethylase inhibitors.
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Affiliation(s)
- Masoud Keighobadi
- Pharmaceutical Sciences Research Center, Student Research Committee, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, 48157-33971, Iran.
| | - Milad Lagzian
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan 98168-76578, Iran.
| | - Mahdi Fakhar
- Department of Parasitology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
- Molecular and Cell Biology Research Center (MCBRC), Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
| | - Alireza Rafiei
- Molecular and Cell Biology Research Center (MCBRC), Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
- Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
| | - Reza Valadan
- Molecular and Cell Biology Research Center (MCBRC), Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
- Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari 48157-33971, Iran.
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Ke X, Ding GJ, Ma BX, Liu ZQ, Zhang JF, Zheng YG. Characterization of a novel CYP51 from Rhodococcus triatomae and its NADH-ferredoxin reductase-coupled application in lanosterol 14α-demethylation. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Emami S, Tavangar P, Keighobadi M. An overview of azoles targeting sterol 14α-demethylase for antileishmanial therapy. Eur J Med Chem 2017; 135:241-259. [PMID: 28456033 DOI: 10.1016/j.ejmech.2017.04.044] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 02/07/2023]
Abstract
The azole antifungal drugs are an important class of chemotherapeutic agents with broad-spectrum of activity against yeasts and filamentous fungi, act in the ergosterol biosynthetic pathway through inhibition of the cytochrome P450-dependent enzyme sterol 14α-demethylase. Azole antifungals have also been repurposed for treatment of tropical protozoan infections including human leishmaniasis. Recent advances in molecular biology and computational chemistry areas have increased our knowledge about sterol biochemical pathway in Leishmania parasites. Based on the importance of sterol biosynthetic pathway in Leishmania parasites, we reviewed all studies reported on azoles for potential antileishmanial therapy along their structural and biological aspects. This review may help medicinal chemists for design of new azole-derived antileishmanial drugs.
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Affiliation(s)
- Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Pegah Tavangar
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Masoud Keighobadi
- Student Research Committee, Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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Bohlooli F, Sepehri S, Razzaghi-Asl N. Response surface methodology in drug design: A case study on docking analysis of a potent antifungal fluconazole. Comput Biol Chem 2017; 67:158-173. [DOI: 10.1016/j.compbiolchem.2017.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/01/2016] [Accepted: 01/16/2017] [Indexed: 10/20/2022]
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27
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Porta EOJ, Jäger SN, Nocito I, Lepesheva GI, Serra EC, Tekwani BL, Labadie GR. Antitrypanosomal and antileishmanial activity of prenyl-1,2,3-triazoles. MEDCHEMCOMM 2017; 8:1015-1021. [PMID: 28993794 DOI: 10.1039/c7md00008a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A series of prenyl 1,2,3-triazoles were prepared from isoprenyl azides and different alkynes. The dipolar cycloaddition reaction provided exclusively primary azide products as regioisomeric mixtures that were separated by column chromatography and fully characterized. Most of the compounds displayed antiparasitic activity against Trypanosoma cruzi and Leishmania donovani. The most active compounds were assayed as potential TcCYP51 inhibitors.
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Affiliation(s)
- Exequiel O J Porta
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina. Tel
| | - Sebastián N Jäger
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina. Tel
| | - Isabel Nocito
- Instituto de Biología Molecular y Celular (IBR-CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Suipacha 531, S2002LRK, Rosario, Argentina
| | - Galina I Lepesheva
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN37232, USA
| | - Esteban C Serra
- Instituto de Biología Molecular y Celular (IBR-CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Suipacha 531, S2002LRK, Rosario, Argentina
| | - Babu L Tekwani
- National Center for Natural Products Research & Department of Pharmacology, School of Pharmacy, University of Mississippi, University MS 38677, USA
| | - Guillermo R Labadie
- Instituto de Química Rosario, UNR, CONICET, Suipacha 531, S2002LRK, Rosario, Argentina. Tel.,Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
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28
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Hargrove TY, Friggeri L, Wawrzak Z, Qi A, Hoekstra WJ, Schotzinger RJ, York JD, Guengerich FP, Lepesheva GI. Structural analyses of Candida albicans sterol 14α-demethylase complexed with azole drugs address the molecular basis of azole-mediated inhibition of fungal sterol biosynthesis. J Biol Chem 2017; 292:6728-6743. [PMID: 28258218 DOI: 10.1074/jbc.m117.778308] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 02/20/2017] [Indexed: 12/27/2022] Open
Abstract
With some advances in modern medicine (such as cancer chemotherapy, broad exposure to antibiotics, and immunosuppression), the incidence of opportunistic fungal pathogens such as Candida albicans has increased. Cases of drug resistance among these pathogens have become more frequent, requiring the development of new drugs and a better understanding of the targeted enzymes. Sterol 14α-demethylase (CYP51) is a cytochrome P450 enzyme required for biosynthesis of sterols in eukaryotic cells and is the major target of clinical drugs for managing fungal pathogens, but some of the CYP51 key features important for rational drug design have remained obscure. We report the catalytic properties, ligand-binding profiles, and inhibition of enzymatic activity of C. albicans CYP51 by clinical antifungal drugs that are used systemically (fluconazole, voriconazole, ketoconazole, itraconazole, and posaconazole) and topically (miconazole and clotrimazole) and by a tetrazole-based drug candidate, VT-1161 (oteseconazole: (R)-2-(2,4-difluorophenyl)-1,1-difluoro-3-(1H-tetrazol-1-yl)-1-(5-(4-(2,2,2-trifluoroethoxy)phenyl)pyridin-2-yl)propan-2-ol). Among the compounds tested, the first-line drug fluconazole was the weakest inhibitor, whereas posaconazole and VT-1161 were the strongest CYP51 inhibitors. We determined the X-ray structures of C. albicans CYP51 complexes with posaconazole and VT-1161, providing a molecular mechanism for the potencies of these drugs, including the activity of VT-1161 against Candida krusei and Candida glabrata, pathogens that are intrinsically resistant to fluconazole. Our comparative structural analysis outlines phylum-specific CYP51 features that could direct future rational development of more efficient broad-spectrum antifungals.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Laura Friggeri
