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Dudas B, Miteva MA. Computational and artificial intelligence-based approaches for drug metabolism and transport prediction. Trends Pharmacol Sci 2024; 45:39-55. [PMID: 38072723 DOI: 10.1016/j.tips.2023.11.001] [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: 08/02/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/07/2024]
Abstract
Drug metabolism and transport, orchestrated by drug-metabolizing enzymes (DMEs) and drug transporters (DTs), are implicated in drug-drug interactions (DDIs) and adverse drug reactions (ADRs). Reliable and precise predictions of DDIs and ADRs are critical in the early stages of drug development to reduce the rate of drug candidate failure. A variety of experimental and computational technologies have been developed to predict DDIs and ADRs. Recent artificial intelligence (AI) approaches offer new opportunities for better predicting and understanding the complex processes related to drug metabolism and transport. We summarize the role of major DMEs and DTs, and provide an overview of current progress in computational approaches for the prediction of drug metabolism, transport, and DDIs, with an emphasis on AI including machine learning (ML) and deep learning (DL) modeling.
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Affiliation(s)
- Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Maria A Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France.
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2
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Levine DS, Jacobson LD, Bochevarov AD. Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase. J Chem Theory Comput 2023; 19:9302-9317. [PMID: 38085599 DOI: 10.1021/acs.jctc.3c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.
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Affiliation(s)
- Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, Oregon 97204, United States
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States
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3
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Wang Y, Yuan H, Liu N, Tang S, Feng Y, Liu Y, Cai P, Xia L, Zheng W, Chen Y, Zhou Z. High Affinity and FAP-Targeted Radiotracers: A Potential Design Strategy to Improve the Pharmacokinetics and Tumor Uptake for FAP Inhibitors. J Med Chem 2023. [PMID: 37390480 DOI: 10.1021/acs.jmedchem.3c00259] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Fibroblast activation protein (FAP) is overexpressed in cancer-associated fibroblasts, making it an attractive target for both imaging and therapy of malignancy. This study presents a range of novel FAP inhibitors derived from amino derivatives of UAMC1110, incorporating polyethylene glycol and bulky groups containing bifunctional DOTA chelators. The compounds labeled with gallium-68 were developed and characterized to study biodistribution properties and tumor-targeting performance in nude mice bearing U87MG tumor xenografts. Several tracers of interest were screened due to the advantages in imaging and tumor-specific uptake. Positron emission tomography scans revealed that polyethylene glycol-modified 68Ga-3-3 had a rapid penetration within the neoplastic tissue and excellent tumor-to-background contrast. In a comparative biodistribution study, naphthalene-modified 68Ga-6-3 exhibited more significant tumor uptake (∼50% ID/g, 1 h p.i.) than 68Ga-3-3 and 10-fold higher than 68Ga-FAPI-04 under the same conditions. Remarkably, 68Ga-8-1, combining the two structural design strategies, obtains superior imaging performance.
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Affiliation(s)
- Yinwen Wang
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Hongmei Yuan
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Nan Liu
- Department of Nuclear Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China
| | - Sufan Tang
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yue Feng
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Institute of Nuclear Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yang Liu
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Institute of Nuclear Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Ping Cai
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Li Xia
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Wenlu Zheng
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Institute of Nuclear Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yue Chen
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Institute of Nuclear Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Zhijun Zhou
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan 646000, China
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
- Institute of Nuclear Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China
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4
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Huang M, Zhu K, Wang Y, Lou C, Sun H, Li W, Tang Y, Liu G. In Silico Prediction of Metabolic Reaction Catalyzed by Human Aldehyde Oxidase. Metabolites 2023; 13:metabo13030449. [PMID: 36984889 PMCID: PMC10059660 DOI: 10.3390/metabo13030449] [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: 03/07/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Aldehyde oxidase (AOX) plays an important role in drug metabolism. Human AOX (hAOX) is widely distributed in the body, and there are some differences between species. Currently, animal models cannot accurately predict the metabolism of hAOX. Therefore, more and more in silico models have been constructed for the prediction of the hAOX metabolism. These models are based on molecular docking and quantum chemistry theory, which are time-consuming and difficult to automate. Therefore, in this study, we compared traditional machine learning methods, graph convolutional neural network methods, and sequence-based methods with limited data, and proposed a ligand-based model for the metabolism prediction catalyzed by hAOX. Compared with the published models, our model achieved better performance (ACC = 0.91, F1 = 0.77). What's more, we built a web server to predict the sites of metabolism (SOMs) for hAOX. In summary, this study provides a convenient and automatable model and builds a web server named Meta-hAOX for accelerating the drug design and optimization stage.
