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Režen T, Ogris I, Sever M, Merzel F, Golic Grdadolnik S, Rozman D. Evaluation of Selected CYP51A1 Polymorphisms in View of Interactions with Substrate and Redox Partner. Front Pharmacol 2017; 8:417. [PMID: 28713270 PMCID: PMC5492350 DOI: 10.3389/fphar.2017.00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 06/13/2017] [Indexed: 01/16/2023] Open
Abstract
Cholesterol is essential for development, growth, and maintenance of organisms. Mutations in cholesterol biosynthetic genes are embryonic lethal and few polymorphisms have been so far associated with pathologies in humans. Previous analyses show that lanosterol 14α-demethylase (CYP51A1) from the late part of cholesterol biosynthesis has only a few missense mutations with low minor allele frequencies and low association with pathologies in humans. The aim of this study is to evaluate the role of amino acid changes in the natural missense mutations of the hCYP51A1 protein. We searched SNP databases for existing polymorphisms of CYP51A1 and evaluated their effect on protein function. We found rare variants causing detrimental missense mutations of CYP51A1. Some missense variants were also associated with a phenotype in humans. Two missense variants have been prepared for testing enzymatic activity in vitro but failed to produce a P450 spectrum. We performed molecular modeling of three selected missense variants to evaluate the effect of the amino acid substitution on potential interaction with its substrate and the obligatory redox partner POR. We show that two of the variants, R277L and especially D152G, have possibly lower binding potential toward obligatory redox partner POR. D152G and R431H have also potentially lower affinity toward the substrate lanosterol. We evaluated the potential effect of damaging variants also using data from other in vitro CYP51A1 mutants. In conclusion, we propose to include damaging CYP51A1 variants into personalized diagnostics to improve genetic counseling for certain rare disease phenotypes.
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Affiliation(s)
- Tadeja Režen
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
| | - Iza Ogris
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
| | - Marko Sever
- Department of Biomolecular Structure, National Institute of ChemistryLjubljana, Slovenia
| | - Franci Merzel
- Department of Biomolecular Structure, National Institute of ChemistryLjubljana, Slovenia
| | | | - Damjana Rozman
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, University of LjubljanaLjubljana, Slovenia
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Shcherbinin DS, Gnedenko OV, Khmeleva SA, Usanov SA, Gilep AA, Yantsevich AV, Shkel TV, Yushkevich IV, Radko SP, Ivanov AS, Veselovsky AV, Archakov AI. Computer-aided design of aptamers for cytochrome p450. J Struct Biol 2015; 191:112-9. [PMID: 26166326 DOI: 10.1016/j.jsb.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
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Affiliation(s)
- Dmitrii S Shcherbinin
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
| | - Oksana V Gnedenko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Sergey A Usanov
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Aliaksei V Yantsevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Tatsiana V Shkel
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Ivan V Yushkevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Alexis S Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | | | - Alexander I Archakov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
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Kaluzhsiy LA, Gnedenko OV, Gilep AA, Strushkevich NV, Shkel TV, Chernovetsky MA, Ivanov AS, Lisitsa AV, Usanov AS, Stonik VA, Archakov AI. [The screening of the inhibitors of the human cytochrome P450(51) (CYP51A1): the plant and animal structural lanosterol's analogs]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 60:528-37. [PMID: 25386880 DOI: 10.18097/pbmc20146005528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The cholesterol biosynthesis regulation is the important part of the hypercholesterolemia diseases therapy. The inhibition of the post-squalene cholesterol biosynthesis steps provide the alternative to classic statin therapy. Sterol-14a-demethylase (CYP51) is one of the hypothetical targets for it. In this work the screening of the ability to interact with human CYP51 (CYP51A1) for the nature low-weight compounds with steroid-like scaffold were performed by integration of the surface plasmon resonance biosensor and spectral titration methods. The results of the selection were 4 compounds (betulafolientriol, holothurin A, teasaponin, capsicoside A) witch had high affinity to the CYP51A1 active site. These data extend the range of compounds which may be used as specific inhibitors of CYP51 and give the permission to suggest the dynamic of the enzyme.
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Kaluzhskiy LA, Gnedenko OV, Gilep AA, Strushkevich NV, Shkel TV, Chernovetsky MA, Ivanov AS, Lisitsa AV, Usanov AS, Stonik VA, Archakov AI. Screening of human cytochrome P450(51) (CYP51A1) inhibitors: Structural lanosterol analogues of plant and animal origin. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2014. [DOI: 10.1134/s199075081404012x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gnedenko OV, Kaluzhskiy LA, Molnar AA, Yantsevich AV, Mukha DV, Gilep AA, Usanov SA, Stonik VA, Ivanov AS, Lisitsa AV, Archakov AI. The SPR-based biosensor test system for analysis of small compounds interaction with human cytochrome P450 51A1 (CYP51A1). BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2013. [DOI: 10.1134/s1990750813030049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gnedenko O, Kaluzhskiy L, Molnar A, Yantsevich A, Mukha D, Gilep A, Usanov S, Stonik V, Ivanov A, Lisitsa A, Archakov A. SPR-biosensor assay for analysis of small compounds interaction with human cytochrome P450 51A1 (CYP51A1). ACTA ACUST UNITED AC 2013; 59:388-98. [DOI: 10.18097/pbmc20135904388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The SPR assay for human cytochrome P450 51A1's (CYP51A1) ligand screening was developed. Assay has been validated with known azole inhibitors of cytochrome P450s. The studied azoles selectively interacted with human cytochrome P450 51A1, which showed the highest affinity towards ketoconazole. The efficiency of the SPR assay was showed with 19 steroid and triterpene compounds, which were not investigated as potential ligands of CYP51A1.
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Affiliation(s)
- O.V. Gnedenko
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| | - L.A. Kaluzhskiy
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| | - A.A. Molnar
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| | | | | | | | | | - V.A. Stonik
- Pacific Institute of Bioorganic Chemistry, Far East Branch of Russian Academy of Sciences
| | - A.S. Ivanov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| | - A.V. Lisitsa
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
| | - A.I. Archakov
- Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences
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