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zdzislaw Wawrzak
- the Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439
| | - Aidong Qi
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | | | | | - John D York
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Galina I Lepesheva
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, .,the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
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Mgbeahuruike AC, Kovalchuk A, Ubhayasekera W, Nelson DR, Yadav JS. CYPome of the conifer pathogen Heterobasidion irregulare: Inventory, phylogeny, and transcriptional analysis of the response to biocontrol. Fungal Biol 2016; 121:158-171. [PMID: 28089047 DOI: 10.1016/j.funbio.2016.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 10/25/2016] [Accepted: 11/26/2016] [Indexed: 01/16/2023]
Abstract
The molecular mechanisms underlying the interaction of the pathogen, Heterobasidion annosum s.l., the conifer tree and the biocontrol fungus, Phlebiopsis gigantea have not been fully elucidated. Members of the cytochrome P450 (CYP) protein family may contribute to the detoxification of components of chemical defence of conifer trees by H. annosum during infection. Additionally, they may also be involved in the interaction between H. annosum and P. gigantea. A genome-wide analysis of CYPs in Heterobasidion irregulare was carried out alongside gene expression studies. According to the Standardized CYP Nomenclature criteria, the H. irregulare genome has 121 CYP genes and 17 CYP pseudogenes classified into 11 clans, 35 families, and 64 subfamilies. Tandem CYP arrays originating from gene duplications and belonging to the same family and subfamily were found. Phylogenetic analysis showed that all the families of H. irregulare CYPs were monophyletic groups except for the family CYP5144. Microarray analysis revealed the transcriptional pattern for 130 transcripts of CYP-encoding genes during growth on culture filtrate produced by P. gigantea. The high level of P450 gene diversity identified in this study could result from extensive gene duplications presumably caused by the high metabolic demands of H. irregulare in its ecological niches.
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Affiliation(s)
- Anthony C Mgbeahuruike
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, PMB, 420001, Enugu State, Nigeria; Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, University of Nigeria, Nsukka, PMB, 420001, Enugu State, Nigeria.
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, FIN-00014 Helsinki, Finland
| | - Wimal Ubhayasekera
- Structure and Molecular Biology Program, Department of Cell and Molecular Biology, Uppsala University, Box 596, Biomedical Center, SE-751 24, Uppsala, Sweden
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee, Memphis, TN 38163, USA
| | - Jagjit S Yadav
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA
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Miller MB, Patkar P, Singha UK, Chaudhuri M, David Nes W. 24-Methylenecyclopropane steroidal inhibitors: A Trojan horse in ergosterol biosynthesis that prevents growth of Trypanosoma brucei. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:305-313. [PMID: 27939999 DOI: 10.1016/j.bbalip.2016.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 01/09/2023]
Abstract
A new class of steroidal therapeutics based on phylogenetic-guided design of covalent inhibitors that target parasite-specific enzymes of ergosterol biosynthesis is shown to prevent growth of the protozoan-Trypanosoma brucei, responsible for sleeping sickness. In the presence of approximately 15±5μM 26,27-dehydrolanosterol, T. brucei procyclic or blood stream form growth is inhibited by 50%. This compound is actively converted by the parasite to an acceptable substrate of sterol C24-methyl transferase (SMT) that upon position-specific side chain methylation at C26 inactivates the enzyme. Treated cells show dose-dependent depletion of ergosterol and other 24β-methyl sterols with no accumulation of intermediates in contradistinction to profiles typical of tight binding inhibitor treatments to azoles showing loss of ergosterol accompanied by accumulation of toxic 14-methyl sterols. HEK cells accumulate 26,27-dehydrolanosterol without effect on cholesterol biosynthesis. During exposure of cloned TbSMT to 26,27-dehydrozymosterol, the enzyme is gradually inactivated (kcat/kinact=0.13min-1/0.08min-1; partition ratio of 1.6) while 26,27-dehydrolanosterol binds nonproductively. GC-MS analysis of the turnover product and bound intermediate released as a C26-methylated diol (C3-OH and C24-OH) confirmed substrate recognition and covalent binding to TbSMT. This study has potential implications for design of a novel class of chemotherapeutic leads functioning as mechanism-based inhibitors of ergosterol biosynthesis to treat neglected tropical diseases.
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Affiliation(s)
- Matthew B Miller
- Department of Chemistry and Biochemistry and Center for Chemical Biology, Texas Tech University, Lubbock, TX 79409, USA
| | - Presheet Patkar
- Department of Chemistry and Biochemistry and Center for Chemical Biology, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujjal K Singha
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN 37208, USA
| | - Minu Chaudhuri
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN 37208, USA
| | - W David Nes
- Department of Chemistry and Biochemistry and Center for Chemical Biology, Texas Tech University, Lubbock, TX 79409, USA.