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Affiliation(s)
- Mengting Huang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Keyun Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chaofeng Lou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huimin Sun
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Öeren M, Walton PJ, Suri J, Ponting DJ, Hunt PA, Segall MD. Predicting Regioselectivity of AO, CYP, FMO, and UGT Metabolism Using Quantum Mechanical Simulations and Machine Learning. J Med Chem 2022; 65:14066-14081. [PMID: 36239985 DOI: 10.1021/acs.jmedchem.2c01303] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unexpected metabolism in modification and conjugation phases can lead to the failure of many late-stage drug candidates or even withdrawal of approved drugs. Thus, it is critical to predict the sites of metabolism (SoM) for enzymes, which interact with drug-like molecules, in the early stages of the research. This study presents methods for predicting the isoform-specific metabolism for human AOs, FMOs, and UGTs and general CYP metabolism for preclinical species. The models use semi-empirical quantum mechanical simulations, validated using experimentally obtained data and DFT calculations, to estimate the reactivity of each SoM in the context of the whole molecule. Ligand-based models, trained and tested using high-quality regioselectivity data, combine the reactivity of the potential SoM with the orientation and steric effects of the binding pockets of the different enzyme isoforms. The resulting models achieve κ values of up to 0.94 and AUC of up to 0.92.
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Affiliation(s)
- Mario Öeren
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K
| | - Peter J Walton
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K.,School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - James Suri
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K.,School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, U.K
| | - David J Ponting
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, U.K
| | - Peter A Hunt
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K
| | - Matthew D Segall
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K
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Toselli F, Golding M, Nicolaï J, Gillent E, Chanteux H. Drug clearance by aldehyde oxidase: can we avoid clinical failure? Xenobiotica 2022; 52:890-903. [PMID: 36170034 DOI: 10.1080/00498254.2022.2129519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Despite increased awareness of aldehyde oxidase (AO) as a major drug-metabolising enzyme, predicting the pharmacokinetics of its substrates remains challenging. Several drug candidates have been terminated due to high clearance, which were subsequently discovered to be AO substrates. Even retrospective extrapolation of human clearance, from models more sensitive to AO activity, often resulted in underprediction.The questions of the current work thus were: Is there an acceptable degree of in vitro AO metabolism that does not result in high in vivo human clearance? And, if so, how can this be predicted?We built an in vitro/in vivo correlation using known AO substrates, combining multiple in vitro parameters to calculate the blood metabolic clearance mediated by AO (CLbAO). This value was compared with observed blood clearance (CLb-obs), establishing cut-off CLbAO values, to discriminate between low and high CLb-obs. The model was validated using additional literature compounds, and CLb-obs was predicted in the correct category.This simple, categorical, semi-quantitative yet multi-factorial model is readily applicable in drug discovery. Further, it is valuable for high-clearance compounds, as it predicts the CLb group, rather than an exact CLb value, for the substrates of this poorly-characterised enzyme.
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Affiliation(s)
| | | | - Johan Nicolaï
- Development Science, UCB Biopharma, Braine-l'Alleud, Belgium
| | - Eric Gillent
- Development Science, UCB Biopharma, Braine-l'Alleud, Belgium
| | - Hugues Chanteux
- Development Science, UCB Biopharma, Braine-l'Alleud, Belgium
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7
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Non-cytochrome P450 enzymes involved in the oxidative metabolism of xenobiotics: Focus on the regulation of gene expression and enzyme activity. Pharmacol Ther 2021; 233:108020. [PMID: 34637840 DOI: 10.1016/j.pharmthera.2021.108020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/25/2021] [Accepted: 10/04/2021] [Indexed: 12/16/2022]
Abstract
Oxidative metabolism is one of the major biotransformation reactions that regulates the exposure of xenobiotics and their metabolites in the circulatory system and local tissues and organs, and influences their efficacy and toxicity. Although cytochrome (CY)P450s play critical roles in the oxidative reaction, extensive CYP450-independent oxidative metabolism also occurs in some xenobiotics, such as aldehyde oxidase, xanthine oxidoreductase, flavin-containing monooxygenase, monoamine oxidase, alcohol dehydrogenase, or aldehyde dehydrogenase-dependent oxidative metabolism. Drugs form a large portion of xenobiotics and are the primary target of this review. The common reaction mechanisms and roles of non-CYP450 enzymes in metabolism, factors affecting the expression and activity of non-CYP450 enzymes in terms of inhibition, induction, regulation, and species differences in pharmaceutical research and development have been summarized. These non-CYP450 enzymes are detoxifying enzymes, although sometimes they mediate severe toxicity. Synthetic or natural chemicals serve as inhibitors for these non-CYP450 enzymes. However, pharmacokinetic-based drug interactions through these inhibitors have rarely been reported in vivo. Although multiple mechanisms participate in the basal expression and regulation of non-CYP450 enzymes, only a limited number of inducers upregulate their expression. Therefore, these enzymes are considered non-inducible or less inducible. Overall, this review focuses on the potential xenobiotic factors that contribute to variations in gene expression levels and the activities of non-CYP450 enzymes.
