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Xiong J, Cui R, Li Z, Zhang W, Zhang R, Fu Z, Liu X, Li Z, Chen K, Zheng M. Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application. Acta Pharm Sin B 2024; 14:623-634. [PMID: 38322350 PMCID: PMC10840476 DOI: 10.1016/j.apsb.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/07/2023] [Accepted: 10/11/2023] [Indexed: 02/08/2024] Open
Abstract
Aldehyde oxidase (AOX) is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other xenobiotics. AOX-mediated metabolism can result in unexpected outcomes, such as the production of toxic metabolites and high metabolic clearance, which can lead to the clinical failure of novel therapeutic agents. Computational models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism liability. In this study, we developed a novel graph neural network called AOMP for predicting AOX-mediated metabolism. AOMP integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction, while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both tasks. AOMP significantly outperformed the benchmark methods in both cross-validation and external testing. Using AOMP, we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability, which were validated through in vitro experiments. Furthermore, for the convenience of the community, we established the first online service for AOX metabolism prediction based on AOMP, which is freely available at https://aomp.alphama.com.cn.
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Affiliation(s)
- Jiacheng Xiong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongrong Cui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaojun Li
- College of Computer and Information Engineering, Dezhou University, Dezhou 253023, China
- AI Department, Suzhou Alphama Biotechnology Co., Ltd., Suzhou 215000, China
| | - Wei Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runze Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zunyun Fu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Liu
- AI Department, Suzhou Alphama Biotechnology Co., Ltd., Suzhou 215000, China
| | - Zhenghao Li
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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2
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Uehara S, Yasuda M, Higuchi Y, Yoneda N, Kawai K, Suzuki M, Yamazaki H, Suemizu H. SGX523 causes renal toxicity through aldehyde oxidase-mediated less-soluble metabolite formation in chimeric mice with humanized livers. Toxicol Lett 2023; 388:48-55. [PMID: 37806366 DOI: 10.1016/j.toxlet.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
SGX523 is a c-Met tyrosine kinase inhibitor that failed in clinical trials because of renal toxicity caused by crystal deposits in renal tubules. SGX523 is metabolized by aldehyde oxidase (AOX) in a species-dependent manner to the considerably less soluble 2-quinolinone-SGX523, which is likely involved in the clinically observed obstructive nephropathy. This study investigated the metabolism and renal toxicity of SGX523 in chimeric mice with humanized livers (humanized-liver mice). The 2-quinolinone-SGX523 formation activity was higher in humanized-liver mouse and human hepatocytes than in mouse hepatocytes. Additionally, this activity in the liver cytosolic fraction from humanized-liver mice was inhibited by the AOX inhibitors raloxifene and hydralazine. After oral SGX523 administration, higher maximum concentrations, larger areas under the plasma concentration versus time curves, and higher urinary concentrations of 2-quinolinone-SGX523 were observed in humanized-liver mice than in non-humanized mice. Serum creatinine and blood urea nitrogen levels were elevated in humanized-liver mice following repeated oral SGX523 administration. The accumulation of amorphous material in the tubules and infiltration of inflammatory cells around tubules were observed in the kidneys of humanized-liver mice after repeated oral SGX523 administration. These findings demonstrate that humanized-liver mice are useful for understanding the metabolism and toxicity of SGX523.
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Affiliation(s)
- Shotaro Uehara
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan.