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31
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Dauchy FA, Bonhivers M, Landrein N, Dacheux D, Courtois P, Lauruol F, Daulouède S, Vincendeau P, Robinson DR. Trypanosoma brucei CYP51: Essentiality and Targeting Therapy in an Experimental Model. PLoS Negl Trop Dis 2016; 10:e0005125. [PMID: 27855164 PMCID: PMC5113867 DOI: 10.1371/journal.pntd.0005125] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/24/2016] [Indexed: 01/03/2023] Open
Abstract
Trypanosoma brucei gambiense is the main causative agent of Human African Trypanosomiasis (HAT), also known as sleeping sickness. Because of limited alternatives and treatment toxicities, new therapeutic options are urgently needed for patients with HAT. Sterol 14alpha-demethylase (CYP51) is a potential drug target but its essentiality has not been determined in T. brucei. We used a tetracycline-inducible RNAi system to assess the essentiality of CYP51 in T. brucei bloodstream form (BSF) cells and we evaluated the effect of posaconazole, a well-tolerated triazole drug, within a panel of virulent strains in vitro and in a murine model. Expression of CYP51 in several T. brucei cell lines was demonstrated by western blot and its essentiality was demonstrated by RNA interference (CYP51RNAi) in vitro. Following reduction of TbCYP51 expression by RNAi, cell growth was reduced and eventually stopped compared to WT or non-induced cells, showing the requirement of CYP51 in T. brucei. These phenotypes were rescued by addition of ergosterol. Additionally, CYP51RNAi induction caused morphological defects with multiflagellated cells (p<0.05), suggesting cytokinesis dysfunction. The survival of CYP51RNAi Doxycycline-treated mice (p = 0.053) and of CYP51RNAi 5-day pre-induced Doxycycline-treated mice (p = 0.008) were improved compared to WT showing a CYP51 RNAi effect on trypanosomal virulence in mice. The posaconazole concentrations that inhibited parasite growth by 50% (IC50) were 8.5, 2.7, 1.6 and 0.12 μM for T. b. brucei 427 90-13, T. b. brucei Antat 1.1, T. b. gambiense Feo (Feo/ITMAP/1893) and T. b. gambiense Biyamina (MHOM/SD/82), respectively. During infection with these last three virulent strains, posaconazole-eflornithine and nifurtimox-eflornithine combinations showed similar improvement in mice survival (p≤0.001). Our results provide support for a CYP51 targeting based treatment in HAT. Thus posaconazole used in combination may represent a therapeutic alternative for trypanosomiasis.
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Affiliation(s)
- Frédéric-Antoine Dauchy
- University of Bordeaux, laboratoire de parasitologie, France
- IRD-CIRAD-University of Bordeaux, France
- University Hospital of Bordeaux, Department of infectious and tropical diseases, Hôpital Pellegrin, France
- * E-mail:
| | - Mélanie Bonhivers
- University of Bordeaux, Microbiologie Fondamentale et Pathogénicité, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, France
| | - Nicolas Landrein
- University of Bordeaux, Microbiologie Fondamentale et Pathogénicité, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, France
| | - Denis Dacheux
- University of Bordeaux, Microbiologie Fondamentale et Pathogénicité, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, France
- Bordeaux INP, ENSTBB, Microbiologie Fondamentale et Pathogénicité, France
| | - Pierrette Courtois
- University of Bordeaux, laboratoire de parasitologie, France
- IRD-CIRAD-University of Bordeaux, France
| | - Florian Lauruol
- University of Bordeaux, laboratoire de parasitologie, France
- IRD-CIRAD-University of Bordeaux, France
| | - Sylvie Daulouède
- University of Bordeaux, laboratoire de parasitologie, France
- IRD-CIRAD-University of Bordeaux, France
| | - Philippe Vincendeau
- University of Bordeaux, laboratoire de parasitologie, France
- IRD-CIRAD-University of Bordeaux, France
- University Hospital of Bordeaux, laboratoire de parasitologie, Hôpital Pellegrin, France
| | - Derrick R. Robinson
- University of Bordeaux, Microbiologie Fondamentale et Pathogénicité, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, France
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32
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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33
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Durairaj P, Hur JS, Yun H. Versatile biocatalysis of fungal cytochrome P450 monooxygenases. Microb Cell Fact 2016; 15:125. [PMID: 27431996 PMCID: PMC4950769 DOI: 10.1186/s12934-016-0523-6] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/10/2016] [Indexed: 11/19/2022] Open
Abstract
Cytochrome P450 (CYP) monooxygenases, the nature’s most versatile biological catalysts have unique ability to catalyse regio-, chemo-, and stereospecific oxidation of a wide range of substrates under mild reaction conditions, thereby addressing a significant challenge in chemocatalysis. Though CYP enzymes are ubiquitous in all biological kingdoms, the divergence of CYPs in fungal kingdom is manifold. The CYP enzymes play pivotal roles in various fungal metabolisms starting from housekeeping biochemical reactions, detoxification of chemicals, and adaptation to hostile surroundings. Considering the versatile catalytic potentials, fungal CYPs has gained wide range of attraction among researchers and various remarkable strategies have been accomplished to enhance their biocatalytic properties. Numerous fungal CYPs with multispecialty features have been identified and the number of characterized fungal CYPs is constantly increasing. Literature reveals ample reviews on mammalian, plant and bacterial CYPs, however, modest reports on fungal CYPs urges a comprehensive review highlighting their novel catalytic potentials and functional significances. In this review, we focus on the diversification and functional diversity of fungal CYPs and recapitulate their unique and versatile biocatalytic properties. As such, this review emphasizes the crucial issues of fungal CYP systems, and the factors influencing efficient biocatalysis.
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Affiliation(s)
- Pradeepraj Durairaj
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.
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34
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Leaver DJ, Patkar P, Singha UK, Miller MB, Haubrich BA, Chaudhuri M, Nes WD. Fluorinated Sterols Are Suicide Inhibitors of Ergosterol Biosynthesis and Growth in Trypanosoma brucei. ACTA ACUST UNITED AC 2016; 22:1374-83. [PMID: 26496686 DOI: 10.1016/j.chembiol.2015.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/20/2015] [Accepted: 08/28/2015] [Indexed: 11/19/2022]
Abstract
Trypanosoma brucei, the causal agent for sleeping sickness, depends on ergosterol for growth. Here, we describe the effects of a mechanism-based inhibitor, 26-fluorolanosterol (26FL), which converts in vivo to a fluorinated substrate of the sterol C24-methyltransferase essential for sterol methylation and function of ergosterol, and missing from the human host. 26FL showed potent inhibition of ergosterol biosynthesis and growth of procyclic and bloodstream forms while having no effect on cholesterol biosynthesis or growth of human epithelial kidney cells. During exposure of cloned TbSMT to 26-fluorocholesta-5,7,24-trienol, the enzyme is gradually killed as a consequence of the covalent binding of the intermediate C25 cation to the active site (kcat/kinact = 0.26 min(-1)/0.24 min(-1); partition ratio of 1.08), whereas 26FL is non-productively bound. These results demonstrate that poisoning of ergosterol biosynthesis by a 26-fluorinated Δ(24)-sterol is a promising strategy for developing a new treatment for trypanosomiasis.