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8
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Soltani S, Hallaj-Nezhadi S, Rashidi MR. A comprehensive review of in silico approaches for the prediction and modulation of aldehyde oxidase-mediated drug metabolism: The current features, challenges and future perspectives. Eur J Med Chem 2021; 222:113559. [PMID: 34119831 DOI: 10.1016/j.ejmech.2021.113559] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 01/09/2023]
Abstract
The importance of aldehyde oxidase (AOX) in drug metabolism necessitates the development and application of the in silico rational drug design methods as an integral part of drug discovery projects for the early prediction and modulation of AOX-mediated metabolism. The current study represents an up-to-date and thorough review of in silico studies of AOX-mediated metabolism and modulation methods. In addition, the challenges and the knowledge gap that should be covered have been discussed. The importance of aldehyde oxidase (AOX) in drug metabolism is a hot topic in drug discovery. Different strategies are available for the modulation of the AOX-mediated metabolism of drugs. Application of the rational drug design methods as an integral part of drug discovery projects is necessary for the early prediction of AOX-mediated metabolism. The current study represents a comprehensive review of AOX molecular structure, AOX-mediated reactions, AOX substrates, AOX inhibition, approaches to modify AOX-mediated metabolism, prediction of AOX metabolism/substrates/inhibitors, and the AOX related structure-activity relationship (SAR) studies. Furthermore, an up-to-date and thorough review of in silico studies of AOX metabolism has been carried out. In addition, the challenges and the knowledge gap that should be covered in the scientific literature have been discussed in the current review.
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Affiliation(s)
- Somaieh Soltani
- Pharmaceutical Analysis Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Somayeh Hallaj-Nezhadi
- Drug Applied Research Center and Pharmacy Faculty, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Rashidi
- Stem Cell and Regenerative Medicine Institute and Pharmacy faculty, Tabriz University of Medical Sciences, Iran.
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Dhuria NV, Haro B, Kapadia A, Lobo KA, Matusow B, Schleiff MA, Tantoy C, Sodhi JK. Recent developments in predicting CYP-independent metabolism. Drug Metab Rev 2021; 53:188-206. [PMID: 33941024 DOI: 10.1080/03602532.2021.1923728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
As lead optimization efforts have successfully reduced metabolic liabilities due to cytochrome P450 (CYP)-mediated metabolism, there has been an increase in the frequency of involvement of non-CYP enzymes in the metabolism of investigational compounds. Although there have been numerous notable advancements in the characterization of non-CYP enzymes with respect to their localization, reaction mechanisms, species differences and identification of typical substrates, accurate prediction of non-CYP-mediated clearance, with a particular emphasis with the difficulties in accounting for any extrahepatic contributions, remains a challenge. The current manuscript comprehensively summarizes the recent advancements in the prediction of drug metabolism and the in vitro to in vitro extrapolation of clearance for substrates of non-CYP drug metabolizing enzymes.
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Affiliation(s)
- Nikhilesh V Dhuria
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bianka Haro
- School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Amit Kapadia
- California Poison Control Center, University of California San Francisco, San Diego, CA, USA
| | | | - Bernice Matusow
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA
| | - Mary A Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christina Tantoy
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA
| | - Jasleen K Sodhi
- Department of Drug Metabolism and Pharmacokinetics, Plexxikon Inc, Berkeley, CA, USA.,Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, CA, USA
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Organophotocatalytic selective deuterodehalogenation of aryl or alkyl chlorides. Nat Commun 2021; 12:2894. [PMID: 34001911 PMCID: PMC8129137 DOI: 10.1038/s41467-021-23255-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/30/2021] [Indexed: 12/23/2022] Open
Abstract
Development of practical deuteration reactions is highly valuable for organic synthesis, analytic chemistry and pharmaceutic chemistry. Deuterodehalogenation of organic chlorides tends to be an attractive strategy but remains a challenging task. We here develop a photocatalytic system consisting of an aryl-amine photocatalyst and a disulfide co-catalyst in the presence of sodium formate as an electron and hydrogen donor. Accordingly, many aryl chlorides, alkyl chlorides, and other halides are converted to deuterated products at room temperature in air (>90 examples, up to 99% D-incorporation). The mechanistic studies reveal that the aryl amine serves as reducing photoredox catalyst to initiate cleavage of the C-Cl bond, at the same time as energy transfer catalyst to induce homolysis of the disulfide for consequent deuterium transfer process. This economic and environmentally-friendly method can be used for site-selective D-labeling of a number of bioactive molecules and direct H/D exchange of some drug molecules. Deuterodehalogenation of organic chlorides is a useful strategy to install deuterium atoms at specific positions, however, it has several drawbacks. In this study, the authors report an organophotocatalytic system consisting of an aryl-amine-based photocatalyst and a common disulfide co-catalyst, for efficient deuteration of a wide range of aryl chlorides, alkyl chlorides and other halides, at room temperature in air.
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11
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Nimesulide increases the aldehyde oxidase activity of humans and rats. Acta Pharmacol Sin 2020; 41:843-851. [PMID: 31913347 PMCID: PMC7471466 DOI: 10.1038/s41401-019-0336-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/18/2019] [Indexed: 11/09/2022] Open
Abstract
An increasing number of drugs are metabolized by aldehyde oxidase (AOX), but AOX-mediated drug interactions are seldom reported due to the lack of appropriate inhibitors and inducers. A recent study reported that nimesulide (NIM) could increase the liver injury risk of methotrexate. The latter was mainly metabolized by AOX to form hepatotoxic 7-hydroxymethotrexate (7-OH MTX). Thus, we speculated that NIM could induce AOX. In this study, we investigated the potential induction of AOX activity by NIM using methotrexate as the probe substrate. Treatment of primary human and rat hepatocytes with NIM (20 μM) for 24 h caused a 2.0- and 3.1-fold, respectively, increase in 7-OH MTX formation. Oral administration of NIM (100 mg·kg−1·d−1, for 5 days) to rats significantly increased the systematic exposure (6.5-fold), liver distribution (2.5-fold), and excretion (5.2-fold for urinary excretion and 2.1-fold for fecal excretion) of 7-OH MTX. The 7-OH MTX formation in liver cytosol from rats pretreated with 20, 50, and 100 mg·kg−1·d−1 NIM for 5 days increased by 1.9-, 3.2-, and 3.7-fold, respectively, compared with that of rats pretreated with the vehicle. We revealed that the elevation of AOX activity was accompanied by an increase in AOX1 protein levels but not the corresponding mRNA levels. Collectively, our results demonstrate for the first time that NIM can increase the AOX activity of humans and rats, and may raise concerns regarding the risk of drug interactions between NIM and AOX substrates in clinical practice.
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12
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Shah P, Siramshetty VB, Zakharov AV, Southall NT, Xu X, Nguyen DT. Predicting liver cytosol stability of small molecules. J Cheminform 2020; 12:21. [PMID: 33431020 PMCID: PMC7140498 DOI: 10.1186/s13321-020-00426-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/25/2020] [Indexed: 01/28/2023] Open
Abstract
Over the last few decades, chemists have become skilled at designing compounds that avoid cytochrome P (CYP) 450 mediated metabolism. Typical screening assays are performed in liver microsomal fractions and it is possible to overlook the contribution of cytosolic enzymes until much later in the drug discovery process. Few data exist on cytosolic enzyme-mediated metabolism and no reliable tools are available to chemists to help design away from such liabilities. In this study, we screened 1450 compounds for liver cytosol-mediated metabolic stability and extracted transformation rules that might help medicinal chemists in optimizing compounds with these liabilities. In vitro half-life data were collected by performing in-house experiments in mouse (CD-1 male) and human (mixed gender) cytosol fractions. Matched molecular pairs analysis was performed in conjunction with qualitative-structure activity relationship modeling to identify chemical structure transformations affecting cytosolic stability. The transformation rules were prospectively validated on the test set. In addition, selected rules were validated on a diverse chemical library and the resulting pairs were experimentally tested to confirm whether the identified transformations could be generalized. The validation results, comprising nearly 250 library compounds and corresponding half-life data, are made publicly available. The datasets were also used to generate in silico classification models, based on different molecular descriptors and machine learning methods, to predict cytosol-mediated liabilities. To the best of our knowledge, this is the first systematic in silico effort to address cytosolic enzyme-mediated liabilities.
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Affiliation(s)
- Pranav Shah
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Vishal B Siramshetty
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Noel T Southall
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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13
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Zhao J, Cui R, Wang L, Chen Y, Fu Z, Ding X, Cui C, Yang T, Li X, Xu Y, Chen K, Luo X, Jiang H, Zheng M. Revisiting Aldehyde Oxidase Mediated Metabolism in Drug-like Molecules: An Improved Computational Model. J Med Chem 2020; 63:6523-6537. [DOI: 10.1021/acs.jmedchem.9b01895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jihui Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Rongrong Cui
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
| | - Lihao Wang
- Gillings School of Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill, North Carolina 27599, United States
| | - Yingjia Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Zunyun Fu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
| | - Xiaoyu Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Chen Cui
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Tianbiao Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Xutong Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Yuan Xu
- Shanghai EnnovaBio Pharmaceuticals Co., Ltd.,
Room 404, Building 2, Lane 720, Cailun Road, Pudong New Area, Shanghai 200120, China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
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14
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Kim NA, Hong S, Kim KH, Choi DH, Kim JS, Park KE, Choi JY, Shin YK, Jeong SH. New Preclinical Development of a c-Met Inhibitor and Its Combined Anti-Tumor Effect in c-Met-Amplified NSCLC. Pharmaceutics 2020; 12:pharmaceutics12020121. [PMID: 32028611 PMCID: PMC7076440 DOI: 10.3390/pharmaceutics12020121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/14/2020] [Accepted: 01/28/2020] [Indexed: 11/30/2022] Open
Abstract
c-Met is a receptor tyrosine kinase with no commercially available product despite being a pivotal target in cancer progression. Unlike other c-Met inhibitors that fail clinically, ABN401 is a newly synthesized c-Met inhibitor that is not potentially degraded by aldehyde oxidase (AO) in human liver cytosol. This study aimed to determine the physicochemical stability, pharmacokinetics in beagle dogs, and therapeutic effect of ABN401 in a c-Met-amplified non-small-cell lung cancer (NSCLC) patient-derived xenograft (PDX) model. ABN401 was found to be a weak basic compound, with pKa and log P values of 7.49 and 2.46, respectively. It is poorly water-soluble but soluble at acidic pH. The accelerated storage stability is dependent on temperature, but the purity remains at over 97% after 6 months. The bioavailability is approximately 30% in dogs and it is highly efficient in the PDX model, achieving around 90% tumor growth inhibition in combination with erlotinib. These observations indicate that the compound is acceptable for the next phase of trials.
