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Denisov IG, Grinkova YV, Sligar SG. Optical annealing of peroxo-ferric intermediates in CYP17A1 and product formation. J Inorg Biochem 2024; 260:112701. [PMID: 39173495 DOI: 10.1016/j.jinorgbio.2024.112701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
Human cytochrome P450 CYP17A1 catalyzes the hydroxylation of pregnenolone and progesterone at the C17 position, with subsequent C17-C20 bond scission, to form dehydroepiandrosterone and androstenedione respectively. The first hydroxylation reaction is faster in H2O than in D2O, while the second carbon‑carbon bond scission event demonstrates an inverse solvent isotope effect, which is more pronounced for 17-hydroxy pregnenolone. In order to better understand the cause of this difference, we compared the optical absorption spectra of oxygenated CYP17A1 with the four substrates (pregnenolone, progesterone, 17-hydroxy pregnenolone and 17-hydroxy progesterone) in both H2O and D2O. We also studied the temperature-dependent decay of the peroxo-ferric and hydroperoxo-ferric intermediates generated by cryoradiolysis of the corresponding oxygenated heme proteins at 77 K. For both pregnenolone and 17-hydroxypregnenolone, annealing of the peroxo-intermediates was observed at lower temperatures in H2O than in D2O. In contrast, no solvent isotope effect was detected when progesterone or 17-hydroxyprogesterone were used as substrates. These differences are attributed to their different positioning in the P450 active site with respect to the heme bound peroxo (Fe-OO-) moiety, which is in agreement with earlier structural and spectroscopic investigations. Analysis of the samples run in both H2O and in D2O, where 17-hydroxyprogesterone is the substrate, demonstrated significant (∼25%) yield of androstenedione product relative to the oxygenated starting material.
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Affiliation(s)
- Ilia G Denisov
- Departments of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yelena V Grinkova
- Departments of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephen G Sligar
- Departments of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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2
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Potter JR, Rivera S, Young PG, Patterson DC, Namitz KE, Yennawar N, Kincaid JR, Liu Y, Weinert EE. Heme pocket modulates protein conformation and diguanylate cyclase activity of a tetrameric globin coupled sensor. J Inorg Biochem 2024; 258:112638. [PMID: 38878680 DOI: 10.1016/j.jinorgbio.2024.112638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/01/2024]
Abstract
Bacteria use the second messenger cyclic dimeric guanosine monophosphate (c-di-GMP) to control biofilm formation and other key phenotypes in response to environmental signals. Changes in oxygen levels can alter c-di-GMP signaling through a family of proteins termed globin coupled sensors (GCS) that contain diguanylate cyclase domains. Previous studies have found that GCS diguanylate cyclase activity is controlled by ligand binding to the heme within the globin domain, with oxygen binding resulting in the greatest increase in catalytic activity. Herein, we present evidence that heme-edge residues control O2-dependent signaling in PccGCS, a GCS protein from Pectobacterium carotovorum, by modulating heme distortion. Using enzyme kinetics, resonance Raman spectroscopy, small angle X-ray scattering, and multi-wavelength analytical ultracentrifugation, we have developed an integrated model of the full-length PccGCS tetramer and have identified conformational changes associated with ligand binding, heme conformation, and cyclase activity. Taken together, these studies provide new insights into the mechanism by which O2 binding modulates activity of diguanylate cyclase-containing GCS proteins.
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Affiliation(s)
- Jacob R Potter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Shannon Rivera
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Paul G Young
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Dayna C Patterson
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Kevin E Namitz
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA.
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA; Department of Chemistry, University of Akron, Akron, OH 44325, USA.