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Affiliation(s)
- David J Leaver
- Center for Chemical Biology and Department of Chemistry & Biochemistry, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA; Institute of Chemistry and Biomedical Sciences, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu, 210093, P.R. China
| | - Presheet Patkar
- Center for Chemical Biology and Department of Chemistry & Biochemistry, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Ujjal K Singha
- Department of Microbiology and Immunology, Meharry Medical College, 1005 Doctor D. B. Todd Jr. Boulevard, Nashville, TN 37208, USA
| | - Matthew B Miller
- Center for Chemical Biology and Department of Chemistry & Biochemistry, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Brad A Haubrich
- Center for Chemical Biology and Department of Chemistry & Biochemistry, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Minu Chaudhuri
- Department of Microbiology and Immunology, Meharry Medical College, 1005 Doctor D. B. Todd Jr. Boulevard, Nashville, TN 37208, USA
| | - W David Nes
- Center for Chemical Biology and Department of Chemistry & Biochemistry, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA.
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35
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Denisov IG, Mak PJ, Grinkova YV, Bastien D, Bérubé G, Sligar SG, Kincaid JR. The use of isomeric testosterone dimers to explore allosteric effects in substrate binding to cytochrome P450 CYP3A4. J Inorg Biochem 2015; 158:77-85. [PMID: 26774838 DOI: 10.1016/j.jinorgbio.2015.12.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/07/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023]
Abstract
Cytochrome P450 CYP3A4 is the main drug-metabolizing enzyme in the human liver, being responsible for oxidation of 50% of all pharmaceuticals metabolized by human P450 enzymes. Possessing a large substrate binding pocket, it can simultaneously bind several substrate molecules and often exhibits a complex pattern of drug-drug interactions. In order to better understand structural and functional aspects of binding of multiple substrate molecules to CYP3A4 we used resonance Raman and UV-VIS spectroscopy to document the effects of binding of synthetic testosterone dimers of different configurations, cis-TST2 and trans-TST2. We directly demonstrate that the binding of two steroid molecules, which can assume multiple possible configurations inside the substrate binding pocket of monomeric CYP3A4, can lead to active site structural changes that affect functional properties. Using resonance Raman spectroscopy, we have documented perturbations in the ferric and Fe-CO states by these substrates, and compared these results with effects caused by binding of monomeric TST. While the binding of trans-TST2 yields results similar to those obtained with monomeric TST, the binding of cis-TST2 is much tighter and results in significantly more pronounced conformational changes of the porphyrin side chains and Fe-CO unit. In addition, binding of an additional monomeric TST molecule in the remote allosteric site significantly improves binding affinity and the overall spin shift for CYP3A4 with trans-TST2 dimer bound inside the substrate binding pocket. This result provides the first direct evidence for an allosteric effect of the peripheral binding site at the protein-membrane interface on the functional properties of CYP3A4.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States.
| | - Piotr J Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, United States.
| | - Yelena V Grinkova
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States.
| | - Dominic Bastien
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada.
| | - Gervais Bérubé
- Département de chimie, biochimie et physique, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada.
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois, Urbana, IL 61801, United States.
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, United States.
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Clinical Candidate VT-1161's Antiparasitic Effect In Vitro, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme CYP51 from Trypanosoma cruzi. Antimicrob Agents Chemother 2015; 60:1058-66. [PMID: 26643331 DOI: 10.1128/aac.02287-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/23/2015] [Indexed: 01/08/2023] Open
Abstract
A novel antifungal drug candidate, the 1-tetrazole-based agent VT-1161 [(R)-2-(2,4-difluorophenyl)-1,1-difluoro-3-(1H-tetrazol-1-yl)-1-{5-[4-(2,2,2-trifluoroethoxy)phenyl]pyridin-2-yl}propan-2-ol], which is currently in two phase 2b antifungal clinical trials, was found to be a tight-binding ligand (apparent dissociation constant [Kd], 24 nM) and a potent inhibitor of cytochrome P450 sterol 14α-demethylase (CYP51) from the protozoan pathogen Trypanosoma cruzi. Moreover, VT-1161 revealed a high level of antiparasitic activity against amastigotes of the Tulahuen strain of T. cruzi in cellular experiments (50% effective concentration, 2.5 nM) and was active in vivo, causing >99.8% suppression of peak parasitemia in a mouse model of infection with the naturally drug-resistant Y strain of the parasite. The data strongly support the potential utility of VT-1161 in the treatment of Chagas disease. The structural characterization of T. cruzi CYP51 in complex with VT-1161 provides insights into the molecular basis for the compound's inhibitory potency and paves the way for the further rational development of this novel, tetrazole-based inhibitory chemotype both for antiprotozoan chemotherapy and for antifungal chemotherapy.