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Affiliation(s)
- Nam Ah Kim
- College of Pharmacy, Dongguk University-Seoul, Gyeonggi 10326, Korea; (N.A.K.); (K.H.K.)
| | - Sungyoul Hong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea;
| | - Ki Hyun Kim
- College of Pharmacy, Dongguk University-Seoul, Gyeonggi 10326, Korea; (N.A.K.); (K.H.K.)
| | - Du Hyung Choi
- Department of Pharmaceutical Engineering, Inje University, Gyeongnam 50834, Korea;
| | - Joo Seok Kim
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, Korea;
| | - Kyung Eui Park
- R&D Center, ABION Inc., Seoul 08394, Korea; (K.E.P.); (J.Y.C.)
| | - Jun Young Choi
- R&D Center, ABION Inc., Seoul 08394, Korea; (K.E.P.); (J.Y.C.)
| | - Young Kee Shin
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul 08826, Korea;
- R&D Center, ABION Inc., Seoul 08394, Korea; (K.E.P.); (J.Y.C.)
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 08826, Korea
- Correspondence: (Y.K.S.); (S.H.J.); Tel.: +82-2-880-9126 (Y.K.S.); +82-10-5679-0621 (S.H.J.)
| | - Seong Hoon Jeong
- College of Pharmacy, Dongguk University-Seoul, Gyeonggi 10326, Korea; (N.A.K.); (K.H.K.)
- Correspondence: (Y.K.S.); (S.H.J.); Tel.: +82-2-880-9126 (Y.K.S.); +82-10-5679-0621 (S.H.J.)
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15
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Manevski N, King L, Pitt WR, Lecomte F, Toselli F. Metabolism by Aldehyde Oxidase: Drug Design and Complementary Approaches to Challenges in Drug Discovery. J Med Chem 2019; 62:10955-10994. [PMID: 31385704 DOI: 10.1021/acs.jmedchem.9b00875] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aldehyde oxidase (AO) catalyzes oxidations of azaheterocycles and aldehydes, amide hydrolysis, and diverse reductions. AO substrates are rare among marketed drugs, and many candidates failed due to poor pharmacokinetics, interspecies differences, and adverse effects. As most issues arise from complex and poorly understood AO biology, an effective solution is to stop or decrease AO metabolism. This perspective focuses on rational drug design approaches to modulate AO-mediated metabolism in drug discovery. AO biological aspects are also covered, as they are complementary to chemical design and important when selecting the experimental system for risk assessment. The authors' recommendation is an early consideration of AO-mediated metabolism supported by computational and in vitro experimental methods but not an automatic avoidance of AO structural flags, many of which are versatile and valuable building blocks. Preferably, consideration of AO-mediated metabolism should be part of the multiparametric drug optimization process, with the goal to improve overall drug-like properties.
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Affiliation(s)
- Nenad Manevski
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - Lloyd King
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - William R Pitt
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - Fabien Lecomte
- UCB Celltech , 208 Bath Road , Slough SL13WE , United Kingdom
| | - Francesca Toselli
- UCB BioPharma , Chemin du Foriest 1 , 1420 Braine-l'Alleud , Belgium
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16
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Lazzara PR, Moore TW. Scaffold-hopping as a strategy to address metabolic liabilities of aromatic compounds. RSC Med Chem 2019; 11:18-29. [PMID: 33479602 DOI: 10.1039/c9md00396g] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/09/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding and minimizing oxidative metabolism of aromatic compounds is a key hurdle in lead optimization. Metabolic processes not only clear compounds from the body, but they can also transform parent compounds into reactive metabolites. One particularly useful strategy when addressing metabolically labile or oxidation-prone structures is scaffold-hopping. Replacement of an aromatic system with a more electron-deficient ring system can often increase robustness towards cytochrome P450-mediated oxidation while conserving the structural requirements of the pharmacophore. The most common example of this substitution strategy, replacement of a phenyl ring with a pyridyl substituent, is prevalent throughout the literature; however scaffold-hopping encompasses a much wider scope of heterocycle replacement. This review will showcase recent examples where different scaffold-hopping approaches were used to reduce metabolic clearance or block the formation of reactive metabolites. Additionally, we will highlight considerations that should be made to garner the most benefit from a scaffold-hopping strategy for lead optimization.
