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Rao M, McDuffie E, Srivastava S, Plaisted W, Sachs C. Safety Implications of Modulating Nuclear Receptors: A Comprehensive Analysis from Non-Clinical and Clinical Perspectives. Pharmaceuticals (Basel) 2024; 17:875. [PMID: 39065726 PMCID: PMC11279859 DOI: 10.3390/ph17070875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/13/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The unintended modulation of nuclear receptor (NR) activity by drugs can lead to toxicities amongst the endocrine, gastrointestinal, hepatic cardiovascular, and central nervous systems. While secondary pharmacology screening assays include NRs, safety risks due to unintended interactions of small molecule drugs with NRs remain poorly understood. To identify potential nonclinical and clinical safety effects resulting from functional interactions with 44 of the 48 human-expressed NRs, we conducted a systematic narrative review of the scientific literature, tissue expression data, and used curated databases (OFF-X™) (Off-X, Clarivate) to organize reported toxicities linked to the functional modulation of NRs in a tabular and machine-readable format. The top five NRs associated with the highest number of safety alerts from peer-reviewed journals, regulatory agency communications, congresses/conferences, clinical trial registries, and company communications were the Glucocorticoid Receptor (GR, 18,328), Androgen Receptor (AR, 18,219), Estrogen Receptor (ER, 12,028), Retinoic acid receptors (RAR, 10,450), and Pregnane X receptor (PXR, 8044). Toxicities associated with NR modulation include hepatotoxicity, cardiotoxicity, endocrine disruption, carcinogenicity, metabolic disorders, and neurotoxicity. These toxicities often arise from the dysregulation of receptors like Peroxisome proliferator-activated receptors (PPARα, PPARγ), the ER, PXR, AR, and GR. This dysregulation leads to various health issues, including liver enlargement, hepatocellular carcinoma, heart-related problems, hormonal imbalances, tumor growth, metabolic syndromes, and brain function impairment. Gene expression analysis using heatmaps for human and rat tissues complemented the functional modulation of NRs associated with the reported toxicities. Interestingly, certain NRs showed ubiquitous expression in tissues not previously linked to toxicities, suggesting the potential utilization of organ-specific NR interactions for therapeutic purposes.
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Affiliation(s)
- Mohan Rao
- Toxicology Department, Neurocrine Biosciences, Inc., San Diego, CA 92130, USA (C.S.)
| | - Eric McDuffie
- Toxicology Department, Neurocrine Biosciences, Inc., San Diego, CA 92130, USA (C.S.)
| | - Sanjay Srivastava
- Chemistry Department, Neurocrine Biosciences, Inc., San Diego, CA 92130, USA
| | - Warren Plaisted
- Biology Department, Neurocrine Biosciences, Inc., San Diego, CA 92130, USA
| | - Clifford Sachs
- Toxicology Department, Neurocrine Biosciences, Inc., San Diego, CA 92130, USA (C.S.)
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2
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Brown AP, Friedrichs GS, Tang HM, Traebert M, Weber V, Yao N, Yan GX. Electrophysiological Changes in the Rabbit Ventricular Wedge and Human-Induced Pluripotent Stem-Cell Derived (IPSC) Cardiomyocytes Translate to Severe Arrhythmia Observed in a Canine Toxicology Study, Not Predicted by Standard In Vitro Ion Channel Assays. Int J Toxicol 2024; 43:231-242. [PMID: 38327194 DOI: 10.1177/10915818241230900] [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] [Indexed: 02/09/2024]
Abstract
During drug discovery, small molecules are typically assayed in vitro for secondary pharmacology effects, which include ion channels relevant to cardiac electrophysiology. Compound A was an irreversible inhibitor of myeloperoxidase investigated for the treatment of peripheral artery disease. Oral doses in dogs at ≥5 mg/kg resulted in cardiac arrhythmias in a dose-dependent manner (at Cmax, free ≥1.53 μM) that progressed in severity with time. Nevertheless, a panel of 13 different cardiac ion channel (K, Na, and Ca) assays, including hERG, failed to identify pharmacologic risks of the molecule. Compound A and a related Compound B were evaluated for electrophysiological effects in the isolated rabbit ventricular wedge assay. Compounds A and B prolonged QT and Tp-e intervals at ≥1 and ≥.3 μM, respectively, and both prolonged QRS at ≥5 μM. Compound A produced early after depolarizations and premature ventricular complexes at ≥5 μM. These data indicate both compounds may be modulating hERG (Ikr) and Nav1.5 ion channels. In human IPSC cardiomyocytes, Compounds A and B prolonged field potential duration at ≥3 μM and induced cellular dysrhythmia at ≥10 and ≥3 μM, respectively. In a rat toxicology study, heart tissue: plasma concentration ratios for Compound A were ≥19X at 24 hours post-dose, indicating significant tissue distribution. In conclusion, in vitro ion channel assays may not always identify cardiovascular electrophysiological risks observed in vivo, which can be affected by tissue drug distribution. Risk for arrhythmia may increase with a "trappable" ion channel inhibitor, particularly if cardiac tissue drug levels achieve a critical threshold for pharmacologic effects.
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Affiliation(s)
- Alan P Brown
- Novartis Biomedical Research, Cambridge, MA, USA
| | | | | | | | | | - Nancy Yao
- Novartis Biomedical Research, East Hanover, NJ, USA
| | - Gan-Xin Yan
- Lankenau Institute for Medical Research, Wynnewood, PA, USA
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3
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Dorel R, Sun D, Carruthers N, Castanedo GM, Ung PMU, Factor DC, Li T, Baumann H, Janota D, Pang J, Salphati L, Meklemburg R, Korman AJ, Harper HE, Stubblefield S, Payandeh J, McHugh D, Lang BT, Tesar PJ, Dere E, Masureel M, Adams DJ, Volgraf M, Braun MG. Discovery and Optimization of Selective Brain-Penetrant EBP Inhibitors that Enhance Oligodendrocyte Formation. J Med Chem 2024. [PMID: 38470227 DOI: 10.1021/acs.jmedchem.3c02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The inhibition of emopamil binding protein (EBP), a sterol isomerase within the cholesterol biosynthesis pathway, promotes oligodendrocyte formation, which has been proposed as a potential therapeutic approach for treating multiple sclerosis. Herein, we describe the discovery and optimization of brain-penetrant, orally bioavailable inhibitors of EBP. A structure-based drug design approach from literature compound 1 led to the discovery of a hydantoin-based scaffold, which provided balanced physicochemical properties and potency and an improved in vitro safety profile. The long half-lives of early hydantoin-based EBP inhibitors in rodents prompted an unconventional optimization strategy, focused on increasing metabolic turnover while maintaining potency and a brain-penetrant profile. The resulting EBP inhibitor 11 demonstrated strong in vivo target engagement in the brain, as illustrated by the accumulation of EBP substrate zymostenol after repeated dosing. Furthermore, compound 11 enhanced the formation of oligodendrocytes in human cortical organoids, providing additional support for our therapeutic hypothesis.
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Affiliation(s)
- Ruth Dorel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Dawei Sun
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Carruthers
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Peter M-U Ung
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel C Factor
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Tianbo Li
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hannah Baumann
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Danielle Janota
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laurent Salphati
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Meklemburg
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Allison J Korman
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Halie E Harper
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel McHugh
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Bradley T Lang
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Paul J Tesar
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Edward Dere
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthieu Masureel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Drew J Adams
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Matthew Volgraf
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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4
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Talevi A. Computer-Aided Drug Discovery and Design: Recent Advances and Future Prospects. Methods Mol Biol 2024; 2714:1-20. [PMID: 37676590 DOI: 10.1007/978-1-0716-3441-7_1] [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] [Indexed: 09/08/2023]
Abstract
Computer-aided drug discovery and design involve the use of information technologies to identify and develop, on a rational ground, chemical compounds that align a set of desired physicochemical and biological properties. In its most common form, it involves the identification and/or modification of an active scaffold (or the combination of known active scaffolds), although de novo drug design from scratch is also possible. Traditionally, the drug discovery and design processes have focused on the molecular determinants of the interactions between drug candidates and their known or intended pharmacological target(s). Nevertheless, in modern times, drug discovery and design are conceived as a particularly complex multiparameter optimization task, due to the complicated, often conflicting, property requirements.This chapter provides an updated overview of in silico approaches for identifying active scaffolds and guiding the subsequent optimization process. Recent groundbreaking advances in the field have also analyzed the integration of state-of-the-art machine learning approaches in every step of the drug discovery process (from prediction of target structure to customized molecular docking scoring functions), integration of multilevel omics data, and the use of a diversity of computational approaches to assist target validation and assess plausible binding pockets.