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37
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Yu X, Nandekar P, Mustafa G, Cojocaru V, Lepesheva GI, Wade RC. Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design. Biochim Biophys Acta Gen Subj 2015; 1860:67-78. [PMID: 26493722 DOI: 10.1016/j.bbagen.2015.10.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/19/2015] [Accepted: 10/16/2015] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cytochrome P450 sterol 14α-demethylase (CYP51) is an essential enzyme for sterol biosynthesis and a target for anti-parasitic drug design. However, the design of parasite-specific drugs that inhibit parasitic CYP51 without severe side effects remains challenging. The active site of CYP51 is situated in the interior of the protein. Here, we characterize the potential ligand egress routes and mechanisms in Trypanosoma brucei and human CYP51 enzymes. METHODS We performed Random Acceleration Molecular Dynamics simulations of the egress of four different ligands from the active site of models of soluble and membrane-bound T. brucei CYP51 and of soluble human CYP51. RESULTS In the simulations, tunnel 2f, which leads to the membrane, was found to be the predominant ligand egress tunnel for all the ligands studied. Tunnels S, 1 and W, which lead to the cytosol, were also used in T. brucei CYP51, whereas tunnel 1 was the only other tunnel used significantly in human CYP51. The common tunnels found previously in other CYPs were barely used. The ligand egress times were shorter for human than T. brucei CYP51, suggesting lower barriers to ligand passage. Two gating residues, F105 and M460, in T. brucei CYP51 that modulate the opening of tunnels 2f and S were identified. CONCLUSIONS Although the main egress tunnel was the same, differences in the tunnel-lining residues, ligand passage and tunnel usage were found between T. brucei and human CYP51s. GENERAL SIGNIFICANCE The results provide a basis for the design of selective anti-parasitic agents targeting the ligand tunnels.
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Affiliation(s)
- Xiaofeng Yu
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Prajwal Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Vlad Cojocaru
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Galina I Lepesheva
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
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38
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Hargrove TY, Wawrzak Z, Lamb DC, Guengerich FP, Lepesheva GI. Structure-Functional Characterization of Cytochrome P450 Sterol 14α-Demethylase (CYP51B) from Aspergillus fumigatus and Molecular Basis for the Development of Antifungal Drugs. J Biol Chem 2015; 290:23916-34. [PMID: 26269599 DOI: 10.1074/jbc.m115.677310] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/18/2023] Open
Abstract
Aspergillus fumigatus is the opportunistic fungal pathogen that predominantly affects the immunocompromised population and causes 600,000 deaths/year. The cytochrome P450 51 (CYP51) inhibitor voriconazole is currently the drug of choice, yet the treatment efficiency remains low, calling for rational development of more efficient agents. A. fumigatus has two CYP51 genes, CYP51A and CYP51B, which share 59% amino acid sequence identity. CYP51B is expressed constitutively, whereas gene CYP51A is reported to be inducible. We expressed, purified, and characterized A. fumigatus CYP51B, including determination of its substrate preferences, catalytic parameters, inhibition, and x-ray structure in complexes with voriconazole and the experimental inhibitor (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide (VNI). The enzyme demethylated its natural substrate eburicol and the plant CYP51 substrate obtusifoliol at steady-state rates of 17 and 16 min(-1), respectively, but did not metabolize lanosterol, and the topical antifungal drug miconazole was the strongest inhibitor that we identified. The x-ray crystal structures displayed high overall similarity of A. fumigatus CYP51B to CYP51 orthologs from other biological kingdoms but revealed phylum-specific differences relevant to enzyme catalysis and inhibition. The complex with voriconazole provides an explanation for the potency of this relatively small molecule, whereas the complex with VNI outlines a direction for further enhancement of the efficiency of this new inhibitory scaffold to treat humans afflicted with filamentous fungal infections.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zdzislaw Wawrzak
- the Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439
| | - David C Lamb
- Swansea University, Swansea, Wales SA2 8PP, United Kingdom, and
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Galina I Lepesheva
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
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39
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Li ZJ, Guo X, Dawuti G, Aibai S. Antifungal Activity of Ellagic Acid In Vitro and In Vivo. Phytother Res 2015; 29:1019-25. [PMID: 25919446 DOI: 10.1002/ptr.5340] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/27/2015] [Accepted: 03/11/2015] [Indexed: 01/03/2023]
Abstract
Ellagic acid (EA) has been shown to have antioxidant, antibacterial, and anti-inflammatory activities. In Uighur traditional medicine, Euphorbia humifusa Willd is used to treat fungal diseases, and recent studies suggest that it is the EA content which is responsible for its therapeutic effect. However, the effects of EA on antifungal activity have not yet been reported. This study aimed to investigate the inhibitory effect of EA on fungal strains both in vitro and in vivo. The minimal inhibitory concentration (MIC) was determined by the National Committee for Clinical Laboratory Standards (M38-A and M27-A2) standard method in vitro. EA had a broad spectrum of antifungal activity, with MICs for all the tested dermatophyte strains between 18.75 and 58.33 µg/ml. EA was also active against two Candida strains, with MICs between 25.0 and 75.0 µg/ml. It was inactive against Candida glabrata. The susceptibility of six species of dermatophytes to EA was comparable with that of the commercial antifungal, fluconazole. The most sensitive filamentous species was Trichophyton rubrum (MIC = 18.75 µg/ml). Studies on the mechanism of action using an HPLC-based assay and an enzyme linked immunosorbent assay showed that EA inhibited ergosterol biosynthesis and reduced the activity of sterol 14α-demethylase P450 (CYP51) in the Trichophyton rubrum membrane, respectively. An in vivo test demonstrated that topical administration of EA (4.0 and 8.0 mg/cm(2) ) significantly enhanced the cure rate in a guinea-pig infection model of Trichophyton rubrum. The results suggest that EA has the potential to be developed as a natural antifungal agent.
