1
|
Wróbel TM, Bartuzi D, Kaczor AA. Secondary Binding Site of CYP17A1 in Enhanced Sampling Simulations. J Chem Inf Model 2024. [PMID: 39325660 DOI: 10.1021/acs.jcim.4c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Androgens like testosterone and dihydrotestosterone play a key role in prostate cancer progression, making the enzyme CYP17A1, essential for androgen synthesis, a crucial therapeutic target. Recent studies have revealed electron density at the substrate entry channel, suggesting the presence of a secondary binding site. In this study, we calculated the binding free energy landscape of known ligands at this site using Funnel Metadynamics. Our results characterize this binding site and indicate that nonheme-interacting ligands could effectively bind to CYP17A1, providing a novel approach to the design of CYP17A1 inhibitors.
Collapse
Affiliation(s)
- Tomasz M Wróbel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., 20093 Lublin, Poland
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., 20093 Lublin, Poland
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., 20093 Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, 70211 Kuopio, Finland
| |
Collapse
|
2
|
Kędzierski J, Jäger MC, Naeem S, Odermatt A, Smieško M. In silico and in vitro assessment of drugs potentially causing adverse effects by inhibiting CYP17A1. Toxicol Appl Pharmacol 2024; 486:116945. [PMID: 38688424 DOI: 10.1016/j.taap.2024.116945] [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: 01/18/2024] [Revised: 04/11/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Cytochrome P450 enzymes (CYPs) play a crucial role in the metabolism and synthesis of various compound classes. While drug-metabolizing CYP enzymes are frequently investigated as anti-targets, the inhibition of CYP enzymes involved in adrenal steroidogenesis is not well studied. The steroidogenic enzyme CYP17A1 is a dual-function enzyme catalyzing hydroxylase and lyase reactions relevant for the biosynthesis of adrenal glucocorticoids and androgens. Inhibition of CYP17A1-hydroxylase leads to pseudohyperaldosteronism with subsequent excessive mineralocorticoid receptor activation, hypertension and hypokalemia. In contrast, specific inhibition of the lyase function might be beneficial for the treatment of prostate cancer by decreasing adrenal androgen levels. This study combined in silico and in vitro methods to identify drugs inhibiting CYP17A1. The most potent CYP17A1 inhibitors identified are serdemetan, mocetinostat, nolatrexed, liarozole, and talarozole. While some of these drugs are currently under investigation for the treatment of various cancers, their potential for the treatment of prostate cancer is yet to be explored. The DrugBank database was screened for CYP17A1 inhibitors, to increase the awareness for the risk of drug-induced pseudohyperaldosteronism and to highlight drugs so far unknown for their potential to cause side effects resulting from CYP17A1 inhibition.
Collapse
Affiliation(s)
- Jacek Kędzierski
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland.
| | - Marie-Christin Jäger
- Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland.
| | - Sadaf Naeem
- Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Department of Biochemistry, University of Karachi, KU, Circular Road, Karachi, Pakistan
| | - Alex Odermatt
- Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland.
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel 4056, Switzerland; Swiss Centre for Human Applied Toxicology, University of Basel, Missionsstrasse 64, Basel 4055, Switzerland.
| |
Collapse
|
3
|
Exploring the Chemical Space of CYP17A1 Inhibitors Using Cheminformatics and Machine Learning. Molecules 2023; 28:molecules28041679. [PMID: 36838665 PMCID: PMC9966999 DOI: 10.3390/molecules28041679] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 02/12/2023] Open
Abstract
Cytochrome P450 17A1 (CYP17A1) is one of the key enzymes in steroidogenesis that produces dehydroepiandrosterone (DHEA) from cholesterol. Abnormal DHEA production may lead to the progression of severe diseases, such as prostatic and breast cancers. Thus, CYP17A1 is a druggable target for anti-cancer molecule development. In this study, cheminformatic analyses and quantitative structure-activity relationship (QSAR) modeling were applied on a set of 962 CYP17A1 inhibitors (i.e., consisting of 279 steroidal and 683 nonsteroidal inhibitors) compiled from the ChEMBL database. For steroidal inhibitors, a QSAR classification model built using the PubChem fingerprint along with the extra trees algorithm achieved the best performance, reflected by the accuracy values of 0.933, 0.818, and 0.833 for the training, cross-validation, and test sets, respectively. For nonsteroidal inhibitors, a systematic cheminformatic analysis was applied for exploring the chemical space, Murcko scaffolds, and structure-activity relationships (SARs) for visualizing distributions, patterns, and representative scaffolds for drug discoveries. Furthermore, seven total QSAR classification models were established based on the nonsteroidal scaffolds, and two activity cliff (AC) generators were identified. The best performing model out of these seven was model VIII, which is built upon the PubChem fingerprint along with the random forest algorithm. It achieved a robust accuracy across the training set, the cross-validation set, and the test set, i.e., 0.96, 0.92, and 0.913, respectively. It is anticipated that the results presented herein would be instrumental for further CYP17A1 inhibitor drug discovery efforts.