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Affiliation(s)
- Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata (UNLP), La Plata, Argentina.
- Argentinean National Council of Scientific and Technical Research (CONICET), La Plata, Argentina.
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5
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Shahout F, Vanharen M, Saafane A, Gillard J, Girard D, LaPlante SR. Drug Self-Aggregation into Nano-Entities Has the Potential to Induce Immune Responses. Mol Pharm 2023; 20:4031-4040. [PMID: 37421372 DOI: 10.1021/acs.molpharmaceut.3c00196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
The free-state solution behaviors of small molecules profoundly affect their respective properties. It is becoming more obvious that compounds can adopt a three-phase equilibrium when placed in an aqueous solution, among soluble-lone molecule form, self-assembled aggregate form (nano-entities), and solid precipitate form. Recently, correlations have emerged between the existence of self-assemblies into drug nano-entities and unintended side effects. This report describes our pilot study involving a selection of drugs and dyes to explore if there may be a correlation between the existence of drug nano-entities and immune responses. We first implement practical strategies for detecting the drug self-assemblies using a combination of nuclear magnetic resonance (NMR), dynamic light scattering (DLS), transmission electron microscopy (TEM), and confocal microscopy. We then used enzyme-linked immunosorbent assays (ELISA) to monitor the modulation of immune responses on two cellular models, murine macrophage and human neutrophils, upon exposure to the drugs and dyes. The results suggest that exposure to some aggregates correlated with an increase in IL-8 and TNF-α in these model systems. Given this pilot study, further correlations merit pursuing on a larger scale given the importance and potential impact of drug-induced immune-related side effects.
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Affiliation(s)
- Fatma Shahout
- Université du Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Marion Vanharen
- Université du Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Abdelaziz Saafane
- Université du Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - James Gillard
- Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, 2950 Chem. de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Denis Girard
- Université du Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Steven R LaPlante
- Université du Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX Research and Solutions, Inc., 500 Boulevard Cartier Ouest, Laval, Québec H7V 5B7, Canada
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6
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Tredup C, Ndreshkjana B, Schneider NS, Tjaden A, Kemas AM, Youhanna S, Lauschke VM, Berger BT, Krämer A, Berger LM, Röhm S, Knapp S, Farin HF, Müller S. Deep Annotation of Donated Chemical Probes (DCP) in Organotypic Human Liver Cultures and Patient-Derived Organoids from Tumor and Normal Colorectum. ACS Chem Biol 2023; 18:822-836. [PMID: 36944371 PMCID: PMC10127199 DOI: 10.1021/acschembio.2c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Well-characterized small molecules are essential tools for studying the biology and therapeutic relevance of a target protein. However, many compounds reported in the literature and routinely studied in biomedical research lack the potency and selectivity required for mechanistic cellular studies on the function of a given protein. Furthermore, commercially available compounds often do not include useful tools developed by industry as part of their research and development efforts, as they frequently remain proprietary. The freely available donated chemical probe (DCP) library, fueled by generous donations of compounds from industry and academia, enables easy access to a steadily growing collection of these valuable and well-characterized tools. Here, we provide a systematic description of the current DCP library collection and their associated comprehensive characterization data, including a variety of in vitro and cellular assays. Of note, we characterized the set in relevant human primary models by employing hepatotoxicity screening in primary human liver spheroids and viability screening in patient-derived colorectal cancer organoids and matched normal-adjacent epithelium. Taken together, the DCP library represents a well-annotated, openly available collection of tool compounds for studying a wide range of targets, including kinases, G-protein-coupled receptors, and ion channels. As such, it represents a unique resource for the biomedical research community.
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Affiliation(s)
- Claudia Tredup
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Benardina Ndreshkjana
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596Frankfurt am Main, Germany
| | - Natalie S Schneider
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Aurino M Kemas
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
| | - Sonia Youhanna
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376Stuttgart, Germany
- University of Tübingen, 72074Tübingen, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Sandra Röhm
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
- German Cancer Consortium (DKTK), Heidelberg69120, Germany
- German Cancer Research Center (DKFZ), 69120Heidelberg, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
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7
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Cipriano A, Milite C, Feoli A, Viviano M, Pepe G, Campiglia P, Sarno G, Picaud S, Imaide S, Makukhin N, Filippakopoulos P, Ciulli A, Castellano S, Sbardella G. Discovery of Benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain. ChemMedChem 2022; 17:e202200343. [PMID: 36040095 PMCID: PMC9826262 DOI: 10.1002/cmdc.202200343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/29/2022] [Indexed: 01/11/2023]
Abstract
The bromodomain and extra-terminal (BET) family of proteins includes BRD2, BRD3, BRD4, and the testis-specific protein, BRDT, each containing two N-terminal tandem bromodomain (BRD) modules. Potent and selective inhibitors targeting the two bromodomains are required to elucidate their biological role(s), with potential clinical applications. In this study, we designed and synthesized a series of benzimidazole-6-sulfonamides starting from the azobenzene compounds MS436 (7 a) and MS611 (7 b) that exhibited preference for the first (BD1) over the second (BD2) BRD of BET family members. The most-promising compound (9 a) showed good binding potency and improved metabolic stability and selectivity towards BD1 with respect to the parent compounds.
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Affiliation(s)
- Alessandra Cipriano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Ciro Milite
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Alessandra Feoli
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Monica Viviano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giacomo Pepe
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Pietro Campiglia
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giuliana Sarno
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Sarah Picaud
- Nuffield Department of MedicineOxford UniversityOX3 7DQOxfordUK
| | - Satomi Imaide
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Discovery Technology Research LaboratoriesOno Pharmaceutical Co., Ltd.618-8585OsakaJapan
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Oncology R&DTumour Targeted DeliveryAstraZenecaQMB Innovation Centre42 New RoadLondonE1 2AXUK
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK
| | - Sabrina Castellano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Gianluca Sbardella
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
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8
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Adnan M, Koli S, Mohammad T, Siddiqui AJ, Patel M, Alshammari N, Bardakci F, Elasbali AM, Hassan MI. Searching for Novel Anaplastic Lymphoma Kinase Inhibitors: Structure-Guided Screening of Natural Compounds for a Tyrosine Kinase Therapeutic Target in Cancers. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:461-470. [PMID: 35925819 DOI: 10.1089/omi.2022.0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase molecular target with broad importance for drug discovery, especially in the field of cancer therapeutics. ALK belongs to the insulin receptor superfamily that is involved in various malignancies, including non-small cell lung cancer, anaplastic large cell lymphoma, and neuroblastoma. ALK has been shown to play a role in cancer progression and metastasis, making it one of the prime targets to develop novel anticancer therapeutics. In this context, natural compounds can be an important resource to unravel novel ALK inhibitors. In this study, we report a structure-based virtual screening of natural compounds from the ZINC database, with an eye to potential inhibitors of ALK. Molecular docking was performed on a natural compound library, and top hits holding good binding affinity, docking score, and specificity toward ALK were selected. The hits were further evaluated based on the PAINS (pan-assay interference compounds) filter, ADMET (absorption, distribution, metabolism, excretion, toxicity) properties, PASS (prediction of activity spectra for substances) analysis, and two-dimensional interaction of protein-ligand complexes. Importantly, two natural compounds (ZINC03845566 and ZINC03999625) were identified as potential candidates for ALK, having appreciable affinity and specificity toward the ALK binding pocket and depicting drug-like properties as predicted from ADMET analysis and their physicochemical parameters. An all-atom molecular dynamics simulation for 100 ns on ALK promised stable ALK-ligand complexes. Hence, we conclude that ZINC03845566 and ZINC03999625 can act as potential ALK inhibitors against cancers where ALK plays a role, for example, in lung cancer, among others. All in all, these findings inform future discovery and translational research for ALK inhibitors as anticancer drugs.