| | - Masahiko Yasuda
- Pathology Center, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan
| | - Yuichiro Higuchi
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan
| | - Nao Yoneda
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan
| | - Kenji Kawai
- Pathology Center, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan
| | - Masami Suzuki
- Translational Research Division, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida 194-8543, Japan
| | - Hiroshi Suemizu
- Liver Engineering Laboratory, Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki 210-0821, Japan
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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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Uehara S, Yoneda N, Higuchi Y, Yamazaki H, Suemizu H. Oxidative metabolism and pharmacokinetics of the EGFR inhibitor BIBX1382 in chimeric NOG-TKm30 mice transplanted with human hepatocytes. Drug Metab Pharmacokinet 2021; 41:100419. [PMID: 34624627 DOI: 10.1016/j.dmpk.2021.100419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022]
Abstract
The epidermal growth factor receptor inhibitor BIBX1382 has failed in drug development because of poor oral exposure and low bioavailability associated with its extensive metabolism by aldehyde oxidase (AOX) in humans. In this study, we investigated the metabolic profiles and pharmacokinetics of BIBX1382 in chimeric NOG-TKm30 mice with humanized liver (humanized liver mice). After intravenous and oral BIBX1382 administration, increased plasma clearance and decreased oral exposure together with high production of the predominant oxidative metabolite (M1, BIBU1476) and secondary oxidized metabolite (M2) were observed in humanized liver mice. Extensive oxidation rates of BIBX1382 were observed in hepatocytes from humanized liver mice and were suppressed by the typical human AOX1 inhibitors raloxifene and hydralazine. Liver cytosolic fractions from humans, humanized liver mice, cynomolgus monkeys, minipigs, and guinea pigs, but not fractions from dogs, rabbits, rats, and mice, displayed high BIBX1382 clearance and resulted in oxidative metabolite production. These results indicate that humanized liver mice have human-type AOX activity based on the transplanted human liver AOX1 function. Humanized liver mice can be considered an important animal model for understanding the metabolism and pharmacokinetics of AOX drug substrates.
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Affiliation(s)
- Shotaro Uehara
- Central Institute for Experimental Animals, Kawasaki, Japan.
| | - Nao Yoneda
- Central Institute for Experimental Animals, Kawasaki, Japan
| | | | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Japan
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Kozminski KD, Selimkhanov J, Heyward S, Zientek MA. Contribution of Extrahepatic Aldehyde Oxidase Activity to Human Clearance. Drug Metab Dispos 2021; 49:743-749. [PMID: 34162687 DOI: 10.1124/dmd.120.000313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/10/2021] [Indexed: 11/22/2022] Open
Abstract
Aldehyde oxidase (AOX) is a soluble, cytosolic enzyme that metabolizes various N-heterocyclic compounds and organic aldehydes. It has wide tissue distribution with highest levels found in liver, kidney, and lung. Human clearance projections of AOX substrates by in vitro assessments in isolated liver fractions (cytosol, S9) and even hepatocytes have been largely underpredictive of clinical outcomes. Various hypotheses have been suggested as to why this is the case. One explanation is that extrahepatic AOX expression contributes measurably to AOX clearance and is at least partially responsible for the often observed underpredictions. Although AOX expression has been confirmed in several extrahepatic tissues, activities therein and potential contribution to overall human clearance have not been thoroughly studied. In this work, the AOX enzyme activity using the S9 fractions of select extrahepatic human tissues (kidney, lung, vasculature, and intestine) were measured using carbazeran as a probe substrate. Measured activities were scaled to a whole-body clearance using best-available parameters and compared with liver S9 fractions. Here, the combined scaled AOX clearance obtained from the kidney, lung, vasculature, and intestine is very low and amounted to <1% of liver. This work suggests that AOX metabolism from extrahepatic sources plays little role in the underprediction of activity in human. One of the notable outcomes of this work has been the first direct demonstration of AOX activity in human vasculature. SIGNIFICANCE STATEMENT: This work demonstrates aldehyde oxidase (AOX) activity is measurable in a variety of extrahepatic human tissues, including vasculature, yet activities and potential contributions to human clearance are relatively low and insignificant when compared with the liver. Additionally, the modeling of the tissue-specific in vitro kinetic data suggests that AOX may be influenced by the tissue it resides in and thus show different affinity, activity, and modified activity over time.
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Affiliation(s)
- Kirk D Kozminski
- Takeda Pharmaceuticals Limited, San Diego, California (K.D.K., J.S., M.A.Z.); and BioIVT, Baltimore, Maryland (S.H.)
| | - Jangir Selimkhanov
- Takeda Pharmaceuticals Limited, San Diego, California (K.D.K., J.S., M.A.Z.); and BioIVT, Baltimore, Maryland (S.H.)
| | - Scott Heyward
- Takeda Pharmaceuticals Limited, San Diego, California (K.D.K., J.S., M.A.Z.); and BioIVT, Baltimore, Maryland (S.H.)
| | - Michael A Zientek
- Takeda Pharmaceuticals Limited, San Diego, California (K.D.K., J.S., M.A.Z.); and BioIVT, Baltimore, Maryland (S.H.)