Collapse
|
4
|
Gumede NJ. Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PL pro Inhibitors. Molecules 2022; 27:8569. [PMID: 36500659 PMCID: PMC9741453 DOI: 10.3390/molecules27238569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
A global pandemic caused by the SARS-CoV-2 virus that started in 2020 and has wreaked havoc on humanity still ravages up until now. As a result, the negative impact of travel restrictions and lockdowns has underscored the importance of our preparedness for future pandemics. The main thrust of this work was based on addressing this need by traversing chemical space to design inhibitors that target the SARS-CoV-2 papain-like protease (PLpro). Pathfinder-based retrosynthesis analysis was used to generate analogs of GRL-0617 using commercially available building blocks by replacing the naphthalene moiety. A total of 10 models were built using active learning QSAR, which achieved good statistical results such as an R2 > 0.70, Q2 > 0.64, STD Dev < 0.30, and RMSE < 0.31, on average for all models. A total of 35 ideas were further prioritized for FEP+ calculations. The FEP+ results revealed that compound 45 was the most active compound in this series with a ΔG of −7.28 ± 0.96 kcal/mol. Compound 5 exhibited a ΔG of −6.78 ± 1.30 kcal/mol. The inactive compounds in this series were compound 91 and compound 23 with a ΔG of −5.74 ± 1.06 and −3.11 ± 1.45 kcal/mol. The combined strategy employed here is envisaged to be of great utility in multiparameter lead optimization efforts, to traverse chemical space, maintaining and/or improving the potency as well as the property space of synthetically aware design ideas.
Collapse
Affiliation(s)
- Njabulo Joyfull Gumede
- Department of Chemistry, Mangosuthu University of Technology, P.O. Box 12363, Jacobs 4026, South Africa
| |
Collapse
|
5
|
Padmakar Darne C, Velaparthi U, Saulnier M, Frennesson D, Liu P, Huang A, Tokarski J, Fura A, Spires T, Newitt J, Spires VM, Obermeier MT, Elzinga PA, Gottardis MM, Jayaraman L, Vite GD, Balog A. The Discovery of BMS-737 as a Potent, CYP17 Lyase-Selective Inhibitor for the Treatment of Castration-Resistant Prostate Cancer. Bioorg Med Chem Lett 2022; 75:128951. [PMID: 36031020 DOI: 10.1016/j.bmcl.2022.128951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/14/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022]
Abstract
We report herein, the discovery of BMS-737 (compound 33) as a potent, non-steroidal, reversible small molecule inhibitor demonstrating 11-fold selectivity for CYP17 lyase over CYP17 hydroxylase, as well as a clean xenobiotic CYP profile for the treatment of castration-resistant prostate cancer (CRPC). Extensive SAR studies on the initial lead 1 at three different regions of the molecule resulted in the identification of BMS-737, which demonstrated a robust 83% lowering of testosterone without any significant perturbation of the mineralocorticoid and glucocorticoid levels in cynomologous monkeys in a 1-day PK/PD study.
Collapse
Affiliation(s)
| | - Upender Velaparthi
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States.
| | - Mark Saulnier
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - David Frennesson
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Peiying Liu
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Audris Huang
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - John Tokarski
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Aberra Fura
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Thomas Spires
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - John Newitt
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Vanessa M Spires
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Mary T Obermeier
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Paul A Elzinga
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Marco M Gottardis
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Lata Jayaraman
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Gregory D Vite
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| | - Aaron Balog
- Bristol-Myers Squibb Company, P.O. Box 4000, Princeton, NJ 08543, United States
| |
Collapse
|
6
|
Investigation of new schiff base transition metal (II) complexes theoretical, antidiabetic and molecular docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
7
|
Design and synthesis of 6-amino-quinoxaline-alkynyl as potential aromatase (CYP19A1) inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|