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Affiliation(s)
- Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, Saudi Arabia
| | - Saadgee Koli
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, India
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | | | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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9
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Katz D, Fike K, Longenberger J, Placko S, Philippe-Venec L, Chervenak A. AlphaLogD determination: An optimized Reversed-Phase Liquid Chromatography method to measure lipophilicity on neutral and basic small and Beyond-Rule-of-Five compounds. J Chromatogr A 2022; 1674:463146. [DOI: 10.1016/j.chroma.2022.463146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/21/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
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10
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Attah AF, Akindele OO, Nnamani PO, Jonah UJ, Sonibare MA, Moody JO. Moringa oleifera Seed at the Interface of Food and Medicine: Effect of Extracts on Some Reproductive Parameters, Hepatic and Renal Histology. Front Pharmacol 2022; 13:816498. [PMID: 35350756 PMCID: PMC8958002 DOI: 10.3389/fphar.2022.816498] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
The lipid-rich Seed of Moringa oleifera has been promoted as an effective water clarifier. Aside its vital nutritional application as an emerging food additive, the seed has continued to gain a wider acceptance in various global ethnomedicines for managing several communicable and lifestyle diseases, howbeit, its potential toxic effect, particularly on fertility and pregnancy outcomes has remained uninvestigated; the effect of Moringa oleifera seed (MOSE) aqueous-methanol extracts on fertility and pregnancy outcome, was investigated in vivo using female Wistar rats that were divided into 50, 100, 300 and 500 mg per kilogram body weight. Group six was given Moringa oleifera seed treated water ad-libitum (ad-libitum group). Organs harvested for histological assessment included ovary, uterus, liver and kidney. In addition to HPLC fingerprint and a preliminary peptide detection, we determined the physico-chemical characteristics and mineral content of MOSE using standard methods. Data were analyzed with significance at p ≤ 0.05. There was no significant difference in the estrus cycle, mating index, gestation survival index, gestation index, fertility index and sex ratio among all groups. Gestation length was reduced in some groups. While the male pup birth weight was comparable among the different groups, female pups birth weights were significantly reduced in 50 and 100 mg groups. Anogenital distance indices of female pups in ad libitum group were significantly increased. Pathologies were observed in liver and kidneys of dams while kidneys of pups presented a dose dependent reduction in the number of glomeruli. There were no observed pathological changes in the ovary and uterus. This study showed for the first time in rodents, that the lipid-rich MOSE is unsafe to the kidney of rodents while the lipid-free MOSE appears to be safe at doses up to 300 mg/kg body weight. Findings from this study suggested that the female pups were masculinized. In conclusion, the lipid-rich seed extracts of MOSE appear to be unsafe during pregnancy, induce hepatic and renal toxicity while the lipid-free MOSE excludes inherent toxicity as the hydrophobic part has been linked to toxicity as observed in this study due to the developmental programming effect on female offspring in rodents.
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Affiliation(s)
- Alfred F Attah
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria.,Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin, Nigeria
| | - Opeyemi O Akindele
- Laboratory for Reproductive Physiology and Developmental Programming, Department of Physiology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Petra O Nnamani
- Drug Delivery and Nanomedicines Research Unit/Public Health and Environmental Sustainability (PHES) Research Group, Department of Pharmaceutics, University of Nigeria, Nsukka, Nigeria
| | | | - Mubo A Sonibare
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Jones O Moody
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
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11
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Ueda H, Hirakawa Y, Miyano T, Imono M, Tse JY, Uchiyama H, Tozuka Y, Kadota K. Design of a Stable Coamorphous System Using Lactose as an Antiplasticizing Agent for Diphenhydramine Hydrochloride with a Low Glass Transition Temperature. Mol Pharm 2022; 19:1209-1218. [PMID: 35316068 DOI: 10.1021/acs.molpharmaceut.2c00057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coamorphous systems comprising small molecules are emerging as counterparts to polymeric solid dispersions. However, the glass transition temperatures (Tgs) of coamorphous materials are relatively low because of the lack of polymeric carriers with higher Tgs. This study aimed to investigate the applicability of lactose (LAC) as an antiplasticizing coformer to a coamorphous system. Diphenhydramine hydrochloride (DPH) was selected as a model drug (Tg = 16 °C). Differential scanning calorimetry showed a comelting point in addition to a decrease in the neat melting points depending on the composition of the physical mixtures, suggesting that the mixture of DPH-LAC was eutectic. The melting point of the eutectic mixture was calculated according to the Schröder-van Laar equation. The heat of fusion of the eutectic mixture was maximized at a 70:30 molar ratio of DPH to LAC; at this point, the melting peaks of the pure components disappeared. The heat flow profiles following the melting and cooling of DPH-LAC physical mixtures at the ratios from 10:90 to 90:10 showed a single Tg, suggesting the formation of a coamorphous system. Lactose showed a Tg of over 100 °C, and the Tg of DPH increased with the molar ratio of LAC; it was 84 °C at a 10:90 molar ratio of DPH to LAC. The Raman image indicated the formation of a homogeneous dispersion of DPH and LAC in the coamorphous system. Peak shifts in the infrared spectra indicated the presence of intermolecular interactions between the amino group of DPH and the hydroxyl group of LAC. Principal component analysis of the infrared spectra revealed a significant change at the 70:30 molar ratio of DPH to LAC, which was in agreement with the results of the thermal analysis. A stability test at 40 °C revealed rapid crystallization of the supercooled liquid DPH. The coamorphous samples containing 10-50% of LAC remained in an amorphous state for 21 days, and no crystallization was observed for the samples containing >60% of LAC for 28 days. The relatively lower Tg (less than 40 °C) of the coamorphous system containing 10-50% of LAC might have caused crystallization during storage. These findings indicate that LAC, which is a safe and widely used pharmaceutical excipient, can be applied to coamorphous systems as an antiplasticizing coformer.
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Affiliation(s)
- Hiroshi Ueda
- Physical Chemistry, Laboratory for Medicinal Chemistry Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Yuya Hirakawa
- Chemical Modality 2, Laboratory for Advanced Medicine Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Tetsuya Miyano
- Physical Chemistry, Laboratory for Medicinal Chemistry Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Masaaki Imono
- Physical Chemistry, Laboratory for Medicinal Chemistry Research, Shionogi & Co., Ltd., Osaka 561-0825, Japan
| | - Jun Yee Tse
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Hiromasa Uchiyama
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Yuichi Tozuka
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Kazunori Kadota
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
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12
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Tanaka Y, Seto M, Kakegawa K, Takami K, Kikuchi F, Yamamoto T, Nakamura M, Daini M, Murakami M, Ohashi T, Kasahara T, Wang J, Ikeda Z, Wada Y, Puenner F, Fujii T, Inazuka M, Sato S, Suzaki T, Oak JH, Takai Y, Kohara H, Kimoto K, Oki H, Mikami S, Sasaki M, Tanaka Y. Discovery of Brain-Penetrant Glucosylceramide Synthase Inhibitors with a Novel Pharmacophore. J Med Chem 2022; 65:4270-4290. [PMID: 35188773 DOI: 10.1021/acs.jmedchem.1c02078] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Inhibition of glucosylceramide synthase (GCS) is a major therapeutic strategy for Gaucher's disease and has been suggested as a potential target for treating Parkinson's disease. Herein, we report the discovery of novel brain-penetrant GCS inhibitors. Assessment of the structure-activity relationship revealed a unique pharmacophore in this series. The lipophilic ortho-substituent of aromatic ring A and the appropriate directionality of aromatic ring B were key for potency. Optimization of the absorption, distribution, metabolism, elimination, toxicity (ADMETox) profile resulted in the discovery of T-036, a potent GCS inhibitor in vivo. Pharmacophore-based scaffold hopping was performed to mitigate safety concerns associated with T-036. The ring opening of T-036 resulted in another potent GCS inhibitor with a lower toxicological risk, T-690, which reduced glucosylceramide in a dose-dependent manner in the plasma and cortex of mice. Finally, we discuss the structural aspects of the compounds that impart a unique inhibition mode and lower the cardiovascular risk.
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Affiliation(s)
- Yuta Tanaka
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaki Seto
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Keiko Kakegawa
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazuaki Takami
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Fumiaki Kikuchi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takeshi Yamamoto
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Minoru Nakamura
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masaki Daini
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masataka Murakami
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomohiro Ohashi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takahito Kasahara
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Junsi Wang
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Zenichi Ikeda
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasufumi Wada
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Florian Puenner
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Takahiro Fujii
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masakazu Inazuka
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Sho Sato
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomohiko Suzaki
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jeong-Ho Oak
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuichi Takai
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hiroshi Kohara
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kouya Kimoto
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Oki
- Axcelead Drug Discovery Partners, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Mikami
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Minoru Sasaki
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuta Tanaka
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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13
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Luxenburger A, Ure EM, Harris L, Cameron SA, Weymouth-Wilson A, Furneaux RH, Pitman J, Hinkley SF. The Synthesis of 12β-Methyl-18-nor-Avicholic Acid Analogues as Potential TGR5 Agonists†. Org Biomol Chem 2022; 20:3511-3527. [DOI: 10.1039/d1ob02401a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quest for new modulators of the Farnesoid-X (FXR) and Takeda G-protein-coupled (TGR5) receptors, bile acids are a popular candidate for drug development. Recently, bile acids endowed with a...