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Affiliation(s)
- Phillip R Lazzara
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Illinois at Chicago , 833 S. Wood Street , Chicago , IL 60612 , USA .
| | - Terry W Moore
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Illinois at Chicago , 833 S. Wood Street , Chicago , IL 60612 , USA . .,University of Illinois Cancer Center , University of Illinois at Chicago , 1801 W. Taylor Street , Chicago , IL 60612 , USA
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17
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Cheshmazar N, Dastmalchi S, Terao M, Garattini E, Hamzeh-Mivehroud M. Aldehyde oxidase at the crossroad of metabolism and preclinical screening. Drug Metab Rev 2019; 51:428-452. [DOI: 10.1080/03602532.2019.1667379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Narges Cheshmazar
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Dalvie D, Di L. Aldehyde oxidase and its role as a drug metabolizing enzyme. Pharmacol Ther 2019; 201:137-180. [PMID: 31128989 DOI: 10.1016/j.pharmthera.2019.05.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/27/2019] [Indexed: 11/29/2022]
Abstract
Aldehyde oxidase (AO) is a cytosolic enzyme that belongs to the family of structurally related molybdoflavoproteins like xanthine oxidase (XO). The enzyme is characterized by broad substrate specificity and marked species differences. It catalyzes the oxidation of aromatic and aliphatic aldehydes and various heteroaromatic rings as well as reduction of several functional groups. The references to AO and its role in metabolism date back to the 1950s, but the importance of this enzyme in the metabolism of drugs has emerged in the past fifteen years. Several reviews on the role of AO in drug metabolism have been published in the past decade indicative of the growing interest in the enzyme and its influence in drug metabolism. Here, we present a comprehensive monograph of AO as a drug metabolizing enzyme with emphasis on marketed drugs as well as other xenobiotics, as substrates and inhibitors. Although the number of drugs that are primarily metabolized by AO are few, the impact of AO on drug development has been extensive. We also discuss the effect of AO on the systemic exposure and clearance these clinical candidates. The review provides a comprehensive analysis of drug discovery compounds involving AO with the focus on developmental candidates that were reported in the past five years with regards to pharmacokinetics and toxicity. While there is only one known report of AO-mediated clinically relevant drug-drug interaction (DDI), a detailed description of inhibitors and inducers of AO known to date has been presented here and the potential risks associated with DDI. The increasing recognition of the importance of AO has led to significant progress in predicting the site of AO-mediated metabolism using computational methods. Additionally, marked species difference in expression of AO makes it is difficult to predict human clearance with high confidence. The progress made towards developing in vivo, in vitro and in silico approaches for predicting AO metabolism and estimating human clearance of compounds that are metabolized by AO have also been discussed.
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Affiliation(s)
- Deepak Dalvie
- Drug Metabolism and Pharmacokinetics, Celgene Corporation, 10300, Campus Point Drive, San Diego, CA 92121, USA.
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, CT 06340, UK
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19
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Affiliation(s)
- Christine Beedham
- Honorary Senior Lecturer, Faculty of Life Sciences, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
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20
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In Vitro Metabolism by Aldehyde Oxidase Leads to Poor Pharmacokinetic Profile in Rats for c-Met Inhibitor MET401. Eur J Drug Metab Pharmacokinet 2019; 44:669-680. [DOI: 10.1007/s13318-019-00557-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Fast Methods for Prediction of Aldehyde Oxidase-Mediated Site-of-Metabolism. Comput Struct Biotechnol J 2019; 17:345-351. [PMID: 30949305 PMCID: PMC6429535 DOI: 10.1016/j.csbj.2019.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/11/2022] Open
Abstract
Aldehyde Oxidase (AO) is an enzyme involved in the metabolism of aldehydes and N-containing heterocyclic compounds. Many drug compounds contain heterocyclic moieties, and AO metabolism has lead to failure of several late-stage drug candidates. Therefore, it is important to take AO-mediated metabolism into account early in the drug discovery process, and thus, to have fast and reliable models to predict the site of metabolism (SOM). We have collected a dataset of 78 substrates of human AO with a total of 89 SOMs and 347 non-SOMs and determined atomic descriptors for each compound. The descriptors comprise NMR shielding and ESP charges from density functional theory (DFT), NMR chemical shift from ChemBioDraw, and Gasteiger charges from RDKit. Additionally, atomic accessibility was considered using 2D-SASA and relative span descriptors from SMARTCyp. Finally, stability of the product, the metabolite, was determined with DFT and also used as a descriptor. All descriptors have AUC larger than 0.75. In particular, descriptors related to the chemical shielding and chemical shift (AUC = 0.96) and ESP charges (AUC = 0.96) proved to be good descriptors. We recommend two simple methods to identify the SOM for a given molecule: 1) use ChemBioDraw to calculate the chemical shift or 2) calculate ESP charges or chemical shift using DFT. The first approach is fast but somewhat difficult to automate, while the second is more time-consuming, but can easily be automated. The two methods predict correctly 93% and 91%, respectively, of the 89 experimentally observed SOMs.
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22
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Zhang JW, Xiao W, Gao ZT, Yu ZT, Zhang JYJ. Metabolism of c-Met Kinase Inhibitors Containing Quinoline by Aldehyde Oxidase, Electron Donating, and Steric Hindrance Effect. Drug Metab Dispos 2018; 46:1847-1855. [PMID: 30209037 DOI: 10.1124/dmd.118.081919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/10/2018] [Indexed: 11/22/2022] Open
Abstract
Some quinoline-containing c-Met kinase inhibitors are aldehyde oxidase (AO) substrates. 3-Substituted quinoline triazolopyridine analogs were synthesized to understand the electron-donating and steric hindrance effects on AO-mediated metabolism. Metabolic stability studies for these quinoline analogs were carried out in liver cytosol from mice, rats, cynomolgus monkeys, and humans. Several 3-N-substituted analogs were found to be unstable in monkey liver cytosolic incubations (half-life, <10 minutes), and five of them (63, 53, 51, 11, and 71) were chosen for additional mechanistic studies. Mono-oxygenation on the quinoline ring was identified by liquid chromatography tandem mass spectrometry. Metabolite formation was inhibited by the AO inhibitors menadione and raloxifene, but not by the xanthine oxidase inhibitor allopurinol. It was found that small electron-donating groups at the 3-quinoline moiety made the analogs more susceptible to AO metabolism, whereas large 3-substituents could reverse the trend. Although species differences were observed, this trend was applicable to all species tested. Small electron-donating substituents at the 3-quinoline moiety increased both affinity (decreased Michaelis constant) and V max maximum velocity toward AO in kinetic studies, whereas large substituents decreased both parameters probably as a result of steric hindrance. Based on our analysis, a common structural feature with high AO liability was proposed. Our finding could provide useful information for chemists to minimize potential AO liability when designing quinoline analogs.
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Affiliation(s)
- Jiang Wei Zhang
- China Novartis Institutes for BioMedical Research, Shanghai, People's Republic of China
| | - Wen Xiao
- China Novartis Institutes for BioMedical Research, Shanghai, People's Republic of China
| | - Zhen Ting Gao
- China Novartis Institutes for BioMedical Research, Shanghai, People's Republic of China
| | - Zheng Tian Yu
- China Novartis Institutes for BioMedical Research, Shanghai, People's Republic of China
| | - Ji Yue Jeff Zhang
- China Novartis Institutes for BioMedical Research, Shanghai, People's Republic of China
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23
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Claesson A, Minidis A. Systematic Approach to Organizing Structural Alerts for Reactive Metabolite Formation from Potential Drugs. Chem Res Toxicol 2018; 31:389-411. [DOI: 10.1021/acs.chemrestox.8b00046] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Alf Claesson
- Awametox AB, Lilldalsvägen 17 A, SE-14461 Rönninge, Sweden
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24
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Dick RA. Refinement of In Vitro Methods for Identification of Aldehyde Oxidase Substrates Reveals Metabolites of Kinase Inhibitors. Drug Metab Dispos 2018; 46:846-859. [DOI: 10.1124/dmd.118.080960] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023] Open
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25
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Koniarczyk JL, Hesk D, Overgard A, Davies IW, McNally A. A General Strategy for Site-Selective Incorporation of Deuterium and Tritium into Pyridines, Diazines, and Pharmaceuticals. J Am Chem Soc 2018; 140:1990-1993. [PMID: 29377684 DOI: 10.1021/jacs.7b11710] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Methods to incorporate deuterium and tritium atoms into organic molecules are valuable for medicinal chemistry. The prevalence of pyridines and diazines in pharmaceuticals means that new ways to label these heterocycles will present opportunities in drug design and facilitate absorption, distribution, metabolism, and excretion (ADME) studies. A broadly applicable protocol is presented wherein pyridines, diazines, and pharmaceuticals are converted into heterocyclic phosphonium salts and then isotopically labeled. The isotopes are incorporated in high yields and, in general, with exclusive regioselectivity.
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Affiliation(s)
- J Luke Koniarczyk
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
| | - David Hesk
- Department of Process Research & Development, MRL, Merck Sharp & Dohme Corp. , Rahway, New Jersey 07065, United States
| | - Alix Overgard
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Ian W Davies
- Department of Process Research & Development, MRL, Merck Sharp & Dohme Corp. , Rahway, New Jersey 07065, United States
| | - Andrew McNally
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
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26
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Direct comparison of the four aldehyde oxidase enzymes present in mouse gives insight into their substrate specificities. PLoS One 2018; 13:e0191819. [PMID: 29370288 PMCID: PMC5784979 DOI: 10.1371/journal.pone.0191819] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/11/2018] [Indexed: 12/13/2022] Open
Abstract
Mammalian aldehyde oxidases (AOXs) are molybdo-flavoenzymes which are present in many tissues in various mammalian species, including humans and rodents. Different species contain a different number of AOX isoforms. In particular, the reasons why mammals other than humans express a multiplicity of tissue-specific AOX enzymes is unknown. In mouse, the isoforms mAOX1, mAOX3, mAOX4 and mAOX2 are present. We previously established a codon-optimized heterologous expression systems for the mAOX1-4 isoforms in Escherichia coli that gives yield to sufficient amounts of active protein for kinetic characterizations and sets the basis in this study for site-directed mutagenesis and structure-function studies. A direct and simultaneous comparison of the enzymatic properties and characteristics of the four enzymes on a larger number of substrates has never been performed. Here, thirty different structurally related aromatic, aliphatic and N-heterocyclic compounds were used as substrates, and the kinetic parameters of all four mAOX enzymes were directly compared. The results show that especially mAOX4 displays a higher substrate selectivity, while no major differences between mAOX1, mAOX2 and mAOX3 were identified. Generally, mAOX1 was the enzyme with the highest catalytic turnover for most substrates. To understand the factors that contribute to the substrate specificity of mAOX4, site-directed mutagenesis was applied to substitute amino acids in the substrate-binding funnel by the ones present in mAOX1, mAOX3, and mAOX2. An increase in activity was obtained by the amino acid exchange M1088V in the active site identified to be specific for mAOX4, to the amino acid identified in mAOX3.
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27
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Zheng M, Zhao J, Cui C, Fu Z, Li X, Liu X, Ding X, Tan X, Li F, Luo X, Chen K, Jiang H. Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies. Med Res Rev 2018; 38:914-950. [DOI: 10.1002/med.21483] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Mingyue Zheng
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jihui Zhao
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Chen Cui
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Zunyun Fu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Xutong Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Xiaohong Liu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
- School of Life Science and Technology; ShanghaiTech University; Shanghai China
| | - Xiaoyu Ding
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Xiaoqin Tan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Fei Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
- Department of Chemistry, College of Sciences; Shanghai University; Shanghai China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
- School of Life Science and Technology; ShanghaiTech University; Shanghai China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
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28
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Crouch RD, Blobaum AL, Felts AS, Conn PJ, Lindsley CW. Species-Specific Involvement of Aldehyde Oxidase and Xanthine Oxidase in the Metabolism of the Pyrimidine-Containing mGlu5-Negative Allosteric Modulator VU0424238 (Auglurant). Drug Metab Dispos 2017; 45:1245-1259. [DOI: 10.1124/dmd.117.077552] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/20/2017] [Indexed: 01/10/2023] Open
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29
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Montefiori M, Jørgensen FS, Olsen L. Aldehyde Oxidase: Reaction Mechanism and Prediction of Site of Metabolism. ACS OMEGA 2017; 2:4237-4244. [PMID: 30023718 PMCID: PMC6044498 DOI: 10.1021/acsomega.7b00658] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/11/2017] [Indexed: 05/16/2023]
Abstract
Aldehyde oxidase (AO) is a molybdenum-containing enzyme involved in the clearance of drug compounds containing aldehydes and N-containing heterocyclic fragments. AO has gained considerable interest in recent years because of examples of too fast clearance of drug compounds in development. Thus, it is important to be able to predict AO-mediated drug metabolism. Therefore, we have characterized the structural and energetic aspects of different mechanisms with density functional theory using the molybdenum cofactor as a model for the reactive part of the enzyme. For a series of 6-substituted 4-quinazolinones, the trend in activation energies is the same for three tested reaction mechanisms. Using the concerted mechanism as a model for the enzymatic reaction, the transition states (TSs) for the formation of all possible metabolites for a series of known AO substrates were determined. The lowest activation energies correspond in all cases to the experimentally observed sites of metabolism (SOMs). Various molecular properties were calculated and investigated as more easily determinable markers for reactivity. The stabilities of both intermediates and products correlate to some extent with the TS energies and may be used to predict the SOM. The electrostatic-potential-derived charges are also good markers for the prediction of the experimental SOM for this set of compounds and may pave the way for the development of fast methods for the prediction of SOM for AO substrates.
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30
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Kumar R, Joshi G, Kler H, Kalra S, Kaur M, Arya R. Toward an Understanding of Structural Insights of Xanthine and Aldehyde Oxidases: An Overview of their Inhibitors and Role in Various Diseases. Med Res Rev 2017; 38:1073-1125. [DOI: 10.1002/med.21457] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/05/2017] [Accepted: 06/13/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Raj Kumar
- Laboratory for Drug Design and Synthesis, Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences; Central University of Punjab; Bathinda 151001 India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences; Central University of Punjab; Bathinda 151001 India
| | - Harveen Kler
- Laboratory for Drug Design and Synthesis, Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences; Central University of Punjab; Bathinda 151001 India
| | - Sourav Kalra
- Laboratory for Drug Design and Synthesis, Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences; Central University of Punjab; Bathinda 151001 India
- Centre for Human Genetics and Molecular Medicine
| | - Manpreet Kaur
- Laboratory for Drug Design and Synthesis, Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences; Central University of Punjab; Bathinda 151001 India
| | - Ramandeep Arya
- Laboratory for Drug Design and Synthesis, Centre for Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences; Central University of Punjab; Bathinda 151001 India
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