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Affiliation(s)
- Zhi-Jian Li
- Department of Pharmacology and Toxicology Laboratory, Xinjiang Institute of Traditional Uighur Medicine, Urumqi, Xinjiang, 830049, China
| | - Xin Guo
- Department of Pharmacology and Toxicology Laboratory, Xinjiang Institute of Traditional Uighur Medicine, Urumqi, Xinjiang, 830049, China
| | - Gulina Dawuti
- Xinjiang Hospital of Traditional Uighur Medicine, Urumqi, Xinjiang, 830049, China
| | - Silafu Aibai
- Department of Pharmacology and Toxicology Laboratory, Xinjiang Institute of Traditional Uighur Medicine, Urumqi, Xinjiang, 830049, China
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Lepesheva GI, Hargrove TY, Rachakonda G, Wawrzak Z, Pomel S, Cojean S, Nde PN, Nes WD, Locuson CW, Calcutt MW, Waterman MR, Daniels JS, Loiseau PM, Villalta F. VFV as a New Effective CYP51 Structure-Derived Drug Candidate for Chagas Disease and Visceral Leishmaniasis. J Infect Dis 2015; 212:1439-48. [DOI: 10.1093/infdis/jiv228] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/08/2015] [Indexed: 11/14/2022] Open
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Yu X, Cojocaru V, Mustafa G, Salo-Ahen OMH, Lepesheva GI, Wade RC. Dynamics of CYP51: implications for function and inhibitor design. J Mol Recognit 2015; 28:59-73. [PMID: 25601796 DOI: 10.1002/jmr.2412] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/14/2014] [Accepted: 07/24/2014] [Indexed: 12/12/2022]
Abstract
Sterol 14α-demethylase (cytochrome P450 family 51 (CYP51)) is an essential enzyme occurring in all biological kingdoms. In eukaryotes, it is located in the membrane of the endoplasmic reticulum. Selective inhibitors of trypanosomal CYP51s that do not affect the human CYP51 have been discovered in vitro and found to cure acute and chronic mouse Chagas disease without severe side effects in vivo. Crystal structures indicate that CYP51 may be more rigid than most CYPs, and it has been proposed that this property may facilitate antiparasitic drug design. Therefore, to investigate the dynamics of trypanosomal CYP51, we built a model of membrane-bound Trypanosoma brucei CYP51 and then performed molecular dynamics simulations of T. brucei CYP51 in membrane-bound and soluble forms. We compared the dynamics of T. brucei CYP51 with those of human CYP51, CYP2C9, and CYP2E1. In the simulations, the CYP51s display low mobility in the buried active site although overall mobility is similar in all the CYPs studied. The simulations suggest that in CYP51, pathway 2f serves as the major ligand access tunnel, and both pathways 2f (leading to membrane) and S (leading to solvent) can serve as ligand egress tunnels. Compared with the other CYPs, the residues at the entrance of the ligand access tunnels in CYP51 have higher mobility that may be necessary to facilitate the passage of its large sterol ligands. The water (W) tunnel is accessible to solvent during most of the simulations of CYP51, but its width is affected by the conformations of the heme's two propionate groups. These differ from those observed in the other CYPs studied because of differences in their hydrogen-bonding network. Our simulations give insights into the dynamics of CYP51 that complement the available experimental data and have implications for drug design against CYP51 enzymes.
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Affiliation(s)
- Xiaofeng Yu
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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42
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Choi JY, Podust LM, Roush WR. Drug strategies targeting CYP51 in neglected tropical diseases. Chem Rev 2014; 114:11242-71. [PMID: 25337991 PMCID: PMC4254036 DOI: 10.1021/cr5003134] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Jun Yong Choi
- Department
of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Larissa M. Podust
- Center for Discovery and Innovation in Parasitic Diseases, and Department of
Pathology, University of California—San
Francisco, San Francisco, California 94158, United States
| | - William R. Roush
- Department
of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
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Haubrich BA, Singha UK, Miller MB, Nes CR, Anyatonwu H, Lecordier L, Patkar P, Leaver DJ, Villalta F, Vanhollebeke B, Chaudhuri M, Nes WD. Discovery of an ergosterol-signaling factor that regulates Trypanosoma brucei growth. J Lipid Res 2014; 56:331-41. [PMID: 25424002 DOI: 10.1194/jlr.m054643] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ergosterol biosynthesis and homeostasis in the parasitic protozoan Trypanosoma brucei was analyzed by RNAi silencing and inhibition of sterol C24β-methyltransferase (TbSMT) and sterol 14α-demethylase [TbSDM (TbCYP51)] to explore the functions of sterols in T. brucei growth. Inhibition of the amount or activity of these enzymes depletes ergosterol from cells at <6 fg/cell for procyclic form (PCF) cells or <0.01 fg/cell for bloodstream form (BSF) cells and reduces infectivity in a mouse model of infection. Silencing of TbSMT expression by RNAi in PCF or BSF in combination with 25-azalanosterol (AZA) inhibited parasite growth and this inhibition was restored completely by adding synergistic cholesterol (7.8 μM from lipid-depleted media) with small amounts of ergosterol (1.2 μM) to the medium. These observations are consistent with the proposed requirement for ergosterol as a signaling factor to spark cell proliferation while imported cholesterol or the endogenously formed cholesta-5,7,24-trienol act as bulk membrane components. To test the potential chemotherapeutic importance of disrupting ergosterol biosynthesis using pairs of mechanism-based inhibitors that block two enzymes in the post-squalene segment, parasites were treated with AZA and itraconazole at 1 μM each (ED50 values) resulting in parasite death. Taken together, our results demonstrate that the ergosterol pathway is a prime drug target for intervention in T. brucei infection.
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Affiliation(s)
- Brad A Haubrich
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409
| | - Ujjal K Singha
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN 37208
| | - Matthew B Miller
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409
| | - Craigen R Nes
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409
| | - Hosanna Anyatonwu
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409
| | - Laurence Lecordier
- Laboratoire de Parasitologie Moléculaire, IBMM, Université Libre de Bruxelles, B6041 Gosselies, Belgium
| | - Presheet Patkar
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409
| | - David J Leaver
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409 Institute of Chemistry and Biomedical Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Fernando Villalta
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN 37208
| | - Benoit Vanhollebeke
- Laboratoire de Parasitologie Moléculaire, IBMM, Université Libre de Bruxelles, B6041 Gosselies, Belgium
| | - Minu Chaudhuri
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN 37208
| | - W David Nes
- Center for Chemical Biology and Department of Chemistry and Biochemistry Texas Tech University, Lubbock, TX 79409
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Chen W, Lee MK, Jefcoate C, Kim SC, Chen F, Yu JH. Fungal cytochrome p450 monooxygenases: their distribution, structure, functions, family expansion, and evolutionary origin. Genome Biol Evol 2014; 6:1620-34. [PMID: 24966179 PMCID: PMC4122930 DOI: 10.1093/gbe/evu132] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cytochrome P450 (CYP) monooxygenase superfamily contributes a broad array of biological functions in living organisms. In fungi, CYPs play diverse and pivotal roles in versatile metabolism and fungal adaptation to specific ecological niches. In this report, CYPomes in the 47 genomes of fungi belong to the phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota have been studied. The comparison of fungal CYPomes suggests that generally fungi possess abundant CYPs belonging to a variety of families with the two global families CYP51 and CYP61, indicating individuation of CYPomes during the evolution of fungi. Fungal CYPs show highly conserved characteristic motifs, but very low overall sequence similarities. The characteristic motifs of fungal CYPs are distinguishable from those of CYPs in animals, plants, and especially archaea and bacteria. The four representative motifs contribute to the general function of CYPs. Fungal CYP51s and CYP61s can be used as the models for the substrate recognition sites analysis. The CYP proteins are clustered into 15 clades and the phylogenetic analyses suggest that the wide variety of fungal CYPs has mainly arisen from gene duplication. Two large duplication events might have been associated with the booming of Ascomycota and Basidiomycota. In addition, horizontal gene transfer also contributes to the diversification of fungal CYPs. Finally, a possible evolutionary scenario for fungal CYPs along with fungal divergences is proposed. Our results provide the fundamental information for a better understanding of CYP distribution, structure and function, and new insights into the evolutionary events of fungal CYPs along with the evolution of fungi.
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Affiliation(s)
- Wanping Chen
- Department of Food Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, ChinaDepartment of Bacteriology and Genetics, University of Wisconsin-Madison
| | - Mi-Kyung Lee
- Department of Bacteriology and Genetics, University of Wisconsin-Madison
| | - Colin Jefcoate
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison
| | - Sun-Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Dae-Jon, Republic of Korea
| | - Fusheng Chen
- Department of Food Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jae-Hyuk Yu
- Department of Bacteriology and Genetics, University of Wisconsin-Madison
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Vieira DF, Choi JY, Roush WR, Podust LM. Expanding the binding envelope of CYP51 inhibitors targeting Trypanosoma cruzi with 4-aminopyridyl-based sulfonamide derivatives. Chembiochem 2014; 15:1111-20. [PMID: 24771705 PMCID: PMC4091728 DOI: 10.1002/cbic.201402027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 12/29/2022]
Abstract
Chagas disease is a chronic infection caused by the protozoan parasite Trypanosoma cruzi, manifested in progressive cardiomyopathy and/or gastrointestinal dysfunction. Therapeutic options to prevent or treat Chagas disease are limited. CYP51, the enzyme key to the biosynthesis of eukaryotic membrane sterols, is a validated drug target in both fungi and T. cruzi. Sulfonamide derivatives of 4-aminopyridyl-based inhibitors of T. cruzi CYP51 (TcCYP51), including the sub-nanomolar compound 3, have molecular structures distinct from other validated CYP51 inhibitors. They augment the biologically relevant chemical space of molecules targeting TcCYP51. In a 2.08 Å X-ray structure, TcCYP51 is in a conformation that has been influenced by compound 3 and is distinct from the previously characterized ground-state conformation of CYP51 drug-target complexes. That the binding site was modulated in response to an incoming inhibitor for the first time characterizes TcCYP51 as a flexible target rather than a rigid template.
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Affiliation(s)
- Debora F. Vieira
- Department of Pathology, Center for Discovery and Innovation in Parasitic Diseases, University of California San Francisco, 1700 4th Street, San Francisco, California, 94158 (USA), Fax: (+)1 415 502-8193
| | - Jun Yong Choi
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458, (USA), Fax: (+)1 561 228-3052
| | - William R. Roush
- Department of Chemistry, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458, (USA), Fax: (+)1 561 228-3052
| | - Larissa M. Podust
- Department of Pathology, Center for Discovery and Innovation in Parasitic Diseases, University of California San Francisco, 1700 4th Street, San Francisco, California, 94158 (USA), Fax: (+)1 415 502-8193
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46
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Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer. Proc Natl Acad Sci U S A 2014; 111:3865-70. [PMID: 24613931 DOI: 10.1073/pnas.1324245111] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bitopic integral membrane proteins with a single transmembrane helix play diverse roles in catalysis, cell signaling, and morphogenesis. Complete monospanning protein structures are needed to show how interaction between the transmembrane helix and catalytic domain might influence association with the membrane and function. We report crystal structures of full-length Saccharomyces cerevisiae lanosterol 14α-demethylase, a membrane monospanning cytochrome P450 of the CYP51 family that catalyzes the first postcyclization step in ergosterol biosynthesis and is inhibited by triazole drugs. The structures reveal a well-ordered N-terminal amphipathic helix preceding a putative transmembrane helix that would constrain the catalytic domain orientation to lie partly in the lipid bilayer. The structures locate the substrate lanosterol, identify putative substrate and product channels, and reveal constrained interactions with triazole antifungal drugs that are important for drug design and understanding drug resistance.
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47
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Ogungbe IV, Erwin WR, Setzer WN. Antileishmanial phytochemical phenolics: molecular docking to potential protein targets. J Mol Graph Model 2014; 48:105-17. [PMID: 24463105 DOI: 10.1016/j.jmgm.2013.12.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 12/21/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022]
Abstract
A molecular docking analysis has been carried out to examine potential Leishmania protein targets of antiprotozoal plant-derived polyphenolic compounds. A total of 352 phenolic phytochemicals, including 10 aurones, six cannabinoids, 34 chalcones, 20 chromenes, 52 coumarins, 92 flavonoids, 41 isoflavonoids, 52 lignans, 25 quinones, eight stilbenoids, nine xanthones, and three miscellaneous phenolic compounds, were used in the virtual screening study using 24 Leishmania enzymes (52 different protein structures from the Protein Data Bank). Noteworthy protein targets were Leishmania dihydroorotate dehydrogenase, N-myristoyl transferase, phosphodiesterase B1, pteridine reductase, methionyl-tRNA synthetase, tyrosyl-tRNA synthetase, uridine diphosphate-glucose pyrophosphorylase, nicotinamidase, and glycerol-3-phosphate dehydrogenase. Based on in-silico analysis of antiparasitic polyphenolics in this study, two aurones, one chalcone, five coumarins, six flavonoids, one isoflavonoid, three lignans, and one stilbenoid, can be considered to be promising drug leads worthy of further investigation.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William R Erwin
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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48
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Lepesheva GI. Design or screening of drugs for the treatment of Chagas disease: what shows the most promise? Expert Opin Drug Discov 2013; 8:1479-89. [PMID: 24079515 PMCID: PMC3867292 DOI: 10.1517/17460441.2013.845554] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Endemic in Latin America, Chagas disease is now becoming a serious global health problem, and yet has no financial viability for the pharmaceutical industry and remains incurable. In 2012, two antimycotic drugs inhibitors of fungal sterol 14α-demethylase (CYP51) - posaconazole and ravuconazole - entered clinical trials. Availability of the X-ray structure of the orthologous enzyme from the causative agent of the disease, protozoan parasite Trypanosoma cruzi, determined in complexes with posaconazole as well as with several experimental protozoa-specific CYP51 inhibitors opens an excellent opportunity to improve the situation. AREAS COVERED This article summarizes the information available in PubMed and Google on the outcomes of treatment of the chronic Chagas disease. It also outlines the major features of the T. cruzi CYP51 structure and the possible structure-based strategies for rational design of novel T. cruzi specific drugs. EXPERT OPINION There is no doubt that screenings for alternative drug-like molecules as well as mining the T. cruzi genome for novel drug targets are of great value and might eventually lead to groundbreaking discoveries. However, all newly identified molecules must proceed through the long, expensive and low-yielding drug optimization process, and all novel potential drug targets must be validated in terms of their essentiality and druggability. CYP51 is already a well-validated and highly successful target for clinical and agricultural antifungals. With minimal investments into the final stages of their development/trials, T. cruzi-specific CYP51 inhibitors can provide an immediate treatment for Chagas disease, either on their own or in combination with the currently available drugs.
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Affiliation(s)
- Galina I Lepesheva
- Vanderbilt University, Institute for Global Health, School of Medicine, Center for Structural Biology, Department of Biochemistry , 622 RRB, 23rd at Pierce, Nashville, TN 37232 , USA +1 615 343 1373 ; +1 615 322 4349 ;
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49
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Hargrove TY, Wawrzak Z, Alexander PW, Chaplin JH, Keenan M, Charman SA, Perez CJ, Waterman MR, Chatelain E, Lepesheva GI. Complexes of Trypanosoma cruzi sterol 14α-demethylase (CYP51) with two pyridine-based drug candidates for Chagas disease: structural basis for pathogen selectivity. J Biol Chem 2013; 288:31602-15. [PMID: 24047900 DOI: 10.1074/jbc.m113.497990] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Chagas disease, caused by the eukaryotic (protozoan) parasite Trypanosoma cruzi, is an alarming emerging global health problem with no clinical drugs available to treat the chronic stage. Azole inhibitors of sterol 14α-demethylase (CYP51) were proven effective against Chagas, and antifungal drugs posaconazole and ravuconazole have entered clinical trials in Spain, Bolivia, and Argentina. Here we present the x-ray structures of T. cruzi CYP51 in complexes with two alternative drug candidates, pyridine derivatives (S)-(4-chlorophenyl)-1-(4-(4-(trifluoromethyl)phenyl)-piperazin-1-yl)-2-(pyridin-3-yl)ethanone (UDO; Protein Data Bank code 3ZG2) and N-[4-(trifluoromethyl)phenyl]-N-[1-[5-(trifluoromethyl)-2-pyridyl]-4-piperi-dyl]pyridin-3-amine (UDD; Protein Data Bank code 3ZG3). These compounds have been developed by the Drugs for Neglected Diseases initiative (DNDi) and are highly promising antichagasic agents in both cellular and in vivo experiments. The binding parameters and inhibitory effects on sterol 14α-demethylase activity in reconstituted enzyme reactions confirmed UDO and UDD as potent and selective T. cruzi CYP51 inhibitors. Comparative analysis of the pyridine- and azole-bound CYP51 structures uncovered the features that make UDO and UDD T. cruzi CYP51-specific. The structures suggest that although a precise fit between the shape of the inhibitor molecules and T. cruzi CYP51 active site topology underlies their high inhibitory potency, a longer coordination bond between the catalytic heme iron and the pyridine nitrogen implies a weaker influence of pyridines on the iron reduction potential, which may be the basis for the observed selectivity of these compounds toward the target enzyme versus other cytochrome P450s, including human drug-metabolizing P450s. These findings may pave the way for the development of novel CYP51-targeted drugs with optimized metabolic properties that are very much needed for the treatment of human infections caused by eukaryotic microbial pathogens.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232
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50
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Abstract
X-ray crystal structures are available for 29 eukaryotic microsomal, chloroplast, or mitochondrial cytochrome P450s, including two non-monooxygenase P450s. These structures provide a basis for understanding structure-function relations that underlie their distinct catalytic activities. Moreover, structural plasticity has been characterized for individual P450s that aids in understanding substrate binding in P450s that mediate drug clearance.
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Affiliation(s)
- Eric F Johnson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.
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