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14
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Kralj S, Jukič M, Bren U. Commercial SARS-CoV-2 Targeted, Protease Inhibitor Focused and Protein-Protein Interaction Inhibitor Focused Molecular Libraries for Virtual Screening and Drug Design. Int J Mol Sci 2021; 23:393. [PMID: 35008818 PMCID: PMC8745317 DOI: 10.3390/ijms23010393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
Since December 2019, the new SARS-CoV-2-related COVID-19 disease has caused a global pandemic and shut down the public life worldwide. Several proteins have emerged as potential therapeutic targets for drug development, and we sought out to review the commercially available and marketed SARS-CoV-2-targeted libraries ready for high-throughput virtual screening (HTVS). We evaluated the SARS-CoV-2-targeted, protease-inhibitor-focused and protein-protein-interaction-inhibitor-focused libraries to gain a better understanding of how these libraries were designed. The most common were ligand- and structure-based approaches, along with various filtering steps, using molecular descriptors. Often, these methods were combined to obtain the final library. We recognized the abundance of targeted libraries offered and complimented by the inclusion of analytical data; however, serious concerns had to be raised. Namely, vendors lack the information on the library design and the references to the primary literature. Few references to active compounds were also provided when using the ligand-based design and usually only protein classes or a general panel of targets were listed, along with a general reference to the methods, such as molecular docking for the structure-based design. No receptor data, docking protocols or even references to the applied molecular docking software (or other HTVS software), and no pharmacophore or filter design details were given. No detailed functional group or chemical space analyses were reported, and no specific orientation of the libraries toward the design of covalent or noncovalent inhibitors could be observed. All libraries contained pan-assay interference compounds (PAINS), rapid elimination of swill compounds (REOS) and aggregators, as well as focused on the drug-like model, with the majority of compounds possessing their molecular mass around 500 g/mol. These facts do not bode well for the use of the reviewed libraries in drug design and lend themselves to commercial drug companies to focus on and improve.
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Affiliation(s)
- Sebastjan Kralj
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (S.K.); (M.J.)
| | - Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (S.K.); (M.J.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (S.K.); (M.J.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
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15
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A probable means to an end: exploring P131 pharmacophoric scaffold to identify potential inhibitors of Cryptosporidium parvum inosine monophosphate dehydrogenase. J Mol Model 2021; 27:35. [PMID: 33423140 DOI: 10.1007/s00894-020-04663-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were identified and subsequently adopted to create a pharmacophore model for virtual screening in the ZINC database. This search generated eight ADMET-compliant hits that were examined thoroughly to fit into the active site of CpIMPDH via molecular docking. Three compounds ZINC46542062, ZINC58646829, and ZINC89780094, with favorable docking scores of - 8.3 kcal/mol, - 8.2 kcal/mol, and - 7.5 kcal/mol, were selected. The potential inhibitory mechanism of these compounds was probed using molecular dynamics simulation and Molecular Mechanics Generalized Poisson Boltzmann Surface Area (MM/PBSA) analyses. Results revealed that one of the hits (ZINC46542062) exhibited a lower binding free energy of - 39.52 kcal/mol than P131, which had - 34.6 kcal/mol. Conformational perturbation induced by the binding of the identified hits to CpIMPDH was similar to P131, suggesting a similarity in inhibitory mechanisms. Also, in silico investigation of the properties of the hit compounds implied superior physicochemical properties with regards to their synthetic accessibility, lipophilicity, and number of hydrogen bond donors and acceptors in comparison with P131. ZINC46542062 was identified as a promising hit compound with the highest binding affinity to the target protein and favorable physicochemical and pharmacokinetic properties relative to P131. The identified compounds can serve as a basis for conducting further experimental investigations toward the development of anticryptosporidials, which can overcome the challenges of existing therapeutic options. Graphical abstract P131 and the identified compounds docked in the NAD+ binding site of Cryptosporidium parvum IMPDH.
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16
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Saravanakumar A, Sadighi A, Ryu R, Akhlaghi F. Physicochemical Properties, Biotransformation, and Transport Pathways of Established and Newly Approved Medications: A Systematic Review of the Top 200 Most Prescribed Drugs vs. the FDA-Approved Drugs Between 2005 and 2016. Clin Pharmacokinet 2020; 58:1281-1294. [PMID: 30972694 DOI: 10.1007/s40262-019-00750-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Enzyme-mediated biotransformation of pharmacological agents is a crucial step in xenobiotic detoxification and drug disposition. Herein, we investigated the metabolism and physicochemical properties of the top 200 most prescribed drugs (established) as well as drugs approved by the US Food and Drug Administration (FDA) between 2005 and 2016 (newly approved). OBJECTIVE Our objective was to capture the changing trends in the routes of administration, physicochemical properties, and prodrug medications, as well as the contributions of drug-metabolizing enzymes and transporters to drug clearance. METHODS The University of Washington Drug Interaction Database (DIDB®) as well as other online resources (e.g., CenterWatch.com, Drugs.com, DrugBank.ca, and PubChem.ncbi.nlm.nih.gov) was used to collect and stratify the dataset required for exploring the above-mentioned trends. RESULTS Analyses revealed that ~ 90% of all drugs in the established and newly approved drug lists were administered systemically (oral or intravenous). Meanwhile, the portion of biologics (molecular weight > 1 kDa) was 15 times greater in the newly approved list than established drugs. Additionally, there was a 4.5-fold increase in the number of compounds with a high calculated partition coefficient (cLogP > 3) and a high total polar surface area (> 75 Å2) in the newly approved drug vs. the established category. Further, prodrugs in established or newly approved lists were found to be converted to active compounds via hydrolysis, demethylases, and kinases. The contribution of cytochrome P450 (CYP) 3A4, as the major biotransformation pathway, has increased from 40% in the established drug list to 64% in the newly approved drug list. Moreover, the role of CYP1A2, CYP2C19, and CYP2D6 were decreased as major metabolizing enzymes among the newly approved medications. Among non-CYP major metabolizers, the contribution of alcohol dehydrogenases/aldehyde dehydrogenases (ADH/ALDH) and sulfotransferases decreased in the newly approved drugs compared with the established list. Furthermore, the highest contribution among uptake and efflux transporters was found for Organic Anion Transporting Polypeptide 1B1 (OATP1B1) and P-glycoprotein (P-gp), respectively. CONCLUSIONS The higher portion of biologics in the newly approved drugs compared with the established list confirmed the growing demands for protein- and antibody-based therapies. Moreover, the larger number of hydrophilic drugs found in the newly approved list suggests that the probability of toxicity is likely to decrease. With regard to CYP-mediated major metabolism, CYP3A5 showed an increased involvement owing to the identification of unique probe substrates to differentiate CYP3As. Furthermore, the contribution of OATP1B1 and P-gp did not show a significant shift in the newly approved drugs as compared to the established list because of their broad substrate specificity.
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Affiliation(s)
- Anitha Saravanakumar
- Clinical Pharmacokinetics Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Office 495 A, 7 Greenhouse Road, Kingston, RI, 02881, USA
| | - Armin Sadighi
- Clinical Pharmacokinetics Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Office 495 A, 7 Greenhouse Road, Kingston, RI, 02881, USA
| | - Rachel Ryu
- Clinical Pharmacokinetics Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Office 495 A, 7 Greenhouse Road, Kingston, RI, 02881, USA
| | - Fatemeh Akhlaghi
- Clinical Pharmacokinetics Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Office 495 A, 7 Greenhouse Road, Kingston, RI, 02881, USA.
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17
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Norman BH. Drug Induced Liver Injury (DILI). Mechanisms and Medicinal Chemistry Avoidance/Mitigation Strategies. J Med Chem 2020; 63:11397-11419. [PMID: 32511920 DOI: 10.1021/acs.jmedchem.0c00524] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Adverse drug reactions (ADRs) are a common cause of attrition in drug discovery and development and drug-induced liver injury (DILI) is a leading cause of preclinical and clinical drug terminations. This perspective outlines many of the known DILI mechanisms and assessment methods used to evaluate and mitigate DILI risk. Literature assessments and retrospective analyses using verified DILI-associated drugs from the Liver Tox Knowledge Base (LTKB) have been used to derive the predictive value of each end point, along with combination approaches of multiple methods. In vitro assays to assess inhibition of the bile salt export pump (BSEP), mitotoxicity, reactive metabolite (RM) formation, and hepatocyte cytolethality, along with physicochemical properties and clinical dose provide useful DILI predictivity. This Perspective also highlights some of the strategies used by medicinal chemists to reduce DILI risk during the optimization of drug candidates.
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Affiliation(s)
- Bryan H Norman
- Norman Drug Discovery Training and Consulting, LLC, 8540 Bluefin Circle, Indianapolis, Indiana 46236, United States
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18
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Rana P, Kogut S, Wen X, Akhlaghi F, Aleo MD. Most Influential Physicochemical and In Vitro Assay Descriptors for Hepatotoxicity and Nephrotoxicity Prediction. Chem Res Toxicol 2020; 33:1780-1790. [PMID: 32338883 DOI: 10.1021/acs.chemrestox.0c00040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Drug-induced organ injury is a major reason for drug candidate attrition in preclinical and clinical drug development. The liver, kidneys, and heart have been recognized as the most common organ systems affected in safety-related attrition or the subject of black box warnings and postmarket drug withdrawals. In silico physicochemical property calculations and in vitro assays have been utilized separately in the early stages of the drug discovery and development process to predict drug safety. In this study, we combined physicochemical properties and in vitro cytotoxicity assays including mitochondrial dysfunction to build organ-specific univariate and multivariable logistic regression models to achieve odds ratios for the prediction of clinical hepatotoxicity, nephrotoxicity, and cardiotoxicity using 215 marketed drugs. The multivariable hepatotoxic predictive model showed an odds ratio of 6.2 (95% confidence interval (CI) 1.7-22.8) or 7.5 (95% CI 3.2-17.8) for mitochondrial inhibition or drug plasma Cmax >1 μM for drugs associated with liver injury, respectively. The multivariable nephrotoxicity predictive model showed an odds ratio of 5.8 (95% CI 2.0-16.9), 6.4 (95% CI 1.1-39.3), or 15.9 (95% CI 2.8-89.0) for drug plasma Cmax >1 μM, mitochondrial inhibition, or hydrogen-bond-acceptor atoms >7 for drugs associated with kidney injury, respectively. Conversely, drugs with a total polar surface area ≥75 Å were 79% (odds ratio 0.21, 95% CI 0.061-0.74) less likely to be associated with kidney injury. Drugs belonging to the extended clearance classification system (ECCS) class 4, where renal secretion is the primary clearance mechanism (low permeability drugs that are bases/neutrals), were 4 (95% CI 1.8-9.5) times more likely to to be associated with kidney injury with this data set. Alternatively, ECCS class 2 drugs, where hepatic metabolism is the primary clearance (high permeability drugs that are bases/neutrals) were 77% less likely (odds ratio 0.23 95% CI 0.095-0.54) to to be associated with kidney injury. A cardiotoxicity model was poorly defined using any of these drug physicochemical attributes. Combining in silico physicochemical properties descriptors along with in vitro toxicity assays can be used to build predictive toxicity models to select small molecule therapeutics with less potential to cause liver and kidney organ toxicity.
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Affiliation(s)
- Payal Rana
- Drug Safety Research and Development, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Stephen Kogut
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Xuerong Wen
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Fatemeh Akhlaghi
- College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Michael D Aleo
- Drug Safety Research and Development, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
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19
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Yukawa T, Naven R. Utility of Physicochemical Properties for the Prediction of Toxicological Outcomes: Takeda Perspective. ACS Med Chem Lett 2020; 11:203-209. [PMID: 32071689 DOI: 10.1021/acsmedchemlett.9b00536] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2020] [Indexed: 01/17/2023] Open
Abstract
The role that physicochemical properties play toward increasing the likelihood of toxicity findings in in vivo studies has been well reported, albeit sometimes with different conclusions. We decided to understand the role that physicochemical properties play toward the prediction of in vivo toxicological outcomes for Takeda chemistry using 284 internal compounds. In support of the previously reported "3/75 rule", reducing lipophilicity of molecules decreases toxicity odds noticeably; however, we also found that the trend of toxicity odds is different between compounds classified by their ionization state. For basic molecules, the odds of in vivo toxicity outcomes were significantly impacted by both lipophilicity and polar surface area, whereas neutral molecules were impacted less so. Through an analysis of several project-related compounds, we herein demonstrate that the utilization of the 3/75 rule coupled with consideration of ionization state is a rational strategy for medicinal chemistry design of safer drugs.
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Affiliation(s)
- Tomoya Yukawa
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Russell Naven
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
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20
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Brown DG, Smith GF, Wobst HJ. Promiscuity of in Vitro Secondary Pharmacology Assays and Implications for Lead Optimization Strategies. J Med Chem 2019; 63:6251-6275. [PMID: 31714773 DOI: 10.1021/acs.jmedchem.9b01625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We conducted an analysis on screening data generated from 1445 compounds against a panel of 130 enzymes, ion channels, and receptors to assess secondary pharmacological risks. Hit rates of these targets as well as physicochemical properties for those hits were evaluated. A majority of targets yielded hits with higher clogP, molecular weight, and more basic character than inactive compounds. Although most targets favored lipophilic hits, the average clogP of hits at a given target did not correlate with its hit rate. Furthermore, a matched pair analysis was completed to determine structural changes that impacted off-target activities. A correlation of binding assays used in this analysis illustrated that some pharmacologically related binding assays are highly correlative and may be substituted for a smaller set of surrogate assays.
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Affiliation(s)
- Dean G Brown
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Graham F Smith
- Data Science and Artificial Intelligence, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Heike J Wobst
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
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21
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Tadano G, Komano K, Yoshida S, Suzuki S, Nakahara K, Fuchino K, Fujimoto K, Matsuoka E, Yamamoto T, Asada N, Ito H, Sakaguchi G, Kanegawa N, Kido Y, Ando S, Fukushima T, Teisman A, Urmaliya V, Dhuyvetter D, Borghys H, Van Den Bergh A, Austin N, Gijsen HJM, Yamano Y, Iso Y, Kusakabe KI. Discovery of an Extremely Potent Thiazine-Based β-Secretase Inhibitor with Reduced Cardiovascular and Liver Toxicity at a Low Projected Human Dose. J Med Chem 2019; 62:9331-9337. [DOI: 10.1021/acs.jmedchem.9b01140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Aleo MD, Shah F, Allen S, Barton HA, Costales C, Lazzaro S, Leung L, Nilson A, Obach RS, Rodrigues AD, Will Y. Moving beyond Binary Predictions of Human Drug-Induced Liver Injury (DILI) toward Contrasting Relative Risk Potential. Chem Res Toxicol 2019; 33:223-238. [DOI: 10.1021/acs.chemrestox.9b00262] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Scott Allen
- Drug Safety Research and Development, Investigative Toxicology, Pfizer Worldwide Research & Development, One Burtt Road, Andover, Massachusetts 01810, United States
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23
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Exploring the Chemical Space of Cytochrome P450 Inhibitors Using Integrated Physicochemical Parameters, Drug Efficiency Metrics and Decision Tree Models. COMPUTATION 2019. [DOI: 10.3390/computation7020026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The cytochrome P450s (CYPs) play a central role in the metabolism of various endogenous and exogenous compounds including drugs. CYPs are vulnerable to inhibition and induction which can lead to adverse drug reactions. Therefore, insights into the underlying mechanism of CYP450 inhibition and the estimation of overall CYP inhibitor properties might serve as valuable tools during the early phases of drug discovery. Herein, we present a large data set of inhibitors against five major metabolic CYPs (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) for the evaluation of important physicochemical properties and ligand efficiency metrics to define property trends across various activity levels (active, efficient and inactive). Decision tree models for CYP inhibition were developed with an accuracy >90% for both the training set and 10-folds cross validation. Overall, molecular weight (MW), hydrogen bond acceptors/donors (HBA/HBD) and lipophilicity (clogP/logPo/w) represent important physicochemical descriptors for CYP450 inhibitors. However, highly efficient CYP inhibitors show mean MW, HBA, HBD and logP values between 294.18–482.40,5.0–8.2,1–7.29 and 1.68–2.57, respectively. Our results might help in optimization of toxicological profiles associated with new chemical entities (NCEs), through a better understanding of inhibitor properties leading to CYP-mediated interactions.
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24
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Analysis of solvent-exposed and buried co-crystallized ligands: a case study to support the design of novel protein–protein interaction inhibitors. Drug Discov Today 2019; 24:551-559. [DOI: 10.1016/j.drudis.2018.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/03/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
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25
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Furtado D, Björnmalm M, Ayton S, Bush AI, Kempe K, Caruso F. Overcoming the Blood-Brain Barrier: The Role of Nanomaterials in Treating Neurological Diseases. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1801362. [PMID: 30066406 DOI: 10.1002/adma.201801362] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/09/2018] [Indexed: 05/24/2023]
Abstract
Therapies directed toward the central nervous system remain difficult to translate into improved clinical outcomes. This is largely due to the blood-brain barrier (BBB), arguably the most tightly regulated interface in the human body, which routinely excludes most therapeutics. Advances in the engineering of nanomaterials and their application in biomedicine (i.e., nanomedicine) are enabling new strategies that have the potential to help improve our understanding and treatment of neurological diseases. Herein, the various mechanisms by which therapeutics can be delivered to the brain are examined and key challenges facing translation of this research from benchtop to bedside are highlighted. Following a contextual overview of the BBB anatomy and physiology in both healthy and diseased states, relevant therapeutic strategies for bypassing and crossing the BBB are discussed. The focus here is especially on nanomaterial-based drug delivery systems and the potential of these to overcome the biological challenges imposed by the BBB. Finally, disease-targeting strategies and clearance mechanisms are explored. The objective is to provide the diverse range of researchers active in the field (e.g., material scientists, chemists, engineers, neuroscientists, and clinicians) with an easily accessible guide to the key opportunities and challenges currently facing the nanomaterial-mediated treatment of neurological diseases.
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Affiliation(s)
- Denzil Furtado
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Mattias Björnmalm
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Department of Materials, Department of Bioengineering, and the Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Scott Ayton
- Melbourne Dementia Research Centre, The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Ashley I Bush
- Melbourne Dementia Research Centre, The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, 3052, Australia
- Cooperative Research Center for Mental Health, Parkville, Victoria, 3052, Australia
| | - Kristian Kempe
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
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26
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Affiliation(s)
| | - Kevin Beaumont
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Tristan S. Maurer
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
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27
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Nicolas CI, Mansouri K, Phillips KA, Grulke CM, Richard AM, Williams AJ, Rabinowitz J, Isaacs KK, Yau A, Wambaugh JF. Rapid experimental measurements of physicochemical properties to inform models and testing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 636:901-909. [PMID: 29729507 PMCID: PMC6214190 DOI: 10.1016/j.scitotenv.2018.04.266] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 04/14/2023]
Abstract
The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(Kow) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(Kow) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data.
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Affiliation(s)
- Chantel I Nicolas
- ScitoVation, LLC 6 Davis Drive, Durham, NC 27703, USA; National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Kamel Mansouri
- ScitoVation, LLC 6 Davis Drive, Durham, NC 27703, USA; National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
| | - Katherine A Phillips
- National Exposure Research Laboratory, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA
| | - Christopher M Grulke
- National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA
| | - Ann M Richard
- National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA
| | - Antony J Williams
- National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA
| | - James Rabinowitz
- National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA
| | - Kristin K Isaacs
- National Exposure Research Laboratory, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA
| | - Alice Yau
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - John F Wambaugh
- National Center for Computational Toxicology, Office of Research and Development, US EPA, Research Triangle Park, NC 27711, USA.
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28
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He C, Wan H. Drug metabolism and metabolite safety assessment in drug discovery and development. Expert Opin Drug Metab Toxicol 2018; 14:1071-1085. [DOI: 10.1080/17425255.2018.1519546] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Chunyong He
- Department of DMPK/Tox, Shanghai Hengrui Pharmaceutical Co., Ltd., Shanghai, P. R. China
| | - Hong Wan
- Department of DMPK/Tox, Shanghai Hengrui Pharmaceutical Co., Ltd., Shanghai, P. R. China
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29
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Diastereoselective synthesis of fused cyclopropyl-3-amino-2,4-oxazine β-amyloid cleaving enzyme (BACE) inhibitors and their biological evaluation. Bioorg Med Chem Lett 2018; 28:1111-1115. [DOI: 10.1016/j.bmcl.2018.01.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 11/19/2022]
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30
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Shi J, Gu Z, Jurica EA, Wu X, Haque LE, Williams KN, Hernandez AS, Hong Z, Gao Q, Dabros M, Davulcu AH, Mathur A, Rampulla RA, Gupta AK, Jayaram R, Apedo A, Moore DB, Liu H, Kunselman LK, Brady EJ, Wilkes JJ, Zinker BA, Cai H, Shu YZ, Sun Q, Dierks EA, Foster KA, Xu C, Wang T, Panemangalore R, Cvijic ME, Xie C, Cao GG, Zhou M, Krupinski J, Whaley JM, Robl JA, Ewing WR, Ellsworth BA. Discovery of Potent and Orally Bioavailable Dihydropyrazole GPR40 Agonists. J Med Chem 2018; 61:681-694. [DOI: 10.1021/acs.jmedchem.7b00982] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Jun Shi
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Zhengxiang Gu
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Elizabeth Anne Jurica
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Ximao Wu
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Lauren E. Haque
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Kristin N. Williams
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Andres S. Hernandez
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Zhenqiu Hong
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Qi Gao
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Marta Dabros
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Akin H. Davulcu
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Arvind Mathur
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Richard A. Rampulla
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Arun Kumar Gupta
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Ramya Jayaram
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Atsu Apedo
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Douglas B. Moore
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Heng Liu
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Lori K. Kunselman
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Edward J. Brady
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Jason J. Wilkes
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Bradley A. Zinker
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Hong Cai
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Yue-Zhong Shu
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Qin Sun
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Elizabeth A. Dierks
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Kimberly A. Foster
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Carrie Xu
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Tao Wang
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Reshma Panemangalore
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Mary Ellen Cvijic
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Chunshan Xie
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Gary G. Cao
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Min Zhou
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - John Krupinski
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Jean M. Whaley
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Jeffrey A. Robl
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - William R. Ewing
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
| | - Bruce Alan Ellsworth
- Research and Development, Bristol-Myers Squibb Co., P.O. Box 4000, Princeton, New Jersey 08540-4000, United States
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31
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Abstract
The term drug design describes the search of novel compounds with biological activity, on a systematic basis. In its most common form, it involves modification of a known active scaffold or linking known active scaffolds, although de novo drug design (i.e., from scratch) is also possible. Though highly interrelated, identification of active scaffolds should be conceptually separated from drug design. Traditionally, the drug design process has focused on the molecular determinants of the interactions between the drug and its known or intended molecular target. Nevertheless, current drug design also takes into consideration other relevant processes than influence drug efficacy and safety (e.g., bioavailability, metabolic stability, interaction with antitargets).This chapter provides an overview on possible approaches to identify active scaffolds (including in silico approximations to approach that task) and computational methods to guide the subsequent optimization process. It also discusses in which situations each of the overviewed techniques is more appropriate.
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Affiliation(s)
- Alan Talevi
- Laboratorio de Investigación y Desarrollo de Bioactivos (LIDeB), Faculty of Exact Sciences, National University of La Plata (UNLP), Buenos Aires, Argentina.
- Argentinean National Council of Scientific and Technical Research (CONICET), Buenos Aires, Argentina.
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32
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Hevener KE. Computational Toxicology Methods in Chemical Library Design and High-Throughput Screening Hit Validation. Methods Mol Biol 2018; 1800:275-285. [PMID: 29934898 DOI: 10.1007/978-1-4939-7899-1_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery of molecular toxicity in a clinical drug candidate can have a significant impact on both the cost and timeline of the drug discovery process. Early identification of potentially toxic compounds during screening library preparation or, alternatively, during the hit validation process, is critical to ensure that valuable time and resources are not spent pursuing compounds that may possess a high propensity for human toxicity. This chapter focuses on the application of computational molecular filters, applied either prescreening or postscreening, to identify and remove known reactive and/or potentially toxic compounds from consideration in drug discovery campaigns.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA.
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33
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Rodrigues DA, Pinheiro PDSM, Ferreira TTDSC, Thota S, Fraga CAM. Structural basis for the agonist action at free fatty acid receptor 1 (FFA1R or GPR40). Chem Biol Drug Des 2017; 91:668-680. [DOI: 10.1111/cbdd.13131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/02/2017] [Accepted: 10/14/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
- Programa de Pós-Graduação em Química; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal; Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
| | - Thayssa Tavares da Silva Cunha Ferreira
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal; Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
| | - Sreekanth Thota
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN); Center for Technological Development in Health (CDTS); Fundação Oswaldo Cruz - Ministério da Saúde; Rio de Janeiro RJ Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
- Programa de Pós-Graduação em Química; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal; Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
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34
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Croaker A, King GJ, Pyne JH, Anoopkumar-Dukie S, Simanek V, Liu L. Carcinogenic potential of sanguinarine, a phytochemical used in 'therapeutic' black salve and mouthwash. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 774:46-56. [PMID: 29173498 DOI: 10.1016/j.mrrev.2017.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/17/2017] [Accepted: 09/02/2017] [Indexed: 02/07/2023]
Abstract
Black salves are escharotic skin cancer therapies in clinical use since the mid 19th century. Sanguinaria canadensis, a major ingredient of black salve formulations, contains a number of bioactive phytochemicals including the alkaloid sanguinarine. Despite its prolonged history of clinical use, conflicting experimental results have prevented the carcinogenic potential of sanguinarine from being definitively determined. Sanguinarine has a molecular structure similar to known polyaromatic hydrocarbon carcinogens and is a DNA intercalator. Sanguinarine also generates oxidative and endoplasmic reticulum stress resulting in the unfolded protein response and the formation of 8-hydroxyguanine genetic lesions. Sanguinarine has been the subject of contradictory in vitro and in vivo genotoxicity and murine carcinogenesis test results that have delayed its carcinogenic classification. Despite this, epidemiological studies have linked mouthwash that contains sanguinarine with the development of oral leukoplakia. Sanguinarine is also proposed as an aetiological agent in gallbladder carcinoma. This literature review investigates the carcinogenic potential of sanguinarine. Reasons for contradictory genotoxicity and carcinogenesis results are explored, knowledge gaps identified and a strategy for determining the carcinogenic potential of sanguinarine especialy relating to black salve are discussed. As patients continue to apply black salve, especially to skin regions suffering from field cancerization and skin malignancies, an understanding of the genotoxic and carcinogenic potential of sanguinarine is of urgent clinical relevance.
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Affiliation(s)
- Andrew Croaker
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia; Wesley Medical Research Institute, Wesley Hospital, Auchenflower, QLD, Australia; Quality Use of Medicines Network, Queensland, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - John H Pyne
- School of Medicine, University of Queensland, St Lucia, QLD, Australia
| | - Shailendra Anoopkumar-Dukie
- Quality Use of Medicines Network, Queensland, Australia; School of Pharmacy and Pharmacology, Griffith University, Gold Coast Campus, Gold Coast, QLD, Australia
| | - Vilim Simanek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.
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35
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Sebastián-Pérez V, Roca C, Awale M, Reymond JL, Martinez A, Gil C, Campillo NE. Medicinal and Biological Chemistry (MBC) Library: An Efficient Source of New Hits. J Chem Inf Model 2017; 57:2143-2151. [PMID: 28813151 DOI: 10.1021/acs.jcim.7b00401] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identification of new hits is one of the biggest challenges in drug discovery. Creating a library of well-characterized drug-like compounds is a key step in this process. Our group has developed an in-house chemical library called the Medicinal and Biological Chemistry (MBC) library. This collection has been successfully used to start several medicinal chemistry programs and developed in an accumulation of more than 30 years of experience in drug design and discovery of new drugs for unmet diseases. It contains over 1000 compounds, mainly heterocyclic scaffolds. In this work, analysis of drug-like properties and comparative study with well-known libraries by using different computer software are presented here.
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Affiliation(s)
- Víctor Sebastián-Pérez
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carlos Roca
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
| | - Ana Martinez
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carmen Gil
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Nuria E Campillo
- Centro de Investigaciones Biológicas (CIB, CSIC) , Ramiro de Maeztu 9, 28040 Madrid, Spain
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Low JD, Bartberger MD, Chen K, Cheng Y, Fielden MR, Gore V, Hickman D, Liu Q, Allen Sickmier E, Vargas HM, Werner J, White RD, Whittington DA, Wood S, Minatti AE. Development of 2-aminooxazoline 3-azaxanthene β-amyloid cleaving enzyme (BACE) inhibitors with improved selectivity against Cathepsin D. MEDCHEMCOMM 2017; 8:1196-1206. [PMID: 30108829 PMCID: PMC6072065 DOI: 10.1039/c7md00106a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/20/2017] [Indexed: 12/20/2022]
Abstract
As part of an ongoing effort at Amgen to develop a disease-modifying therapy for Alzheimer's disease, we have previously used the aminooxazoline xanthene (AOX) scaffold to generate potent and orally efficacious BACE1 inhibitors. While AOX-BACE1 inhibitors demonstrated acceptable cardiovascular safety margins, a retinal pathological finding in rat toxicological studies demanded further investigation. It has been widely postulated that such retinal toxicity might be related to off-target inhibition of Cathepsin D (CatD), a closely related aspartyl protease. We report the development of AOX-BACE1 inhibitors with improved selectivity against CatD by following a structure- and property-based approach. Our efforts culminated in the discovery of a picolinamide-substituted 3-aza-AOX-BACE1 inhibitor absent of retinal effects in an early screening rat toxicology study.
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Affiliation(s)
- Jonathan D Low
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - Michael D Bartberger
- Department of Molecular Engineering , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Kui Chen
- Department Discovery Technologies , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Yuan Cheng
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - Mark R Fielden
- Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Vijay Gore
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - Dean Hickman
- Department of Pharmacokinetics and Drug Metabolism , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Qingyian Liu
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
| | - E Allen Sickmier
- Department of Molecular Engineering , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA
| | - Hugo M Vargas
- Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Jonathan Werner
- Comparative Biology and Safety Sciences , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Ryan D White
- Department of Medicinal Chemistry , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA
| | - Douglas A Whittington
- Department of Molecular Engineering , Amgen Inc. , 360 Binney Street , Cambridge , MA 02142 , USA
| | - Stephen Wood
- Department of Neuroscience , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA
| | - Ana E Minatti
- Department of Medicinal Chemistry , Amgen Inc. , One Amgen Center Drive , Thousand Oaks , CA 91320 , USA . ; Tel: +1 805 447 4721
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Wenlock MC. Designing safer oral drugs. MEDCHEMCOMM 2017; 8:571-577. [PMID: 30108773 PMCID: PMC6072361 DOI: 10.1039/c6md00706f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/16/2017] [Indexed: 09/29/2023]
Abstract
Designing an oral drug such that its estimated dose to humans is both efficacious and safe is challenging. During the early design stage, where in vitro or preclinical species in vivo safety data are limited, heuristic-based criteria often related to physicochemical properties are used for guidance. The causal relationship between a compound's log P and its human in vivo toxicity is considered. With respect to designing efficacious oral drugs that potentially have reduced toxicity liabilities, an alternative heuristic-based criterion is proposed based on the amount of compound in the body at steady state. In humans, a threshold for the amount of compound in the body at steady state of 0.5 mg kg-1 is suggested. The criterion is based on the minimum toxic blood-plasma concentration that produces clinically relevant side effects or symptoms in humans for 242 oral drugs. It can be used to estimate a therapeutic window against which a compound's estimated in vivo plasma levels for a particular dose size and frequency can be assessed. The relationship between this criterion and acceptable oral dose sizes for different charge types with different in vivo plasma clearances is discussed.
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Affiliation(s)
- M C Wenlock
- InSilicoLynx Ltd , BioHub at Alderley Park , Mereside, Alderley Park , Cheshire , SK10 4TG , UK .
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38
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Ford KA. Refinement, Reduction, and Replacement of Animal Toxicity Tests by Computational Methods. ILAR J 2017; 57:226-233. [DOI: 10.1093/ilar/ilw031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/12/2016] [Indexed: 12/16/2022] Open
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Hett EC, Kyne RE, Gopalsamy A, Tones MA, Xu H, Thio GL, Nolan E, Jones LH. Selectivity Determination of a Small Molecule Chemical Probe Using Protein Microarray and Affinity Capture Techniques. ACS COMBINATORIAL SCIENCE 2016; 18:611-615. [PMID: 27494431 DOI: 10.1021/acscombsci.6b00089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small molecule selectivity is an essential component of candidate drug selection and target validation. New technologies are required to better understand off-target effects, with particular emphasis needed on broad protein profiling. Here, we describe the use of a tritiated chemical probe and a 9000 human protein microarray to discern the binding selectivity of an inhibitor of the mRNA decapping scavenger enzyme DcpS. An immobilized m7GTP resin was also used to assess the selectivity of a DcpS inhibitor against mRNA cap-associated proteins in whole cell extracts. These studies confirm the exquisite selectivity of diaminoquinazoline DcpS inhibitors, and highlight the utility of relatively simple protein microarray and affinity enrichment technologies in drug discovery and chemical biology.
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Affiliation(s)
- Erik C. Hett
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Robert E. Kyne
- Medicine
Design, Pfizer, East Point Road, Groton, Connecticut 06340, United States
| | - Ariamala Gopalsamy
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Michael A. Tones
- Rare
Disease Research Unit, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Hua Xu
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Guene L. Thio
- Protein
and Cell Analysis, Life Sciences Solutions, Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, California 92008, United States
| | - Edward Nolan
- Protein
and Cell Analysis, Life Sciences Solutions, Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, California 92008, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
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Kell DB, Pretorius E. On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr Biol (Camb) 2016; 7:1339-77. [PMID: 26345428 DOI: 10.1039/c5ib00158g] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have recently highlighted (and added to) the considerable evidence that blood can contain dormant bacteria. By definition, such bacteria may be resuscitated (and thus proliferate). This may occur under conditions that lead to or exacerbate chronic, inflammatory diseases that are normally considered to lack a microbial component. Bacterial cell wall components, such as the endotoxin lipopolysaccharide (LPS) of Gram-negative strains, are well known as potent inflammatory agents, but should normally be cleared. Thus, their continuing production and replenishment from dormant bacterial reservoirs provides an easy explanation for the continuing, low-grade inflammation (and inflammatory cytokine production) that is characteristic of many such diseases. Although experimental conditions and determinants have varied considerably between investigators, we summarise the evidence that in a great many circumstances LPS can play a central role in all of these processes, including in particular cell death processes that permit translocation between the gut, blood and other tissues. Such localised cell death processes might also contribute strongly to the specific diseases of interest. The bacterial requirement for free iron explains the strong co-existence in these diseases of iron dysregulation, LPS production, and inflammation. Overall this analysis provides an integrative picture, with significant predictive power, that is able to link these processes via the centrality of a dormant blood microbiome that can resuscitate and shed cell wall components.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK.
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa.
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41
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Plate-based diversity subset screening generation 2: an improved paradigm for high-throughput screening of large compound files. Mol Divers 2016; 20:789-803. [PMID: 27631533 PMCID: PMC5055576 DOI: 10.1007/s11030-016-9692-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/29/2016] [Indexed: 01/07/2023]
Abstract
High-throughput screening (HTS) is an effective method for lead and probe discovery that is widely used in industry and academia to identify novel chemical matter and to initiate the drug discovery process. However, HTS can be time consuming and costly and the use of subsets as an efficient alternative to screening entire compound collections has been investigated. Subsets may be selected on the basis of chemical diversity, molecular properties, biological activity diversity or biological target focus. Previously, we described a novel form of subset screening: plate-based diversity subset (PBDS) screening, in which the screening subset is constructed by plate selection (rather than individual compound cherry-picking), using algorithms that select for compound quality and chemical diversity on a plate basis. In this paper, we describe a second-generation approach to the construction of an updated subset: PBDS2, using both plate and individual compound selection, that has an improved coverage of the chemical space of the screening file, whilst only selecting the same number of plates for screening. We describe the validation of PBDS2 and its successful use in hit and lead discovery. PBDS2 screening became the default mode of singleton (one compound per well) HTS for lead discovery in Pfizer.
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Edwards CD, Luscombe C, Eddershaw P, Hessel EM. Development of a Novel Quantitative Structure-Activity Relationship Model to Accurately Predict Pulmonary Absorption and Replace Routine Use of the Isolated Perfused Respiring Rat Lung Model. Pharm Res 2016; 33:2604-16. [PMID: 27401409 PMCID: PMC5040732 DOI: 10.1007/s11095-016-1983-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/22/2016] [Indexed: 12/23/2022]
Abstract
Purpose We developed and tested a novel Quantitative Structure-Activity Relationship (QSAR) model to better understand the physicochemical drivers of pulmonary absorption, and to facilitate compound design through improved prediction of absorption. The model was tested using a large array of both existing and newly designed compounds. Methods Pulmonary absorption data was generated using the isolated perfused respiring rat lung (IPRLu) model for 82 drug discovery compounds and 17 marketed drugs. This dataset was used to build a novel QSAR model based on calculated physicochemical properties. A further 9 compounds were used to test the model’s predictive capability. Results The QSAR model performed well on the 9 compounds in the “Test set” with a predicted versus observed correlation of R2 = 0.85, and >65% of compounds correctly categorised. Calculated descriptors associated with permeability and hydrophobicity positively correlated with pulmonary absorption, whereas those associated with charge, ionisation and size negatively correlated. Conclusions The novel QSAR model described here can replace routine generation of IPRLu model data for ranking and classifying compounds prior to synthesis. It will also provide scientists working in the field of inhaled drug discovery with a deeper understanding of the physicochemical drivers of pulmonary absorption based on a relevant respiratory compound dataset.
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Affiliation(s)
- Chris D Edwards
- Refractory Respiratory Inflammation DPU, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
| | | | - Peter Eddershaw
- Refractory Respiratory Inflammation DPU, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Edith M Hessel
- Refractory Respiratory Inflammation DPU, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
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43
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Legehar A, Xhaard H, Ghemtio L. IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data. J Cheminform 2016; 8:33. [PMID: 27303447 PMCID: PMC4906584 DOI: 10.1186/s13321-016-0141-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/20/2016] [Indexed: 02/05/2023] Open
Abstract
Background The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. Description We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. Conclusion IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.FDA approved drug data integration for predictive modeling ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0141-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashenafi Legehar
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
| | - Henri Xhaard
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland ; Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Leo Ghemtio
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00790 Helsinki, Finland
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Andrić F, Bajusz D, Rácz A, Šegan S, Héberger K. Multivariate assessment of lipophilicity scales-computational and reversed phase thin-layer chromatographic indices. J Pharm Biomed Anal 2016; 127:81-93. [PMID: 27155738 DOI: 10.1016/j.jpba.2016.04.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/04/2016] [Accepted: 04/01/2016] [Indexed: 01/17/2023]
Abstract
Needs for fast, yet reliable means of assessing the lipophilicities of diverse compounds resulted in the development of various in silico and chromatographic approaches that are faster, cheaper, and greener compared to the traditional shake-flask method. However, at present no accepted "standard" approach exists for their comparison and selection of the most appropriate one(s). This is of utmost importance when it comes to the development of new lipophilicity indices, or the assessment of the lipophilicity of newly synthesized compounds. In this study, 50 well-known, diverse compounds of significant pharmaceutical and environmental importance have been selected and examined. Octanol-water partition coefficients have been measured with the shake-flask method for most of them. Their retentions have been studied in typical reversed thin-layer chromatographic systems, involving the most frequently employed stationary phases (octadecyl- and cyano-modified silica), and acetonitrile and methanol as mobile phase constituents. Twelve computationally estimated logP-s and twenty chromatographic indices together with the shake-flask octanol-water partition coefficient have been investigated with classical chemometric approaches-such as principal component analysis (PCA), hierarchical cluster analysis (HCA), Pearson's and Spearman's correlation matrices, as well as novel non-parametric methods: sum of ranking differences (SRD) and generalized pairwise correlation method (GPCM). Novel SRD and GPCM methods have been introduced based on the Comparisons with One VAriable (lipophilicity metric) at a Time (COVAT). For the visualization of COVAT results, a heatmap format was introduced. Analysis of variance (ANOVA) was applied to reveal the dominant factors between computational logPs and various chromatographic measures. In consensus-based comparisons, the shake-flask method performed the best, closely followed by computational estimates, while the chromatographic estimates often overlap with in silico assessments, mostly with methods involving octadecyl-modified silica stationary phases. The ones that employ cyano-modified silica perform generally worse. The introduction of alternative coloring schemes for the covariance matrices and SRD/GPCM heatmaps enables the discovery of intrinsic relationships among lipophilicity scales and the selection of best/worst measures. Closest to the recommended logKOW values are ClogP and the first principal component scores obtained on octadecyl-silica stationary phase in combination with methanol-water mobile phase, while the usage of slopes derived from Soczewinski-Matyisik equation should be avoided.
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Affiliation(s)
- Filip Andrić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest XI., Magyar Tudósok krt. 2, Hungary
| | - Anita Rácz
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest XI., