1
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Claesson A. Use of Structural Alerts for Reactive Metabolites in the Application SpotRM. Chem Res Toxicol 2024; 37:1231-1245. [PMID: 39088358 DOI: 10.1021/acs.chemrestox.4c00205] [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: 08/03/2024]
Abstract
Reactive metabolite (RM) formation is widely accepted as playing a crucial role in causing idiosyncratic adverse drug reactions (IADRs), where the liver is most affected. An important goal of drug design is to avoid selection of drug candidates giving rise to RMs and therefore risk causing problems later on involving IADRs. The simplest, initial approach is to avoid test structures that have substructures known or strongly suspected to be associated with IADRs. However, as is evident from the many case reports of IADRs, in most cases a clear association with any (bio)chemical mechanism is lacking, which makes it hard to establish any structure-toxicity relationship. Separate studies of RM formation, in vitro and in vivo, have led to likely evidence and to establishing many structural alerts (SAs) that can be used for fast selection/deselection of planned test compounds. As a background to a discussion of the concept, 25 kinase inhibitor drugs with known problems of hepatotoxicity were probed against a set of SAs contained in the application SpotRM. A clear majority of the probed drugs show liabilities as evident by being flagged by more than one of the fairly established types of SAs. At the same time, no clear SAs were found in three drugs, which is discussed in the broader context of usefulness and selection tactics of SAs in drug design.
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Affiliation(s)
- Alf Claesson
- Awametox AB, Lilldalsvägen 17 A, SE-14461 Rönninge, Sweden
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2
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Yu G, Wang R, Liu X, Li Y, Li L, Wang X, Huang Y, Pan G. Screening and identification of reactive metabolic compounds of Cortex Periplocae based on glutathione capture-mass spectrometry. J Nat Med 2024:10.1007/s11418-024-01835-w. [PMID: 39103725 DOI: 10.1007/s11418-024-01835-w] [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: 11/30/2023] [Accepted: 07/21/2024] [Indexed: 08/07/2024]
Abstract
As a traditional Chinese medicine (TCM), Cortex Periplocae (CP) has a wide range of pharmacological effects, as well as toxic side effects. The main toxic components of it are cardiac glycosides, which tend to cause cardiotoxicity. Currently, it has also been reported in studies to cause hepatotoxicity, but it is not clear whether the hepatotoxicity is related to the toxicity caused by the reactive metabolites. This study aims to investigate the target components of CP that generate reactive metabolic toxicity. The fluorescent probe method was used to detect glutathione (GSH)-trapped reactive metabolites in a co-incubation system of CP extract with rat liver microsomes. Identification of GSH conjugates was performed by LC-MS/MS and that of the possible precursor components that produce reactive metabolites was conducted by UPLC-Q-TOF/MS. Cell viability assays were performed on HepG2 and L02 cells to determine the cytotoxicity of the target components. The findings of our study demonstrate that the extract derived from CP has the ability to generate metabolites that exhaust the intracellular GSH levels, resulting in the formation of GSH conjugates and subsequent cytotoxic effects. Through the utilization of the UPLC-Q-TOF/MS technique, we were able to accurately determine the molecular weight of the precursor compound in CP to be 355.1023. The primary evidence to determining the GSH conjugetes relies on the appearance of characteristic product ions resulting from central neutral loss (CNL) scanning of 129 Da and product scanning of m/z 660 in the positive MS/MS spectrum. Through analysis, it was ultimately ascertained that the presence of chlorogenic acid (CGA) and its isomers, namely neochlorogenic acid (NCGA) and cryptochlorogenic acid (CCGA), could lead to the production of GSH conjugates, resulting in cytotoxicity at elevated levels. Taking these findings into consideration, the underlying cause for the potential hepatotoxicity of CP was initially determined.
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Affiliation(s)
- Guantong Yu
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ruirui Wang
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaomei Liu
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuhong Li
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lin Li
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoming Wang
- Tianjin University of Traditional Chinese Medicine, Tianjin, China.
| | - Yuhong Huang
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Guixiang Pan
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.
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3
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Akagi Y, Yamakoshi H, Iwabuchi Y. Development of a fluorous trapping reagent for rapid detection of electrophilic reactive metabolites. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3810-3814. [PMID: 38855885 DOI: 10.1039/d4ay00577e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
A cysteine-based fluorous trapping reagent, Rf8CYS, was developed. Rf8CYS formed adducts with soft and hard electrophilic reactive metabolites. These fluorous-tagged adducts were purified via both fluorous solid-phase extraction and the direct injection method. The highly sensitive mass spectrometric detection of an unprecedented adduct of the ticlopidine metabolite was realized.
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Affiliation(s)
- Yusuke Akagi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan.
- Toxicology Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, Japan
| | - Hiroyuki Yamakoshi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan.
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Japan.
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4
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Christmann U, Garriga L, Llorente AV, Díaz JL, Pascual R, Bordas M, Dordal A, Porras M, Yeste S, Reinoso RF, Vela JM, Almansa C. WLB-87848, a Selective σ 1 Receptor Agonist, with an Unusually Positioned NH Group as Positive Ionizable Moiety and Showing Neuroprotective Activity. J Med Chem 2024; 67:9150-9164. [PMID: 38753759 DOI: 10.1021/acs.jmedchem.4c00288] [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: 05/18/2024]
Abstract
The synthesis and pharmacological activity of a new series of thieno[2,3-d]pyrimidin-4(3H)-one derivatives as sigma-1 receptor (σ1R) ligands are reported. A hit from a high-throughput screening program was evolved into a highly potent and selective σ1R agonist (14qR) that contains a free NH group as positive ionizable moiety, not fulfilling the usual pharmacophoric features of the σ1R. The compound shows good physicochemical and ADMET characteristics, displays an agonist profile in the binding immunoglobulin protein/σ1R association assay, induces neuron viability in an in vitro model of β-amyloid peptide intoxication, and presents positive results against recognition memory impairment induced by hippocampal injection of Aβ peptide in rats after oral treatment, altogether making 14qR (WLB-87848) an interesting candidate for neuroprotection.
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Affiliation(s)
- Ute Christmann
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Lourdes Garriga
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Ana Virginia Llorente
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - José Luis Díaz
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Rosalía Pascual
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Magda Bordas
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Albert Dordal
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Mónica Porras
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Sandra Yeste
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Raquel F Reinoso
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - José Miguel Vela
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
| | - Carmen Almansa
- Welab Barcelona, Parc Científic Barcelona, C/Baldiri Reixac 4-8, Barcelona 08028, Spain
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5
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Thomson P, Fragkas N, Kafu LM, Aithal GP, Lucena MI, Terracciano L, Meng X, Pirmohamed M, Brees D, Kullak‐Ublick GA, Odermatt A, Hammond T, Kammüller M, Naisbitt DJ. Patients with naproxen-induced liver injury display T-cell memory responses toward an oxidative (S)-O-desmethyl naproxen metabolite but not the acyl glucuronide. Allergy 2024; 79:200-214. [PMID: 37515456 PMCID: PMC10952231 DOI: 10.1111/all.15830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/30/2023] [Accepted: 06/13/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Exposure to nonsteroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen (IBU) and naproxen (NAP) is associated with idiosyncratic drug-induced liver injury (DILI). Carboxylate bioactivation into reactive metabolites (e.g., acyl glucuronides, AG) and resulting T-cell activation is hypothesized as causal for this adverse event. However, conclusive evidence supporting this is lacking. METHODS In this work, we identify CD4+ and CD8+ T-cell hepatic infiltration in a biopsy from an IBU DILI patient. Lymphocyte transformation test and IFN-γ ELIspot, conducted on peripheral blood mononuclear cells (PBMCs) of patients with NAP-DILI, were used to explore drug-specific T-cell activation. T-cell clones (TCC) were generated and tested for drug specificity, phenotype/function, and pathways of T-cell activation. Cells were exposed to NAP, its oxidative metabolite 6-O-desmethyl NAP (DM-NAP), its AG or synthesized NAP-AG human-serum albumin adducts (NAP-AG adduct). RESULTS CD4+ and CD8+ T-cells from patients expressing a range of different Vβ receptors were stimulated to proliferate and secrete IFN-γ and IL-22 when exposed to DM-NAP, but not NAP, NAP-AG or the NAP-AG adduct. Activation of the CD4+ TCC was HLA-DQ-restricted and dependent on antigen presenting cells (APC); most TCC were activated with DM-NAP-pulsed APC, while fixation of APC blocked the T-cell response. Cross-reactivity was not observed with structurally-related drugs. CONCLUSION Our results confirm hepatic T-cell infiltrations in NSAID-induced DILI, and show a T-cell memory response toward DM-NAP indicating an immune-mediated basis for the adverse event. Whilst bioactivation at the carboxylate group is widely hypothesized to be pathogenic for NSAID associated DILI, we found no evidence of this with NAP.
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Affiliation(s)
- Paul Thomson
- Molecular& Clinical PharmacologyUniversity of LiverpoolLiverpoolUK
| | - Nik Fragkas
- Novartis Institutes for BioMedical ResearchBaselSwitzerland
| | - Laila M. Kafu
- Molecular& Clinical PharmacologyUniversity of LiverpoolLiverpoolUK
| | - Guruprasad P. Aithal
- NIHR Nottingham Biomedical Research Centre and Nottingham Digestive Diseases Centre, Translational Medical Sciences, West Block, Queen's Medical CentreUniversity of NottinghamNottinghamUK
| | - M. Isabel Lucena
- Unidad de Gestión Clínica de Aparato Digestivo y Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga‐IBIMA, Hospital Universitario Virgen de la VictoriaUniversidad de Málaga, CIBERehdMalagaSpain
| | | | - Xiaoli Meng
- Molecular& Clinical PharmacologyUniversity of LiverpoolLiverpoolUK
| | - Munir Pirmohamed
- Molecular& Clinical PharmacologyUniversity of LiverpoolLiverpoolUK
| | | | - Gerd A. Kullak‐Ublick
- University Hospital ZurichUniversity of ZurichZurichSwitzerland
- Novartis Global Drug DevelopmentBaselSwitzerland
| | - Alex Odermatt
- Division of Molecular & Systems Toxicology, Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
| | - Thomas Hammond
- Division of Molecular & Systems Toxicology, Department of Pharmaceutical SciencesUniversity of BaselBaselSwitzerland
- Oncology Safety, Clinical Pharmacology and Safety Sciences R&DCambridgeUK
| | | | - Dean J. Naisbitt
- Molecular& Clinical PharmacologyUniversity of LiverpoolLiverpoolUK
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6
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Zhu Z, Yao Z, Zheng X, Qi G, Li Y, Mazur N, Gao X, Gong Y, Cong B. Drug-target affinity prediction method based on multi-scale information interaction and graph optimization. Comput Biol Med 2023; 167:107621. [PMID: 37907030 DOI: 10.1016/j.compbiomed.2023.107621] [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: 07/18/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Abstract
Drug-target affinity (DTA) prediction as an emerging and effective method is widely applied to explore the strength of drug-target interactions in drug development research. By predicting these interactions, researchers can assess the potential efficacy and safety of candidate drugs at an early stage, narrowing down the search space for therapeutic targets and accelerating the discovery and development of new drugs. However, existing DTA prediction models mainly use graphical representations of drug molecules, which lack information on interactions between individual substructures, thus affecting prediction accuracy and model interpretability. Therefore, transformer and diffusion on drug graphs in DTA prediction (TDGraphDTA) are introduced to predict drug-target interactions using multi-scale information interaction and graph optimization. An interactive module is integrated into feature extraction of drug and target features at different granularity levels. A diffusion model-based graph optimization module is proposed to improve the representation of molecular graph structures and enhance the interpretability of graph representations while obtaining optimal feature representations. In addition, TDGraphDTA improves the accuracy and reliability of predictions by capturing relationships and contextual information between molecular substructures. The performance of the proposed TDGraphDTA in DTA prediction was verified on three publicly available benchmark datasets (Davis, Metz, and KIBA). Compared with state-of-the-art baseline models, it achieved better results in terms of consistency index, R-squared, etc. Furthermore, compared with some existing methods, the proposed TDGraphDTA is demonstrated to have better structure capturing capabilities by visualizing the feature capturing capabilities of the model using Grad-AAM toxicity labels in the ToxCast dataset. The corresponding source codes are available at https://github.com/Lamouryz/TDGraph.
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Affiliation(s)
- Zhiqin Zhu
- College of Automation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Zheng Yao
- College of Automation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Xin Zheng
- College of Automation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Guanqiu Qi
- Computer Information Systems Department, State University of New York at Buffalo State, Buffalo, NY 14222, USA.
| | - Yuanyuan Li
- College of Automation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Neal Mazur
- Computer Information Systems Department, State University of New York at Buffalo State, Buffalo, NY 14222, USA.
| | - Xinbo Gao
- College of Automation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Yifei Gong
- Faculty of applied science & engineering, the Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto at Toronto, ON M5S, Canada.
| | - Baisen Cong
- Diagnostics Digital, DH(Shanghai) Diagnostics Co, Ltd, a Danaher company, Shanghai, 200335, China.
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7
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Murray M. Mechanisms and Clinical Significance of Pharmacokinetic Drug Interactions Mediated by FDA and EMA-approved Hepatitis C Direct-Acting Antiviral Agents. Clin Pharmacokinet 2023; 62:1365-1392. [PMID: 37731164 DOI: 10.1007/s40262-023-01302-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2023] [Indexed: 09/22/2023]
Abstract
The treatment of patients infected with the hepatitis C virus (HCV) has been revolutionised by the development of direct-acting antiviral agents (DAAs) that target specific HCV proteins involved in viral replication. The first DAAs were associated with clinical problems such as adverse drug reactions and pharmacokinetic drug-drug interactions (DDIs). Current FDA/EMA-approved treatments are combinations of DAAs that simultaneously target the HCV N5A-protein, the HCV N5B-polymerase and the HCV NS3/4A-protease. Adverse events and DDIs are less likely with these DAA combinations but several DDIs of potential clinical significance remain. Much of the available information on the interaction of DAAs with CYP drug-metabolising enzymes and influx and efflux transporters is contained in regulatory summaries and is focused on DDIs of likely clinical importance. Important DDIs perpetrated by current DAAs include increases in the pharmacokinetic exposure to statins and dabigatran. Some mechanistic information can be deduced. Although the free concentrations of DAAs in serum are very low, a number of these DDIs are likely mediated by the inhibition of systemic influx transporters, especially OATP1B1/1B3. Other DDIs may arise by DAA-mediated inhibition of intestinal efflux transporters, which increases the systemic concentrations of some coadministered drugs. Conversely, DAAs are victims of DDIs mediated by cyclosporin, ketoconazole, omeprazole and HIV antiretroviral drug combinations, especially when boosted by ritonavir and, to a lesser extent, cobicistat. In addition, concurrent administration of inducers, such as rifampicin, carbamazepine and efavirenz, decreases exposure to some DAAs. Drug-drug interactions that increase the accumulation of HCV N3/4A-protease inhibitors like grazoprevir may exacerbate hepatic injury in HCV patients.
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Affiliation(s)
- Michael Murray
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, New South Wales, 2006, Australia.
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8
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Salas-Estrada L, Provasi D, Qiu X, Kaniskan HÜ, Huang XP, DiBerto JF, Lamim Ribeiro JM, Jin J, Roth BL, Filizola M. De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework. J Chem Inf Model 2023; 63:5056-5065. [PMID: 37555591 PMCID: PMC10466374 DOI: 10.1021/acs.jcim.3c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Indexed: 08/10/2023]
Abstract
Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown to abolish brain reward deficits in rodents during withdrawal, as well as to reduce the escalation of opioid use in rats with extended access to opioids. Although KOR antagonists represent promising candidates for the treatment of opioid addiction, very few potent selective KOR antagonists are known to date and most of them exhibit significant safety concerns. Here, we used a generative deep-learning framework for the de novo design of chemotypes with putative KOR antagonistic activity. Molecules generated by models trained with this framework were prioritized for chemical synthesis based on their predicted optimal interactions with the receptor. Our models and proposed training protocol were experimentally validated by binding and functional assays.
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Affiliation(s)
- Leslie Salas-Estrada
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Davide Provasi
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xing Qiu
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Husnu Ümit Kaniskan
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xi-Ping Huang
- National
Institute of Mental Health, Psychoactive Drug Screening Program, Department
of Pharmacology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey F. DiBerto
- National
Institute of Mental Health, Psychoactive Drug Screening Program, Department
of Pharmacology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - João Marcelo Lamim Ribeiro
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jian Jin
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
- Mount
Sinai Center for Therapeutics Discovery, Departments of Oncological
Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Bryan L. Roth
- National
Institute of Mental Health, Psychoactive Drug Screening Program, Department
of Pharmacology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
- Division
of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Marta Filizola
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
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9
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Salas-Estrada L, Provasi D, Qui X, Kaniskan HÜ, Huang XP, DiBerto JF, Ribeiro JML, Jin J, Roth BL, Filizola M. De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.537995. [PMID: 37162828 PMCID: PMC10168226 DOI: 10.1101/2023.04.25.537995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown to abolish brain reward deficits in rodents during withdrawal, as well as to reduce the escalation of opioid use in rats with extended access to opioids. Although KOR antagonists represent promising candidates for the treatment of opioid addiction, very few potent selective KOR antagonists are known to date and most of them exhibit significant safety concerns. Here, we used a generative deep learning framework for the de novo design of chemotypes with putative KOR antagonistic activity. Molecules generated by models trained with this framework were prioritized for chemical synthesis based on their predicted optimal interactions with the receptor. Our models and proposed training protocol were experimentally validated by binding and functional assays.
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10
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Jurica EA, Wu X, Williams KN, Haque LE, Rampulla RA, Mathur A, Zhou M, Cao G, Cai H, Wang T, Liu H, Xu C, Kunselman LK, Antrilli TM, Hicks MB, Sun Q, Dierks EA, Apedo A, Moore DB, Foster KA, Cvijic ME, Panemangalore R, Khandelwal P, Wilkes JJ, Zinker BA, Robertson DG, Janovitz EB, Galella M, Li YX, Li J, Ramar T, Jalagam PR, Jayaram R, Whaley JM, Barrish JC, Robl JA, Ewing WR, Ellsworth BA. Optimization of Physicochemical Properties of Pyrrolidine GPR40 AgoPAMs Results in a Differentiated Profile with Improved Pharmacokinetics and Reduced Off-Target Activities. Bioorg Med Chem 2023; 85:117273. [PMID: 37030194 DOI: 10.1016/j.bmc.2023.117273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
GPR40 AgoPAMs are highly effective antidiabetic agents that have a dual mechanism of action, stimulating both glucose-dependent insulin and GLP-1 secretion. The early lipophilic, aromatic pyrrolidine and dihydropyrazole GPR40 AgoPAMs from our laboratory were highly efficacious in lowering plasma glucose levels in rodents but possessed off-target activities and triggered rebound hyperglycemia in rats at high doses. A focus on increasing molecular complexity through saturation and chirality in combination with reducing polarity for the pyrrolidine AgoPAM chemotype resulted in the discovery of compound 46, which shows significantly reduced off-target activities as well as improved aqueous solubility, rapid absorption, and linear PK. In vivo, compound 46 significantly lowers plasma glucose levels in rats during an oral glucose challenge yet does not demonstrate the reactive hyperglycemia effect at high doses that was observed with earlier GPR40 AgoPAMs.
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Affiliation(s)
- Elizabeth A Jurica
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States.
| | - Ximao Wu
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Kristin N Williams
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Lauren E Haque
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Richard A Rampulla
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Arvind Mathur
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Min Zhou
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Gary Cao
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Hong Cai
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Tao Wang
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Heng Liu
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Carrie Xu
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Lori K Kunselman
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Thomas M Antrilli
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Michael B Hicks
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Qin Sun
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Elizabeth A Dierks
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Atsu Apedo
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Douglas B Moore
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Kimberly A Foster
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Mary Ellen Cvijic
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Reshma Panemangalore
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Purnima Khandelwal
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Jason J Wilkes
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Bradley A Zinker
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Donald G Robertson
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Evan B Janovitz
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Michael Galella
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Yi-Xin Li
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Julia Li
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Thangeswaran Ramar
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Prasada Rao Jalagam
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Ramya Jayaram
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Jean M Whaley
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Joel C Barrish
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Jeffrey A Robl
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - William R Ewing
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Bruce A Ellsworth
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
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11
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Yan C, Peng T, Zhang T, Wang Y, Li N, Wang K, Jiang X. Molecular mechanisms of hepatotoxicity induced by compounds occurring in Evodiae Fructus. Drug Metab Rev 2023; 55:75-93. [PMID: 36803497 DOI: 10.1080/03602532.2023.2180027] [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: 02/22/2023]
Abstract
Evodiae Fructus (EF) is a common herbal medicine with thousands of years of medicinal history in China, which has been demonstrated with many promising pharmacological effects on cancer, cardiovascular diseases and Alzheimer's disease. However, there have been increasing reports of hepatotoxicity associated with EF consumption. Unfortunately, in a long term, many implicit constituents of EF as well as their toxic mechanisms remain poorly understood. Recently, metabolic activation of hepatotoxic compounds of EF to generate reactive metabolites (RMs) has been implicated. Herein, we capture metabolic reactions relevant to hepatotoxicity of these compounds. Initially, catalyzed by the hepatic cytochrome P450 enzymes (CYP450s), the hepatotoxic compounds of EF are oxidized to generate RMs. Subsequently, the highly electrophilic RMs could react with nucleophilic groups contained in biomolecules, such as hepatic proteins, enzymes, and nucleic acids to form conjugates and/or adducts, leading to a sequence of toxicological consequences. In addition, currently proposed biological pathogenesis, including oxidative stress, mitochondrial damage and dysfunction, endoplasmic reticulum (ER) stress, hepatic metabolism disorder, and cell apoptosis are represented. In short, this review updates the knowledge on the pathways of metabolic activation of seven hepatotoxic compounds of EF and provides considerable insights into the relevance of proposed molecular hepatotoxicity mechanisms from a biochemical standpoint, for the purpose of providing a theoretical guideline for the rational application of EF in clinics.
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Affiliation(s)
- Caiqin Yan
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Ting Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China.,Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Tingting Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China.,Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Yuan Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China.,Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Na Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Kai Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
| | - Xijuan Jiang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, P.R. China
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12
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Liao J, Chen H, Wei L, Wei L. GSAML-DTA: An interpretable drug-target binding affinity prediction model based on graph neural networks with self-attention mechanism and mutual information. Comput Biol Med 2022; 150:106145. [PMID: 37859276 DOI: 10.1016/j.compbiomed.2022.106145] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/23/2022] [Accepted: 09/24/2022] [Indexed: 11/03/2022]
Abstract
Identifying drug-target affinity (DTA) has great practical importance in the process of designing efficacious drugs for known diseases. Recently, numerous deep learning-based computational methods have been developed to predict drug-target affinity and achieved impressive performance. However, most of them construct the molecule (drug or target) encoder without considering the weights of features of each node (atom or residue). Besides, they generally combine drug and target representations directly, which may contain irrelevant-task information. In this study, we develop GSAML-DTA, an interpretable deep learning framework for DTA prediction. GSAML-DTA integrates a self-attention mechanism and graph neural networks (GNNs) to build representations of drugs and target proteins from the structural information. In addition, mutual information is introduced to filter out redundant information and retain relevant information in the combined representations of drugs and targets. Extensive experimental results demonstrate that GSAML-DTA outperforms state-of-the-art methods for DTA prediction on two benchmark datasets. Furthermore, GSAML-DTA has the interpretation ability to analyze binding atoms and residues, which may be conducive to chemical biology studies from data. Overall, GSAML-DTA can serve as a powerful and interpretable tool suitable for DTA modelling.
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Affiliation(s)
- Jiaqi Liao
- School of Software, Shandong University, Jinan, China
| | - Haoyang Chen
- School of Software, Shandong University, Jinan, China
| | - Lesong Wei
- Department of Computer Science, University of Tsukuba, Tsukuba, 3058577, Japan.
| | - Leyi Wei
- School of Software, Shandong University, Jinan, China.
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13
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Thomas M, O'Boyle NM, Bender A, de Graaf C. Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. J Cheminform 2022; 14:68. [PMID: 36192789 PMCID: PMC9531503 DOI: 10.1186/s13321-022-00646-z] [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: 04/14/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
A plethora of AI-based techniques now exists to conduct de novo molecule generation that can devise molecules conditioned towards a particular endpoint in the context of drug design. One popular approach is using reinforcement learning to update a recurrent neural network or language-based de novo molecule generator. However, reinforcement learning can be inefficient, sometimes requiring up to 105 molecules to be sampled to optimize more complex objectives, which poses a limitation when using computationally expensive scoring functions like docking or computer-aided synthesis planning models. In this work, we propose a reinforcement learning strategy called Augmented Hill-Climb based on a simple, hypothesis-driven hybrid between REINVENT and Hill-Climb that improves sample-efficiency by addressing the limitations of both currently used strategies. We compare its ability to optimize several docking tasks with REINVENT and benchmark this strategy against other commonly used reinforcement learning strategies including REINFORCE, REINVENT (version 1 and 2), Hill-Climb and best agent reminder. We find that optimization ability is improved ~ 1.5-fold and sample-efficiency is improved ~ 45-fold compared to REINVENT while still delivering appealing chemistry as output. Diversity filters were used, and their parameters were tuned to overcome observed failure modes that take advantage of certain diversity filter configurations. We find that Augmented Hill-Climb outperforms the other reinforcement learning strategies used on six tasks, especially in the early stages of training or for more difficult objectives. Lastly, we show improved performance not only on recurrent neural networks but also on a reinforcement learning stabilized transformer architecture. Overall, we show that Augmented Hill-Climb improves sample-efficiency for language-based de novo molecule generation conditioning via reinforcement learning, compared to the current state-of-the-art. This makes more computationally expensive scoring functions, such as docking, more accessible on a relevant timescale.
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Affiliation(s)
- Morgan Thomas
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Noel M O'Boyle
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Chris de Graaf
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
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14
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Kang L, Duan Y, Chen C, Li S, Li M, Chen L, Wen Z. Structure-Activity Relationship (SAR) Model for Predicting Teratogenic Risk of Antiseizure Medications in Pregnancy by Using Support Vector Machine. Front Pharmacol 2022; 13:747935. [PMID: 35281912 PMCID: PMC8914116 DOI: 10.3389/fphar.2022.747935] [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: 08/04/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022] Open
Abstract
Teratogenicity is one of the main concerns in clinical medications of pregnant women. Prescription of antiseizure medications (ASMs) in women with epilepsy during pregnancy may cause teratogenic effects on the fetus. Although large scale epilepsy pregnancy registries played an important role in evaluating the teratogenic risk of ASMs, for most ASMs, especially the newly approved ones, the potential teratogenic risk cannot be effectively assessed due to the lack of evidence. In this study, the analyses are performed on any medication, with a focus on ASMs. We curated a list containing the drugs with potential teratogenicity based on the US Food and Drug Administration (FDA)-approved drug labeling, and established a support vector machine (SVM) model for detecting drugs with high teratogenic risk. The model was validated by using the post-marketing surveillance data from US FDA Spontaneous Adverse Events Reporting System (FAERS) and applied to the prediction of potential teratogenic risk of ASMs. Our results showed that our proposed model outperformed the state-of-art approaches, including logistic regression (LR), random forest (RF) and extreme gradient boosting (XGBoost), when detecting the high teratogenic risk of drugs (MCC and recall rate were 0.312 and 0.851, respectively). Among 196 drugs with teratogenic potential reported by FAERS, 136 (69.4%) drugs were correctly predicted. For the eight commonly used ASMs, 4 of them were predicted as high teratogenic risk drugs, including topiramate, phenobarbital, valproate and phenytoin (predicted probabilities of teratogenic risk were 0.69, 0.60 0.59, and 0.56, respectively), which were consistent with the statement in FDA-approved drug labeling and the high reported prevalence of teratogenicity in epilepsy pregnancy registries. In addition, the structural alerts in ASMs that related to the genotoxic carcinogenicity and mutagenicity, idiosyncratic adverse reaction, potential electrophilic agents and endocrine disruption were identified and discussed. Our findings can be a good complementary for the teratogenic risk assessment in drug development and facilitate the determination of pharmacological therapies during pregnancy.
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Affiliation(s)
- Liyuan Kang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yifei Duan
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Chen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Shihai Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Lei Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, China
- Medical Big Data Center, Sichuan University, Chengdu, China
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15
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Ding Z, Wang X, Zhang N, Sun C, Zhao G, Peng Y, Zheng J. Metabolic Activation of Perampanel Mediated by CYP1A2. Chem Res Toxicol 2022; 35:490-498. [PMID: 35200000 DOI: 10.1021/acs.chemrestox.1c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Perampanel (PRP), a noncompetitive α-amino-3-hydroxy-5-methyl-4-isoxazolepropanoic acid (AMPA) receptor antagonist with high selectivity, has been used as a new adjuvant for the treatment of fractional seizures with or without primary generalized tonic-clonic seizures and secondary generalized seizures in epilepsy patients over the age of 12. Adverse events such as liver injury have been reported during the clinical application of PRP. The purpose of the study is to explore the in vitro and in vivo metabolic activation of PRP. Two GSH conjugates were detected in rat liver microsomal incubations containing PRP, GSH, and NADPH. The two GSH conjugates were both obtained from the bile of rats and rat primary hepatocytes after exposure to PRP. Similar microsomal incubations complemented with N-acetylcysteine (NAC) in place of GSH offered two NAC conjugates. As expected, the NAC conjugates were detected in the urine of PRP-treated rats. One of the two NAC conjugates was identified as NAC conjugate 12 verified by chemical synthesis. The individual human recombinant P450 enzyme incubation assay demonstrated that CYP1A2 dominated the catalysis for the metabolic activation of PRP. Pretreatment with α-naphthoflavone (NTF) decreased the formation of PRP-derived GSH conjugates in both livers of rats and cultured primary hepatocytes after being treated with PRP. Additionally, NTF was found to decrease the susceptibility of primary hepatocytes to the cytotoxicity of PRP. The findings indicate that PRP was metabolized to the corresponding epoxide, which could participate in PRP-induced cytotoxicity.
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Affiliation(s)
- Zifang Ding
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Xu Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Ning Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Chen Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Guode Zhao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Ying Peng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Jiang Zheng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China.,State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou 550025, P.R. China.,Key Laboratory of Environmental Pollution, Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou 550025, P.R. China
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16
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Yang Z, Zhong W, Zhao L, Yu-Chian Chen C. MGraphDTA: deep multiscale graph neural network for explainable drug-target binding affinity prediction. Chem Sci 2022; 13:816-833. [PMID: 35173947 PMCID: PMC8768884 DOI: 10.1039/d1sc05180f] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Predicting drug-target affinity (DTA) is beneficial for accelerating drug discovery. Graph neural networks (GNNs) have been widely used in DTA prediction. However, existing shallow GNNs are insufficient to capture the global structure of compounds. Besides, the interpretability of the graph-based DTA models highly relies on the graph attention mechanism, which can not reveal the global relationship between each atom of a molecule. In this study, we proposed a deep multiscale graph neural network based on chemical intuition for DTA prediction (MGraphDTA). We introduced a dense connection into the GNN and built a super-deep GNN with 27 graph convolutional layers to capture the local and global structure of the compound simultaneously. We also developed a novel visual explanation method, gradient-weighted affinity activation mapping (Grad-AAM), to analyze a deep learning model from the chemical perspective. We evaluated our approach using seven benchmark datasets and compared the proposed method to the state-of-the-art deep learning (DL) models. MGraphDTA outperforms other DL-based approaches significantly on various datasets. Moreover, we show that Grad-AAM creates explanations that are consistent with pharmacologists, which may help us gain chemical insights directly from data beyond human perception. These advantages demonstrate that the proposed method improves the generalization and interpretation capability of DTA prediction modeling.
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Affiliation(s)
- Ziduo Yang
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China +862039332153
| | - Weihe Zhong
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China +862039332153
| | - Lu Zhao
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China +862039332153
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University Guangzhou 510655 China
| | - Calvin Yu-Chian Chen
- Artificial Intelligence Medical Center, School of Intelligent Systems Engineering, Sun Yat-sen University Shenzhen 510275 China +862039332153
- Department of Medical Research, China Medical University Hospital Taichung 40447 Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University Taichung 41354 Taiwan
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17
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Thomas M, Smith RT, O'Boyle NM, de Graaf C, Bender A. Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. J Cheminform 2021; 13:39. [PMID: 33985583 PMCID: PMC8117600 DOI: 10.1186/s13321-021-00516-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
Deep generative models have shown the ability to devise both valid and novel chemistry, which could significantly accelerate the identification of bioactive compounds. Many current models, however, use molecular descriptors or ligand-based predictive methods to guide molecule generation towards a desirable property space. This restricts their application to relatively data-rich targets, neglecting those where little data is available to sufficiently train a predictor. Moreover, ligand-based approaches often bias molecule generation towards previously established chemical space, thereby limiting their ability to identify truly novel chemotypes. In this work, we assess the ability of using molecular docking via Glide-a structure-based approach-as a scoring function to guide the deep generative model REINVENT and compare model performance and behaviour to a ligand-based scoring function. Additionally, we modify the previously published MOSES benchmarking dataset to remove any induced bias towards non-protonatable groups. We also propose a new metric to measure dataset diversity, which is less confounded by the distribution of heavy atom count than the commonly used internal diversity metric. With respect to the main findings, we found that when optimizing the docking score against DRD2, the model improves predicted ligand affinity beyond that of known DRD2 active molecules. In addition, generated molecules occupy complementary chemical and physicochemical space compared to the ligand-based approach, and novel physicochemical space compared to known DRD2 active molecules. Furthermore, the structure-based approach learns to generate molecules that satisfy crucial residue interactions, which is information only available when taking protein structure into account. Overall, this work demonstrates the advantage of using molecular docking to guide de novo molecule generation over ligand-based predictors with respect to predicted affinity, novelty, and the ability to identify key interactions between ligand and protein target. Practically, this approach has applications in early hit generation campaigns to enrich a virtual library towards a particular target, and also in novelty-focused projects, where de novo molecule generation either has no prior ligand knowledge available or should not be biased by it.
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Affiliation(s)
- Morgan Thomas
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Robert T Smith
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Noel M O'Boyle
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Chris de Graaf
- Computational Chemistry, Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK.
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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18
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Bauer MR, Di Fruscia P, Lucas SCC, Michaelides IN, Nelson JE, Storer RI, Whitehurst BC. Put a ring on it: application of small aliphatic rings in medicinal chemistry. RSC Med Chem 2021; 12:448-471. [PMID: 33937776 PMCID: PMC8083977 DOI: 10.1039/d0md00370k] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
Aliphatic three- and four-membered rings including cyclopropanes, cyclobutanes, oxetanes, azetidines and bicyclo[1.1.1]pentanes have been increasingly exploited in medicinal chemistry for their beneficial physicochemical properties and applications as functional group bioisosteres. This review provides a historical perspective and comparative up to date overview of commonly applied small rings, exemplifying key principles with recent literature examples. In addition to describing the merits and advantages of each ring system, potential hazards and liabilities are also illustrated and explained, including any significant chemical or metabolic stability and toxicity risks.
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Affiliation(s)
- Matthias R Bauer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Paolo Di Fruscia
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Simon C C Lucas
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | | | - Jennifer E Nelson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - R Ian Storer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
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19
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Ma J, Risher N, Northcutt V, Moon YC, Weetall M, Welch E, Colacino J, Almstead N, Kong R. Ataluren metabolism: Ataluren-O-1β-acyl glucuronide is a stable circulating metabolite in mouse, rat, dog and human. Drug Metab Pharmacokinet 2021; 38:100393. [PMID: 33872944 DOI: 10.1016/j.dmpk.2021.100393] [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: 12/31/2020] [Revised: 03/07/2021] [Accepted: 03/23/2021] [Indexed: 11/28/2022]
Abstract
Ataluren is an aromatic acid derivative with a 1,2,4-oxodiazole moiety. Ataluren-O-1β-acyl glucuronide is a prominent circulatory metabolite in mice, rats, dogs, and humans following oral administration of ataluren. The objective of this paper was to evaluate the stability in vitro and in vivo of ataluren-O-1β-acyl glucuronide metabolite. Ultrahigh performance liquid chromatography-mass spectrometry methods were developed to separate and monitor ataluren-O-1β-acyl glucuronide and its possible migration isomers. In vitro stability was assessed in phosphate buffered saline as well as in control rat and human plasma. The disappearance of ataluren-O-1β-acyl glucuronide and the formation of migration isomers were monitored by the ultrahigh performance liquid chromatography-mass spectrometry methods. In vitro, ataluren-O-1β-acyl glucuronide underwent isomerization with an estimated half-life of approximately 1 h. However, ataluren-O-1β-acyl glucuronide was stable and was the only detectable acyl glucuronide following oral administration of ataluren in mice, rats, dogs, and humans using the same analytical methods. Ataluren acyl glucuronide in mouse, rat, dog, and human plasma could be hydrolyzed by β-glucuronidase, further confirming the structure of O-1β-acyl glucuronide. These results demonstrated that ataluren-O-1β-acyl glucuronide did not undergo migration in vivo. No clinical safety concern related to ataluren-O-1β-acyl glucuronide migration has been detected.
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Affiliation(s)
- Jiyuan Ma
- PTC Therapeutics, Inc., South Plainfield, NJ, USA.
| | | | | | | | | | - Ellen Welch
- PTC Therapeutics, Inc., South Plainfield, NJ, USA.
| | | | | | - Ronald Kong
- PTC Therapeutics, Inc., South Plainfield, NJ, USA.
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20
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Hughes TB, Flynn N, Dang NL, Swamidass SJ. Modeling the Bioactivation and Subsequent Reactivity of Drugs. Chem Res Toxicol 2021; 34:584-600. [PMID: 33496184 DOI: 10.1021/acs.chemrestox.0c00417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrophilically reactive drug metabolites are implicated in many adverse drug reactions. In this mechanism-termed bioactivation-metabolic enzymes convert drugs into reactive metabolites that often conjugate to nucleophilic sites within biological macromolecules like proteins. Toxic metabolite-product adducts induce severe immune responses that can cause sometimes fatal disorders, most commonly in the form of liver injury, blood dyscrasia, or the dermatologic conditions toxic epidermal necrolysis and Stevens-Johnson syndrome. This study models four of the most common metabolic transformations that result in bioactivation: quinone formation, epoxidation, thiophene sulfur-oxidation, and nitroaromatic reduction, by synthesizing models of metabolism and reactivity. First, the metabolism models predict the formation probabilities of all possible metabolites among the pathways studied. Second, the exact structures of these metabolites are enumerated. Third, using these structures, the reactivity model predicts the reactivity of each metabolite. Finally, a feedfoward neural network converts the metabolism and reactivity predictions to a bioactivation prediction for each possible metabolite. These bioactivation predictions represent the joint probability that a metabolite forms and that this metabolite subsequently conjugates to protein or glutathione. Among molecules bioactivated by these pathways, we predicted the correct pathway with an AUC accuracy of 89.98%. Furthermore, the model predicts whether molecules will be bioactivated, distinguishing bioactivated and nonbioactivated molecules with 81.06% AUC. We applied this algorithm to withdrawn drugs. The known bioactivation pathways of alclofenac and benzbromarone were identified by the algorithm, and high probability bioactivation pathways not yet confirmed were identified for safrazine, zimelidine, and astemizole. This bioactivation model-the first of its kind that jointly considers both metabolism and reactivity-enables drug candidates to be quickly evaluated for a toxicity risk that often evades detection during preclinical trials. The XenoSite bioactivation model is available at http://swami.wustl.edu/xenosite/p/bioactivation.
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Affiliation(s)
- Tyler B Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Noah Flynn
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Na Le Dang
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
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21
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Guengerich FP. A history of the roles of cytochrome P450 enzymes in the toxicity of drugs. Toxicol Res 2021; 37:1-23. [PMID: 32837681 PMCID: PMC7431904 DOI: 10.1007/s43188-020-00056-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 05/22/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
The history of drug metabolism began in the 19th Century and developed slowly. In the mid-20th Century the relationship between drug metabolism and toxicity became appreciated, and the roles of cytochrome P450 (P450) enzymes began to be defined in the 1960s. Today we understand much about the metabolism of drugs and many aspects of safety assessment in the context of a relatively small number of human P450s. P450s affect drug toxicity mainly by either reducing exposure to the parent molecule or, in some cases, by converting the drug into a toxic entity. Some of the factors involved are enzyme induction, enzyme inhibition (both reversible and irreversible), and pharmacogenetics. Issues related to drug toxicity include drug-drug interactions, drug-food interactions, and the roles of chemical moieties of drug candidates in drug discovery and development. The maturation of the field of P450 and drug toxicity has been facilitated by advances in analytical chemistry, computational capability, biochemistry and enzymology, and molecular and cell biology. Problems still arise with P450s and drug toxicity in drug discovery and development, and in the pharmaceutical industry the interaction of scientists in medicinal chemistry, drug metabolism, and safety assessment is critical for success.
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Affiliation(s)
- F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, 638B Robinson Research Building, 2200 Pierce Avenue, Nashville, TN 37232-0146 USA
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22
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Domenico A, Nicola G, Daniela T, Fulvio C, Nicola A, Orazio N. De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization. J Chem Inf Model 2020; 60:4582-4593. [PMID: 32845150 DOI: 10.1021/acs.jcim.0c00517] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Artificial intelligence and multiobjective optimization represent promising solutions to bridge chemical and biological landscapes by addressing the automated de novo design of compounds as a result of a humanlike creative process. In the present study, we conceived a novel pair-based multiobjective approach implemented in an adapted SMILES generative algorithm based on recurrent neural networks for the automated de novo design of new molecules whose overall features are optimized by finding the best trade-offs among relevant physicochemical properties (MW, logP, HBA, HBD) and additional similarity-based constraints biasing specific biological targets. In this respect, we carried out the de novo design of chemical libraries targeting neuraminidase, acetylcholinesterase, and the main protease of severe acute respiratory syndrome coronavirus 2. Several quality metrics were employed to assess drug-likeness, chemical feasibility, diversity content, and validity. Molecular docking was finally carried out to better evaluate the scoring and posing of the de novo generated molecules with respect to X-ray cognate ligands of the corresponding molecular counterparts. Our results indicate that artificial intelligence and multiobjective optimization allow us to capture the latent links joining chemical and biological aspects, thus providing easy-to-use options for customizable design strategies, which are especially effective for both lead generation and lead optimization. The algorithm is freely downloadable at https://github.com/alberdom88/moo-denovo and all of the data are available as Supporting Information.
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Affiliation(s)
- Alberga Domenico
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Gambacorta Nicola
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Trisciuzzi Daniela
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy.,Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Ciriaco Fulvio
- Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Amoroso Nicola
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
| | - Nicolotti Orazio
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, I-70126 Bari, Italy
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23
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García M, Virgili M, Alonso M, Alegret C, Fernández B, Port A, Pascual R, Monroy X, Vidal-Torres A, Serafini MT, Vela JM, Almansa C. 4-Aryl-1-oxa-4,9-diazaspiro[5.5]undecane Derivatives as Dual μ-Opioid Receptor Agonists and σ 1 Receptor Antagonists for the Treatment of Pain. J Med Chem 2020; 63:2434-2454. [PMID: 31743642 DOI: 10.1021/acs.jmedchem.9b01256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The synthesis and pharmacological activity of a new series of 1-oxa-4,9-diazaspiro[5.5]undecane derivatives as potent dual ligands for the sigma-1 receptor (σ1R) and the μ-opioid receptor (MOR) are reported. The different positions of the central scaffold, designed using a merging strategy of both target pharmacophores, were explored using a versatile synthetic approach. Phenethyl derivatives in position 9, substituted pyridyl moieties in position 4 and small alkyl groups in position 2 provided the best profiles. One of the best compounds, 15au, showed a balanced dual profile (i.e., MOR agonism and sigma antagonism) and a potent analgesic activity, comparable to the MOR agonist oxycodone in the paw pressure test in mice. Contrary to oxycodone, as expected from the addition of σ1R antagonism, 15au showed local, peripheral activity in this test, which was reversed by the σ1R agonist PRE-084. At equianalgesic doses, 15au showed less constipation than oxycodone, providing evidence that dual MOR agonism and σ1R antagonism may be a useful strategy for obtaining potent and safer analgesics.
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Affiliation(s)
- Mónica García
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Marina Virgili
- Carrer Baldiri Reixac, Enantia, SL, 10 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Mònica Alonso
- Carrer Baldiri Reixac, Enantia, SL, 10 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Carles Alegret
- Carrer Baldiri Reixac, Enantia, SL, 10 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Begoña Fernández
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Adriana Port
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Rosalía Pascual
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Xavier Monroy
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Alba Vidal-Torres
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - María-Teresa Serafini
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - José Miguel Vela
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Carmen Almansa
- Drug Discovery and Preclinical Development, Carrer Baldiri Reixac, ESTEVE Pharmaceuticals SA, 4-8 Parc Científic de Barcelona, 08028 Barcelona, Spain
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Yang H, Lou C, Li W, Liu G, Tang Y. Computational Approaches to Identify Structural Alerts and Their Applications in Environmental Toxicology and Drug Discovery. Chem Res Toxicol 2020; 33:1312-1322. [DOI: 10.1021/acs.chemrestox.0c00006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hongbin Yang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chaofeng Lou
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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25
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Yadav J, Paragas E, Korzekwa K, Nagar S. Time-dependent enzyme inactivation: Numerical analyses of in vitro data and prediction of drug-drug interactions. Pharmacol Ther 2020; 206:107449. [PMID: 31836452 PMCID: PMC6995442 DOI: 10.1016/j.pharmthera.2019.107449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) enzyme kinetics often do not conform to Michaelis-Menten assumptions, and time-dependent inactivation (TDI) of CYPs displays complexities such as multiple substrate binding, partial inactivation, quasi-irreversible inactivation, and sequential metabolism. Additionally, in vitro experimental issues such as lipid partitioning, enzyme concentrations, and inactivator depletion can further complicate the parameterization of in vitro TDI. The traditional replot method used to analyze in vitro TDI datasets is unable to handle complexities in CYP kinetics, and numerical approaches using ordinary differential equations of the kinetic schemes offer several advantages. Improvement in the parameterization of CYP in vitro kinetics has the potential to improve prediction of clinical drug-drug interactions (DDIs). This manuscript discusses various complexities in TDI kinetics of CYPs, and numerical approaches to model these complexities. The extrapolation of CYP in vitro TDI parameters to predict in vivo DDIs with static and dynamic modeling is discussed, along with a discussion on current gaps in knowledge and future directions to improve the prediction of DDI with in vitro data for CYP catalyzed drug metabolism.
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Affiliation(s)
- Jaydeep Yadav
- Amgen Inc., 360 Binney Street, Cambridge, MA 02142, United States; Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Erickson Paragas
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States.
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26
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Yang ZY, He JH, Lu AP, Hou TJ, Cao DS. Application of Negative Design To Design a More Desirable Virtual Screening Library. J Med Chem 2020; 63:4411-4429. [DOI: 10.1021/acs.jmedchem.9b01476] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Jun-Hong He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, P. R. China
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27
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CHEN LL, CHEN CH, ZHANG XX, WANG Y, WANG SF. Identification of constituents in Gui-Zhi-Jia-Ge-Gen-Tang by LC-IT-MS combined with LC-Q-TOF-MS and elucidation of their metabolic networks in rat plasma after oral administration. Chin J Nat Med 2019; 17:803-821. [DOI: 10.1016/s1875-5364(19)30099-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 10/25/2022]
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28
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Liu Y, Peng Y, Zhang Z, Guo X, Ji M, Zheng J. In vitro and in vivo studies of the metabolic activation of chelidonine. Chem Biol Interact 2019; 308:155-163. [PMID: 31102647 DOI: 10.1016/j.cbi.2019.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/18/2019] [Accepted: 05/08/2019] [Indexed: 11/27/2022]
Abstract
Chelidonium majus L. is a herbal medicine widely employed in Europe and Western Asia. Chelidonine (CHE) is a major constituent of the herb and has been reported to be an inhibitor of the cytochrome P450 enzymes (CYP). The major objective of the present study was to study the metabolic pathways of CHE in order to identify potential reactive metabolites responsible for the enzyme inhibition. Three oxidative metabolites (M1-M3) were detected in human liver microsomal incubations after exposure to CHE. M1 and M2 were two isomers of catechol derivatives, and M3 was a dicatechol compound. The M1-M3 metabolites were also observed in bile of rats given CHE. A total of five glutathione (GSH) conjugates (M4-M8) were detected in microsomes containing CHE, GSH, and NADPH. Moreover, M4 and M6 originated from M1, M5 and M7 resulted from M2, and M8 was a M3-derived GSH conjugate. Three biliary CHE-derived GSH conjugates (M4, M5 and M8) were found in CHE-treated rats. This indicates that CHE was bioactivated to ortho-quinone derivatives both in vitro and in vivo. Recombinant P450 enzyme incubations demonstrated that the CYPs3A4, 1A2, 2C19 and 2D6 were mainly involved in metabolic activation of CHE. This study generated data that may be useful in understanding possible mechanisms of CHE-induced P450 inhibition.
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Affiliation(s)
- Yuyang Liu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110161, PR China
| | - Ying Peng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China
| | - Zhengyu Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China
| | - Xiucai Guo
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China
| | - Mingshan Ji
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, 110161, PR China.
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, 550004, PR China; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China.
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29
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Hu L, Wu F, He J, Zhong L, Song Y, Shao H. Cytotoxicity of safrole in HepaRG cells: studies on the role of CYP1A2-mediated ortho-quinone metabolic activation. Xenobiotica 2019; 49:1504-1515. [PMID: 30865484 DOI: 10.1080/00498254.2019.1590882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Linlin Hu
- The Pharmaceutical Department, Nanjing Zhong-da Hospital, School of Medicine, Southeast University, Nanjing, P.R. China
| | - Fei Wu
- Engineering Research Center of Modern Preparation Technology of TCM of Ministry of Education, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Jie He
- The Pharmaceutical Department, Nanjing Zhong-da Hospital, School of Medicine, Southeast University, Nanjing, P.R. China
| | - Lingjun Zhong
- The Pharmaceutical Department, Nanjing Zhong-da Hospital, School of Medicine, Southeast University, Nanjing, P.R. China
| | - Yifan Song
- The Pharmaceutical Department, Nanjing Zhong-da Hospital, School of Medicine, Southeast University, Nanjing, P.R. China
| | - Hua Shao
- The Pharmaceutical Department, Nanjing Zhong-da Hospital, School of Medicine, Southeast University, Nanjing, P.R. China
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30
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Potęga A, Garwolińska D, Nowicka AM, Fau M, Kot-Wasik A, Mazerska Z. Phase I and phase II metabolism simulation of antitumor-active 2-hydroxyacridinone with electrochemistry coupled on-line with mass spectrometry. Xenobiotica 2019; 49:922-934. [PMID: 30301406 DOI: 10.1080/00498254.2018.1524946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here, we report the metabolic profile and the results of associated metabolic studies of 2-hydroxy-acridinone (2-OH-AC), the reference compound for antitumor-active imidazo- and triazoloacridinones. Electrochemistry coupled with mass spectrometry was applied to simulate the general oxidative metabolism of 2-OH-AC for the first time. The reactivity of 2-OH-AC products to biomolecules was also examined. The usefulness of the electrochemistry for studying the reactive drug metabolite trapping (conjugation reactions) was evaluated by the comparison with conventional electrochemical (controlled-potential electrolysis) and enzymatic (microsomal incubation) approaches. 2-OH-AC oxidation products were generated in an electrochemical thin-layer cell. Their tentative structures were assigned based on tandem mass spectrometry in combination with accurate mass measurements. Moreover, the electrochemical conversion of 2-OH-AC in the presence of reduced glutathione and/or N-acetylcysteine unveiled the formation of reactive metabolite-nucleophilic trapping agent conjugates (m/z 517 and m/z 373, respectively) through the thiol group. This glutathione S-conjugate was also identified after electrolysis experiment as well as was detected in liver microsomes. Summing up, the present work illustrates that the electrochemical simulation of metabolic reactions successfully supports the results of classical electrochemical and enzymatic studies. Therefore, it can be a useful tool for synthesis of drug metabolites, including reactive metabolites.
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Affiliation(s)
- Agnieszka Potęga
- a Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry , Gdańsk University of Technology , Gdańsk , Poland
| | - Dorota Garwolińska
- b Department of Analytical Chemistry, Faculty of Chemistry , Gdańsk University of Technology , Gdańsk , Poland
| | - Anna M Nowicka
- c Laboratory of Theory and Applications of Electrodes, Faculty of Chemistry , University of Warsaw , Warsaw , Poland
| | - Michał Fau
- c Laboratory of Theory and Applications of Electrodes, Faculty of Chemistry , University of Warsaw , Warsaw , Poland
| | - Agata Kot-Wasik
- b Department of Analytical Chemistry, Faculty of Chemistry , Gdańsk University of Technology , Gdańsk , Poland
| | - Zofia Mazerska
- a Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry , Gdańsk University of Technology , Gdańsk , Poland
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Kakutani N, Nanayama T, Nomura Y. Novel risk assessment of reactive metabolites from discovery to clinical stage. J Toxicol Sci 2019; 44:201-211. [DOI: 10.2131/jts.44.201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Nobuyuki Kakutani
- Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute
| | - Toyomichi Nanayama
- Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute
| | - Yukihiro Nomura
- Drug Metabolism & Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute
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32
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Liu R, Zhou F, He H, Wei J, Tian X, Ding L. Metabolism and Bioactivation of Corynoline With Characterization of the Glutathione/Cysteine Conjugate and Evaluation of Its Hepatotoxicity in Mice. Front Pharmacol 2018; 9:1264. [PMID: 30459618 PMCID: PMC6232370 DOI: 10.3389/fphar.2018.01264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/16/2018] [Indexed: 11/24/2022] Open
Abstract
Corynoline (CRL), an isoquinoline alkaloid, is the major constituent derived from Corydalis bungeana Herba, which is a well-known Chinese herbal medicine widely used in many prescriptions. The purpose of this study was to comprehensively investigate the metabolism and bioactivation of CRL, and identify the CYP450 isoforms involved in reactive ortho-benzoquinone metabolites formation and evaluate its hepatotoxicity in mice. Here, high resolution and triple quadrupole mass spectrometry were used for studying the metabolism of CRL. Three metabolites (M1-M3) and four glutathione conjugates (M4-M7) of CRL ortho-benzoquinone reactive metabolite were found in vitro using rat and human liver microsomes supplemented with NADPH and glutathione. Four cysteine conjugates (M8-M11) were trapped in mice besides M1-M7. Using human recombinant CYP450 enzymes and chemical inhibitor method, we found that CYP3A4, CYP2C19, CYP2C9, and CYP2D6 were mainly involved in the bioactivation of CRL. Furthermore, CRL had no obvious hepatotoxicity and did not induce acute liver injuries in the experimental dosage (125-500 mg/kg) used in this study. However, phenomena of abnormal behaviors and low body temperature appeared in mice after drug administration, and three of them were dead. Tissue distribution study of CRL in mice showed that the main target organ of CRL was liver, then kidney, heart, and brain. CRL could traverse the blood-brain barrier, and have relative high concentration in brain. So, we surmise that toxicity effect of CRL on other organs may have occurred, and more attention should be paid on the traditional Chinese medicine contained CRL in clinic.
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Affiliation(s)
- Ruijuan Liu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Fang Zhou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
- Department of Pharmacy, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - He He
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Physiology and Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Jingyao Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Ding
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
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33
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Piska K, Galanty A, Koczurkiewicz P, Żmudzki P, Potaczek J, Podolak I, Pękala E. Usnic acid reactive metabolites formation in human, rat, and mice microsomes. Implication for hepatotoxicity. Food Chem Toxicol 2018; 120:112-118. [DOI: 10.1016/j.fct.2018.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/10/2018] [Accepted: 07/02/2018] [Indexed: 01/05/2023]
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34
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Limban C, Nuţă DC, Chiriţă C, Negreș S, Arsene AL, Goumenou M, Karakitsios SP, Tsatsakis AM, Sarigiannis DA. The use of structural alerts to avoid the toxicity of pharmaceuticals. Toxicol Rep 2018; 5:943-953. [PMID: 30258789 PMCID: PMC6151358 DOI: 10.1016/j.toxrep.2018.08.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/12/2018] [Accepted: 08/29/2018] [Indexed: 01/18/2023] Open
Abstract
In order to identify compounds with potential toxicity problems, particular attention is paid to structural alerts, which are high chemical reactivity molecular fragments or fragments that can be transformed via bioactivation by human enzymes into fragments with high chemical reactivity. The concept has been introduced in order to reduce the likelihood that future candidate substances as pharmaceuticals will have undesirable toxic effects. A significant proportion (∼78–86%) of drugs characterized by residual toxicity contain structural alerts; there is also evidence indicating the formation of active metabolites as a causal factor for the toxicity of 62–69% of these molecules. On the other hand, the pharmacological action of certain drugs depends on the formation of reactive metabolites. Detailed assessment of the potential for the formation of active metabolites is recommended to characterize a biologically active compound. Although many prescribed drugs frequently contain structural alerts and form reactive metabolites, the vast majority of these drugs are administered in low daily doses. Avoiding structural alerts has become almost a norm in new drug design. An in-depth review of the biochemical reactivity of these structural alerts for new drug candidates is critical from a safety point of view and is currently being monitored in the discovery of drugs. The chemical strategies applied to structural alerts in molecules to limit the toxicity are: partial replacement or full replacement of the structural alert; reduction of electronic density; introduction of a structural element of metabolic interest (metabolic switching); multiple approaches.
Therefore, chemical intervention strategies to eliminate bioactivation are often interactive processes; their success depends largely on a close working relationship between drug chemists, pharmacologists and researchers in metabolic science.
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Affiliation(s)
- Carmen Limban
- "Carol Davila" University of Medicine and Pharmacy, Department of Pharmaceutical Chemistry, Traian Vuia 6, Bucharest, 020956, Romania
| | - Diana C Nuţă
- "Carol Davila" University of Medicine and Pharmacy, Department of Pharmaceutical Chemistry, Traian Vuia 6, Bucharest, 020956, Romania
| | - Cornel Chiriţă
- "Carol Davila" University of Medicine and Pharmacy, Department of Pharmacology and Clinical Pharmacy, Traian Vuia 6, Bucharest, 020956, Romania
| | - Simona Negreș
- "Carol Davila" University of Medicine and Pharmacy, Department of Pharmacology and Clinical Pharmacy, Traian Vuia 6, Bucharest, 020956, Romania
| | - Andreea L Arsene
- "Carol Davila" University of Medicine and Pharmacy, Department of Pharmaceutical Microbiology, Traian Vuia 6, Bucharest, 020956, Romania
| | - Marina Goumenou
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, Heraklion, 71409, Crete, Greece
| | - Spyros P Karakitsios
- Aristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece.,HERACLES Research Center on the Exposome and Health, Center for Interdisciplinary Research and Innovation, Balkan Center, Bldg. B, 10th km Thessaloniki-Thermi Road, 57001, Greece
| | - Aristidis M Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, Heraklion, 71409, Crete, Greece
| | - Dimosthenis A Sarigiannis
- Aristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece.,HERACLES Research Center on the Exposome and Health, Center for Interdisciplinary Research and Innovation, Balkan Center, Bldg. B, 10th km Thessaloniki-Thermi Road, 57001, Greece.,University School for Advanced Study (IUSS), Piazza della Vittoria 15, Pavia 27100, Italy
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35
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Bosc D, Vezenkov L, Bortnik S, An J, Xu J, Choutka C, Hannigan AM, Kovacic S, Loo S, Clark PGK, Chen G, Guay-Ross RN, Yang K, Dragowska WH, Zhang F, Go NE, Leung A, Honson NS, Pfeifer TA, Gleave M, Bally M, Jones SJ, Gorski SM, Young RN. A new quinoline-based chemical probe inhibits the autophagy-related cysteine protease ATG4B. Sci Rep 2018; 8:11653. [PMID: 30076329 PMCID: PMC6076261 DOI: 10.1038/s41598-018-29900-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 07/17/2018] [Indexed: 01/06/2023] Open
Abstract
The cysteine protease ATG4B is a key component of the autophagy machinery, acting to proteolytically prime and recycle its substrate MAP1LC3B. The roles of ATG4B in cancer and other diseases appear to be context dependent but are still not well understood. To help further explore ATG4B functions and potential therapeutic applications, we employed a chemical biology approach to identify ATG4B inhibitors. Here, we describe the discovery of 4-28, a styrylquinoline identified by a combined computational modeling, in silico screening, high content cell-based screening and biochemical assay approach. A structure-activity relationship study led to the development of a more stable and potent compound LV-320. We demonstrated that LV-320 inhibits ATG4B enzymatic activity, blocks autophagic flux in cells, and is stable, non-toxic and active in vivo. These findings suggest that LV-320 will serve as a relevant chemical tool to study the various roles of ATG4B in cancer and other contexts.
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Affiliation(s)
- D Bosc
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Inserm, Institut Pasteur de Lille, U1177 Drugs & Molecules for Living Systems, Université de Lille, F-59000, Lille, France
| | - L Vezenkov
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie, 15 avenue Charles Flahault, 34093, Montpellier, France
| | - S Bortnik
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
| | - J An
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
| | - J Xu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - C Choutka
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - A M Hannigan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
| | - S Kovacic
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - S Loo
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - P G K Clark
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - G Chen
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - R N Guay-Ross
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - K Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - W H Dragowska
- Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
| | - F Zhang
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V6H 3Z6, Canada
| | - N E Go
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
| | - A Leung
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
| | - N S Honson
- Centre for Drug Research and Development, 2405 Wesbrook Mall - 4th Floor, Vancouver, BC, V6T 1Z3, Canada
| | - T A Pfeifer
- Centre for Drug Research and Development, 2405 Wesbrook Mall - 4th Floor, Vancouver, BC, V6T 1Z3, Canada
| | - M Gleave
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V6H 3Z6, Canada
| | - M Bally
- Experimental Therapeutics, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
| | - S J Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - S M Gorski
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4E6, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - R N Young
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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36
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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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37
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Ogiyama T, Yamaguchi M, Kurikawa N, Honzumi S, Terayama K, Nagaoka N, Yamamoto Y, Kimura T, Sugiyama D, Inoue SI. Design, synthesis, and pharmacological evaluation of a novel series of hormone sensitive lipase inhibitor. Bioorg Med Chem 2017; 25:4817-4828. [DOI: 10.1016/j.bmc.2017.07.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022]
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38
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La DS, Peterson EA, Bode C, Boezio AA, Bregman H, Chu-Moyer MY, Coats J, DiMauro EF, Dineen TA, Du B, Gao H, Graceffa R, Gunaydin H, Guzman-Perez A, Fremeau R, Huang X, Ilch C, Kornecook TJ, Kreiman C, Ligutti J, Jasmine Lin MH, McDermott JS, Marx I, Matson DJ, McDonough SI, Moyer BD, Nho Nguyen H, Taborn K, Yu V, Weiss MM. The discovery of benzoxazine sulfonamide inhibitors of Na V 1.7: Tools that bridge efficacy and target engagement. Bioorg Med Chem Lett 2017. [DOI: 10.1016/j.bmcl.2017.05.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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39
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Weiss MM, Dineen TA, Marx IE, Altmann S, Boezio A, Bregman H, Chu-Moyer M, DiMauro EF, Feric Bojic E, Foti RS, Gao H, Graceffa R, Gunaydin H, Guzman-Perez A, Huang H, Huang L, Jarosh M, Kornecook T, Kreiman CR, Ligutti J, La DS, Lin MHJ, Liu D, Moyer BD, Nguyen HN, Peterson EA, Rose PE, Taborn K, Youngblood BD, Yu V, Fremeau RT. Sulfonamides as Selective NaV1.7 Inhibitors: Optimizing Potency and Pharmacokinetics While Mitigating Metabolic Liabilities. J Med Chem 2017; 60:5969-5989. [DOI: 10.1021/acs.jmedchem.6b01851] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Thomas Kornecook
- Department
of Neuroscience, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | | | - Joseph Ligutti
- Department
of Neuroscience, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | | | | | - Dong Liu
- Department
of Neuroscience, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Bryan D. Moyer
- Department
of Neuroscience, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
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40
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Spicer JA, Miller CK, O'Connor PD, Jose J, Huttunen KM, Jaiswal JK, Denny WA, Akhlaghi H, Browne KA, Trapani JA. Benzenesulphonamide inhibitors of the cytolytic protein perforin. Bioorg Med Chem Lett 2017; 27:1050-1054. [PMID: 28110869 PMCID: PMC5303009 DOI: 10.1016/j.bmcl.2016.12.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 11/23/2022]
Abstract
The pore-forming protein perforin is a key component of mammalian cell-mediated immunity and essential to the pathway that allows elimination of virus-infected and transformed cells. Perforin activity has also been implicated in certain auto-immune conditions and therapy-induced conditions such as allograft rejection and graft versus host disease. An inhibitor of perforin activity could be used as a highly specific immunosuppressive treatment for these conditions, with reduced side-effects compared to currently accepted therapies. Previously identified first-in-class inhibitors based on a 2-thioxoimidazolidin-4-one core show suboptimal physicochemical properties and toxicity toward the natural killer (NK) cells that secrete perforin in vivo. The current benzenesulphonamide-based series delivers a non-toxic bioisosteric replacement possessing improved solubility.
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Affiliation(s)
- Julie A Spicer
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, A New Zealand Centre for Research Excellence, Auckland, New Zealand.
| | - Christian K Miller
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, A New Zealand Centre for Research Excellence, Auckland, New Zealand
| | - Patrick D O'Connor
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, A New Zealand Centre for Research Excellence, Auckland, New Zealand
| | - Jiney Jose
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, A New Zealand Centre for Research Excellence, Auckland, New Zealand
| | - Kristiina M Huttunen
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jagdish K Jaiswal
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, A New Zealand Centre for Research Excellence, Auckland, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, A New Zealand Centre for Research Excellence, Auckland, New Zealand
| | - Hedieh Akhlaghi
- Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia
| | - Kylie A Browne
- Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
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41
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den Braver MW, Vermeulen NPE, Commandeur JNM. Generic method for the absolute quantification of glutathione S-conjugates: Application to the conjugates of acetaminophen, clozapine and diclofenac. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1046:185-194. [PMID: 28189104 DOI: 10.1016/j.jchromb.2017.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 10/20/2022]
Abstract
Modification of cellular macromolecules by reactive drug metabolites is considered to play an important role in the initiation of tissue injury by many drugs. Detection and identification of reactive intermediates is often performed by analyzing the conjugates formed after trapping by glutathione (GSH). Although sensitivity of modern mass spectrometrical methods is extremely high, absolute quantification of GSH-conjugates is critically dependent on the availability of authentic references. Although 1H NMR is currently the method of choice for quantification of metabolites formed biosynthetically, its intrinsically low sensitivity can be a limiting factor in quantification of GSH-conjugates which generally are formed at low levels. In the present study, a simple but sensitive and generic method for absolute quantification of GSH-conjugates is presented. The method is based on quantitative alkaline hydrolysis of GSH-conjugates and subsequent quantification of glutamic acid and glycine by HPLC after precolumn derivatization with o-phthaldialdehyde/N-acetylcysteine (OPA/NAC). Because of the lower stability of the glycine OPA/NAC-derivate, quantification of the glutamic acid OPA/NAC-derivate appeared most suitable for quantification of GSH-conjugates. The novel method was used to quantify the concentrations of GSH-conjugates of diclofenac, clozapine and acetaminophen and quantification was consistent with 1H NMR, but with a more than 100-fold lower detection limit for absolute quantification.
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Affiliation(s)
- Michiel W den Braver
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Nico P E Vermeulen
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Jan N M Commandeur
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical sciences, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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42
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Yamanobe S, Kawamoto H, Ohtake N. [Design of high-quality compound library and open innovation]. Nihon Yakurigaku Zasshi 2017; 149:180-185. [PMID: 28381662 DOI: 10.1254/fpj.149.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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43
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Zhang XY, Elfarra AA. Potential roles of myeloperoxidase and hypochlorous acid in metabolism and toxicity of alkene hydrocarbons and drug molecules containing olefinic moieties. Expert Opin Drug Metab Toxicol 2016; 13:513-524. [DOI: 10.1080/17425255.2017.1271413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xin-Yu Zhang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai, China
| | - Adnan A. Elfarra
- Department of Comparative Biosciences and the Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA
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44
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Abstract
A number of drugs have been withdrawn from the market or severely restricted in their use because of unexpected toxicities that become apparent only after the launch of new drug entities. Circumstantial evidence suggests that, in most cases, reactive metabolites are responsible for these unexpected toxicities. In this review, a general overview of the types of reactive metabolites and the consequences of their formation are presented. The current approaches to evaluate bioactivation potential of new compounds with particular emphasis on the advantages and limitation of these procedures will be discussed. Reasonable reasons for the excellent safety record of certain drugs susceptible to bioactivation will also be explored and should provide valuable guidance in the use of reactive-metabolite assessments when nominating drug candidates for development. This will, in turn, help us to design and bring safer drugs to the market.
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Affiliation(s)
- Sabry M Attia
- Department of Pharmacology and Toxicology; College of Pharmacy; King Saud University; Riyadh, Saudi Arabia.
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45
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Feng P, Hu X, Wu X, Dong J, Cai X. Characterization of an epoxide-derived metabolite of dictamnine using high-performance liquid chromatography with hybrid linear trap quadrupole orbitrap mass spectrometry. J Sep Sci 2016; 39:4858-4865. [DOI: 10.1002/jssc.201600980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Pinning Feng
- Department of Laboratory Medicine; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou P. R. China
| | - Xinrong Hu
- Department of oncology; Nanxi Mountain hospital; Guilin P. R. China
| | - Xiaoliang Wu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangzhou Guangdong P. R. China
| | - Jun Dong
- Department of General Internal Medicine, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangzhou P. R. China
| | - Xiuyu Cai
- Department of General Internal Medicine, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Guangzhou P. R. China
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46
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Abstract
Drugs can induce liver injury when taken as an over-dose, or even at therapeutic doses in susceptible individuals. Although severe drug-induced liver injury (DILI) is a relatively uncommon clinical event, it is a potentially life threatening adverse drug reaction and is the most common indication for the drug withdrawal. Areas covered: However, the diagnosis of DILI remains a significant challenge, because the establishment of causality is very difficult, and the histopathologic findings of DILI may be indistinguishable from those of other hepatic disorders, such as viral and alcoholic hepatitis. In this review, we provide an overview of recent advances in identification of serologic markers of diagnosis and prognosis, etiologic factors for susceptibility and diagnostic evaluation of DILI, with a focus on its pathogenic mechanisms and the role of liver biopsy. Expert commentary: Further studies of divergent research platforms, using a systems biology approach such as genomics and transcriptomics, may provide a deeper understanding of human drug metabolism and the causes, risk factors, and pathogenesis of DILI.
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Affiliation(s)
- Sun-Jae Lee
- a Department of Pathology, School of Medicine , Catholic University of Daegu , Daegu , Republic of Korea
| | - Youn Ju Lee
- b Department of Pharmacology, School of Medicine , Catholic University of Daegu , Daegu , Republic of Korea
| | - Kwan-Kyu Park
- a Department of Pathology, School of Medicine , Catholic University of Daegu , Daegu , Republic of Korea
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47
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Thompson RA, Isin EM, Ogese MO, Mettetal JT, Williams DP. Reactive Metabolites: Current and Emerging Risk and Hazard Assessments. Chem Res Toxicol 2016; 29:505-33. [DOI: 10.1021/acs.chemrestox.5b00410] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Richard A. Thompson
- DMPK, Respiratory, Inflammation & Autoimmunity iMed, AstraZeneca R&D, 431 83 Mölndal, Sweden
| | - Emre M. Isin
- DMPK, Cardiovascular & Metabolic Diseases iMed, AstraZeneca R&D, 431 83 Mölndal, Sweden
| | - Monday O. Ogese
- Translational Safety, Drug Safety and Metabolism, AstraZeneca R&D, Darwin Building 310, Cambridge Science Park, Milton Rd, Cambridge CB4 0FZ, United Kingdom
| | - Jerome T. Mettetal
- Translational Safety, Drug Safety and Metabolism, AstraZeneca R&D, 35 Gatehouse Dr, Waltham, Massachusetts 02451, United States
| | - Dominic P. Williams
- Translational Safety, Drug Safety and Metabolism, AstraZeneca R&D, Darwin Building 310, Cambridge Science Park, Milton Rd, Cambridge CB4 0FZ, United Kingdom
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48
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Gómez-Lechón MJ, Tolosa L, Donato MT. Metabolic activation and drug-induced liver injury: in vitro approaches for the safety risk assessment of new drugs. J Appl Toxicol 2015; 36:752-68. [PMID: 26691983 DOI: 10.1002/jat.3277] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/21/2015] [Accepted: 11/11/2015] [Indexed: 12/13/2022]
Abstract
Drug-induced liver injury (DILI) is a significant leading cause of hepatic dysfunction, drug failure during clinical trials and post-market withdrawal of approved drugs. Many cases of DILI are unexpected reactions of an idiosyncratic nature that occur in a small group of susceptible individuals. Intensive research efforts have been made to understand better the idiosyncratic DILI and to identify potential risk factors. Metabolic bioactivation of drugs to form reactive metabolites is considered an initiation mechanism for idiosyncratic DILI. Reactive species may interact irreversibly with cell macromolecules (covalent binding, oxidative damage), and alter their structure and activity. This review focuses on proposed in vitro screening strategies to predict and reduce idiosyncratic hepatotoxicity associated with drug bioactivation. Compound incubation with metabolically competent biological systems (liver-derived cells, subcellular fractions), in combination with methods to reveal the formation of reactive intermediates (e.g., formation of adducts with liver proteins, metabolite trapping or enzyme inhibition assays), are approaches commonly used to screen the reactivity of new molecules in early drug development. Several cell-based assays have also been proposed for the safety risk assessment of bioactivable compounds. Copyright © 2015 John Wiley & Sons, Ltd.
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MESH Headings
- Activation, Metabolic
- Animals
- Cell Culture Techniques/trends
- Cell Line
- Cells, Cultured
- Chemical and Drug Induced Liver Injury/epidemiology
- Chemical and Drug Induced Liver Injury/metabolism
- Chemical and Drug Induced Liver Injury/pathology
- Coculture Techniques/trends
- Drug Evaluation, Preclinical/trends
- Drugs, Investigational/adverse effects
- Drugs, Investigational/chemistry
- Drugs, Investigational/pharmacokinetics
- Humans
- In Vitro Techniques/trends
- Liver/cytology
- Liver/drug effects
- Liver/metabolism
- Liver/pathology
- Microfluidics/methods
- Microfluidics/trends
- Microsomes, Liver/drug effects
- Microsomes, Liver/enzymology
- Microsomes, Liver/metabolism
- Models, Biological
- Pluripotent Stem Cells/cytology
- Pluripotent Stem Cells/drug effects
- Pluripotent Stem Cells/metabolism
- Pluripotent Stem Cells/pathology
- Recombinant Proteins/metabolism
- Risk Assessment
- Risk Factors
- Tissue Scaffolds/trends
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Affiliation(s)
- M José Gómez-Lechón
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- CIBEREHD, FIS, Spain
| | - Laia Tolosa
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - M Teresa Donato
- Unidad de Hepatología Experimental, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- CIBEREHD, FIS, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Spain
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49
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Chi M, Peng Y, Zheng J. Characterization of glutathione conjugates derived from reactive metabolites of bakuchiol. Chem Biol Interact 2015; 244:178-86. [PMID: 26712081 DOI: 10.1016/j.cbi.2015.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/26/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
Abstract
Bakuchiol belongs to a family of monoterpene phenols occurring in plant Psoralea corylifolia L., a traditional herbal medicine. Bakuchiol has also demonstrated multiple pharmacologic activities. However, metabolism of bakuchiol had never been investigated. The major objective of the present study was to study the metabolic pathways of bakuchiol in order to identify potential reactive metabolites. A total of five glutathione (GSH) conjugates (M1-M5) were detected in rat/human liver microsomes containing NADPH, GSH, and bakuchiol. M1 and M2 resulted from GSH conjugated on the phenol ring. M3, M4, and M5 were derived from GSH adducted on the side chain. The results displayed that bakuchiol can be bioactivated by oxidation of the phenol moiety to the corresponding ortho-quinone and by epoxidation of the aliphatic side chain to epoxide metabolites. No bakuchiol-derived GSH conjugates were detected in urine of rats given bakuchiol, but six corresponding cysteinylglycine (Cys-Gly) conjugates and mercapturic acids were observed instead. A 2'-iodoxybenzoic acid-mediated oxidation reaction of bakuchiol in the presence of GSH produced M1 and M2, and m-chloroperoxybenzoicacid-mediated oxidation of bakuchiol trapped with GSH generated M3 and M4. The four synthetic metabolites were detected in microsomal incubations. In addition, recombinant P450 enzyme incubations showed that CYP 1A2 was the predominant P450 responsible for the metabolism of bakuchiol. In summary, our results demonstrated that bakuchiol can be bioactivated to quinone and epoxide metabolites. These findings facilitate the understanding of the mechanisms of bakuchiol-induced cytotoxicity.
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Affiliation(s)
- Meina Chi
- College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China
| | - Ying Peng
- College of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China.
| | - Jiang Zheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, PR China; Center for Developmental Therapeutics, Seattle Children's Research Institute, Division of Gastroenterology and Hepatology, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA.
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50
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Svennebring A. The role of intramolecular self-destruction of reactive metabolic intermediates in determining toxicity. J Appl Toxicol 2015; 36:483-500. [DOI: 10.1002/jat.3248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Andreas Svennebring
- Department of Pharmaceutical Biosciences, Faculty of Pharmacy; Uppsala University; Box 591 Uppsala 751 24 Sweden
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