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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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Zhong G, Seaman CJ, Paragas EM, Xi H, Herpoldt KL, King NP, Jones JP, Isoherranen N. Aldehyde Oxidase Contributes to All- Trans-Retinoic Acid Biosynthesis in Human Liver. Drug Metab Dispos 2020; 49:202-211. [PMID: 33355213 DOI: 10.1124/dmd.120.000296] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
All-trans-retinoic acid (atRA) is a critical endogenous signaling molecule. atRA is predominantly synthesized from retinaldehyde by aldehyde dehydrogenase 1A1 (ALDH1A1), but aldehyde oxidase (AOX) may also contribute to atRA biosynthesis. The goal of this study was to test the hypothesis that AOX contributes significantly to atRA formation in human liver. Human recombinant AOX formed atRA from retinaldehyde (Km ∼1.5 ± 0.4 µM; kcat ∼3.6 ± 2.0 minute-1). In human liver S9 fractions (HLS9), atRA formation was observed in the absence of NAD+, suggesting AOX contribution to atRA formation. In the presence of NAD+, Eadie-Hofstee plots of atRA formation in HLS9 indicated that two enzymes contributed to atRA formation. The two enzymes were identified as AOX and ALDH1A1 based on inhibition of atRA formation by AOX inhibitor hydralazine (20%-50% inhibition) and ALDH1A1 inhibitor WIN18,446 (50%-80%inhibition). The expression of AOX in HLS9 was 9.4-24 pmol mg-1 S9 protein, whereas ALDH1A1 expression was 156-285 pmol mg-1 S9 protein measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) quantification of signature peptides. The formation velocity of atRA in the presence of NAD+ correlated significantly with the expression of ALDH1A1 and AOX protein. Taken together, the data show that both AOX and ALDH1A1 contribute to atRA biosynthesis in the human liver, with ALDH1A1 being the high-affinity, low-capacity enzyme and AOX being the low-affinity, high-capacity enzyme. The results suggest that in the case of ALDH1A dysfunction or excess vitamin A, AOX may play an important role in regulating hepatic vitamin A homeostasis and that inhibition of AOX may alter atRA biosynthesis and signaling. SIGNIFICANCE STATEMENT: This study provides direct evidence to show that human AOX converts retinaldehyde to atRA and contributes to hepatic atRA biosynthesis. The finding that AOX may be responsible for 20%-50% of overall hepatic atRA formation suggests that alterations in AOX activity via drug-drug interactions, genetic polymorphisms, or disease states may impact hepatic atRA concentrations and signaling and alter vitamin A homeostasis.
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Affiliation(s)
- Guo Zhong
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Chris J Seaman
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Erickson M Paragas
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Huaqing Xi
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Karla-Luise Herpoldt
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Neil P King
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Jeffrey P Jones
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington (G.Z., C.J.S., H.X., N.I.); Department of Chemistry, Washington State University, Pullman, Washington (E.M.P., J.P.J.); and Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington (K.-L.H., N.P.K.)
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Ferreira P, Cerqueira NMFSA, Fernandes PA, Romão MJ, Ramos MJ. Catalytic Mechanism of Human Aldehyde Oxidase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pedro Ferreira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nuno M. F. Sousa A. Cerqueira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Alexandrino Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Romão
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria João Ramos
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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10
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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: 61] [Impact Index Per Article: 12.2] [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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11
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Inhibition of vertebrate aldehyde oxidase as a therapeutic treatment for cancer, obesity, aging and amyotrophic lateral sclerosis. Eur J Med Chem 2019; 187:111948. [PMID: 31877540 DOI: 10.1016/j.ejmech.2019.111948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 10/25/2022]
Abstract
The aldehyde oxidases (AOXs) are a small sub-family of cytosolic molybdo-flavoenzymes, which are structurally conserved proteins and broadly distributed from plants to animals. AOXs play multiple roles in both physiological and pathological processes and AOX inhibition is of increasing significance in the development of novel drugs and therapeutic strategies. This review provides an overview of the evolution and the action mechanism of AOX and the role of each domain. The review provides an update of the polymorphisms in the human AOX. This review also summarises the physiology of AOX in different organs and its role in drug metabolism. The inhibition of AOX is a promising therapeutic treatment for cancer, obesity, aging and amyotrophic lateral sclerosis.
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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: 40] [Impact Index Per Article: 8.0] [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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Deris-Abdolahpour F, Abdolalipouran-Sadegh L, Dastmalchi S, Hamzeh-Mivehroud M, Zarei O, Dehgan G, Rashidi MR. Effects of Phenothiazines on Aldehyde Oxidase Activity Towards Aldehydes and N-Heterocycles: an In Vitro and In Silico Study. Eur J Drug Metab Pharmacokinet 2019; 44:275-286. [PMID: 30382490 DOI: 10.1007/s13318-018-0514-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Aldehyde oxidase (AOX) is an important molybdenum-containing enzyme with high similarity with xanthine oxidase (XO). AOX involved in the metabolism of a large array of aldehydes and N-heterocyclic compounds and its activity is highly substrate-dependent. OBJECTIVES The aim of this work was to study the effect of five important phenothiazine drugs on AOX activity using benzaldehyde and phenanthridine as aldehyde and N-heterocyclic substrates, respectively. METHODS The effect of trifluperazine, chlorpromazine, perphenazine, thioridazine and promethazine on rat liver AOX was measured spectrophotometrically. To predict the mode of interactions between the studied compounds and AOX, a combination of homology modeling and a molecular docking study was performed. RESULTS All phenothiazines could inhibit AOX activity measured either by phenanthridine or benzaldehyde with almost no effect on XO activity. In the case of benzaldehyde oxidation, the lowest and highest half-maximal inhibitory concentration (IC50) values were obtained for promethazine (IC50 = 0.9 µM), and trifluoperazine (IC50 = 3.9 µM), respectively; whereas perphenazine (IC50 = 4.3 µM), and trifluoperazine (IC50 = 49.6 µM) showed the strongest and weakest inhibitory activity against AOX-catalyzed phenanthridine oxidation, respectively. The in silico findings revealed that the binding site of thioridazine is near the dimer interference, and that hydrophobic interactions are of great importance in all the tested phenothiazines. CONCLUSION The five studied phenothiazine drugs showed dual inhibitory effects on AOX activity towards aldehydes and N-heterocycles as two major classes of enzyme substrates. Most of the interactions between the phenothiazine-related drugs and AOX in the binding pocket showed a hydrophobic nature.
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Affiliation(s)
| | | | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omid Zarei
- Neurosciences Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Gholamreza Dehgan
- Department of Zoology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Mohammad-Reza Rashidi
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, 51664-14766, Iran.
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Yang X, Johnson N, Di L. Evaluation of Cytochrome P450 Selectivity for Hydralazine as an Aldehyde Oxidase Inhibitor for Reaction Phenotyping. J Pharm Sci 2019; 108:1627-1630. [DOI: 10.1016/j.xphs.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/16/2018] [Accepted: 11/02/2018] [Indexed: 12/15/2022]
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Xie J, Saburulla NF, Chen S, Wong SY, Yap ZP, Zhang LH, Lau AJ. Evaluation of Carbazeran 4-Oxidation and O6-Benzylguanine 8-Oxidation as Catalytic Markers of Human Aldehyde Oxidase: Impact of Cytosolic Contamination of Liver Microsomes. Drug Metab Dispos 2018; 47:26-37. [DOI: 10.1124/dmd.118.082099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/15/2018] [Indexed: 12/17/2022] Open
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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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Liu JF, Harbeson SL, Brummel CL, Tung R, Silverman R, Doller D. A Decade of Deuteration in Medicinal Chemistry. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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