| | - Emily E Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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Joshi BP, Bhandare VV, Vankawala M, Patel P, Patel R, Vyas B, Krishnamurty R. Friedelin, a novel inhibitor of CYP17A1 in prostate cancer from Cassia tora. J Biomol Struct Dyn 2023; 41:9695-9720. [PMID: 36373336 DOI: 10.1080/07391102.2022.2145497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022]
Abstract
In prostate cancer (PC), drugs targeting CYP17A1 have shown great success in regulating PC progression. However, successful drug molecules show adverse side effects and therapeutic resistance in PC. Therefore, we proposed to discover the potent phytochemical-based inhibitor against CYP17A1 using virtual screening. In this study, a phytochemicals library of ∼13800 molecules was selected to screen the best possible inhibitors against CYP17A1. A molecular modelling approach investigated detailed intermolecular interactions, their structural stability, and binding affinity. Further, in vitro and in vivo studies were performed to confirm the anticancer activity of identified potential inhibitor against CYP17A1. Friedelin from Cassia tora (CT) is identified as the best possible inhibitor from the screened library. MD simulation study reveals stable binding of Friedelin to conserved binding pocket of CYP17A1 with higher binding affinity than studied control, that is, Orteronel. Friedelin was tested on hormone-sensitive (22Rv1) and insensitive (DU145) cell lines and the IC50 value was found to be 72.025 and 81.766 µg/ml, respectively. CT extract showed a 25.28% IC50 value against 22Rv1, ∼92.6% increase in late Apoptosis/Necrosis, and three folds decrease in early apoptosis in treated cells compared to untreated cells. Further, animal studies show a marked decrease in prostate weight by 39.6% and prostate index by 36.5%, along with a reduction in serum PSA level by 71.7% and testosterone level by 92.4% compared to the testosterone group, which was further validated with histopathological studies. Thus, we propose Friedelin and CT extract as potential leads, which could be taken further for drug development in PC.[Figure: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Mahima Vankawala
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Prittesh Patel
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Surat, Gujarat, India
| | - Rajesh Patel
- Bioinformatics and Supercomputer Lab., Department of Biosciences (UGC-SAP-DRS-II & DST-FIST-I), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Bhavin Vyas
- Department of Pharmacology, Maliba Pharmacy College, Uka Tarsadia University, Tarsadi, Surat, Gujarat, India
| | - Ramar Krishnamurty
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Surat, Gujarat, India
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Denisov IG, Sligar SG. Solvent isotope effects in the catalytic cycle of P450 CYP17A1: Computational modeling of the hydroxylation and lyase reactions. J Inorg Biochem 2023; 243:112202. [PMID: 37004494 PMCID: PMC10128154 DOI: 10.1016/j.jinorgbio.2023.112202] [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: 01/05/2023] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
The catalytic cycle of the cytochromes P450 (CYP) requires two electrons from a protein redox partner and two protons from water to generate the main catalytic intermediate, a ferryl-oxo complex with π-cation on the heme porphyrin ring, termed Compound 1. The protonation steps are at least partially rate-limiting, therefore the steady-state rates of P450 catalysis are usually slower in deuterated solvent (D2O) by a factor of 1.5-3. However, in several P450 systems a pronounced inverse kinetic solvent isotope effect (KSIE ∼0.4-0.7) is observed, where the reaction is faster in D2O. This raises an important mechanistic question: Is this inverse solvent isotope effect compatible with Compound 1 catalyzed reactions, or is it indicative of another catalytic intermediate being involved? In this communication we use exhaustive numerical modeling of the P450 steady-state kinetics to demonstrate that a significant inverse KSIE cannot be obtained for a pure Compound 1 driven catalytic cycle of P450. Rather, an alternative, protonation independent, catalytic intermediate needs to be introduced. This result is applicable to the broad spectrum of P450s in nature, but as an example we use the extensively documented inverse isotope effect in the human steroid biosynthetic P450 CYP17A1 where the involvement of a heme peroxo anion intermediate has been characterized. Based on this analysis, we show that the observation of an inverse KSIE can be used as a general mechanistic probe for reaction cycle intermediates in the cytochromes P450.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America.
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Liu Y, Denisov I, Gregory M, Sligar SG, Kincaid JR. Importance of Asparagine 202 in Manipulating Active Site Structure and Substrate Preference for Human CYP17A1. Biochemistry 2022; 61:583-594. [PMID: 35287432 PMCID: PMC9972851 DOI: 10.1021/acs.biochem.2c00023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The multifunctional cytochrome P450 17A1 (CYP17A1) plays a crucial role in human steroid hormone synthesis (UniProtKB─P05093). It first carries out standard monooxygenase chemistry, converting pregnenolone (PREG) and progesterone (PROG) into 17OH-PREG and 17OH-PROG, utilizing a "Compound I" to initiate hydrogen abstraction and radical recombination in the classic "oxygen rebound" mechanism. Additionally, these hydroxylated products also serve as substrates in a second oxidative cycle which cleaves the 17-20 carbon-carbon bond to form dehydroepiandrosterone and androstenedione, which are key precursors in the generation of powerful androgens and estrogens. Interestingly, in humans, with 17OH-PREG, this so-called lyase reaction is more efficient than with 17OH-PROG, based on Kcat/Km values. In the present work, the asparagine residue at 202 position was replaced by serine, an alteration which can affect substrate orientation and control substrate preference for the lyase reaction. First, we report studies of solvent isotope effects for the N202S CYP17A1 mutant in the presence of 17OH-PREG and 17OH-PROG, which suggest that the ferric peroxo species is the predominant catalytically active intermediate in the lyase step. This conclusion is further supported by employing a combination of cryoradiolysis and resonance Raman techniques to successfully trap and structurally characterize the key reaction intermediates, including the peroxo, the hydroperoxo, and the crucial peroxo-hemiketal intermediate. Collectively, these studies show that the mutation causes active site structural changes that alter the H-bonding interactions with the key Fe-O-O fragment and the degree of protonation of the reactive ferric peroxo intermediate, thereby impacting lyase efficiency.
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Affiliation(s)
- Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Ilia Denisov
- Departments of Chemistry and Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Michael Gregory
- Departments of Chemistry and Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Departments of Chemistry and Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
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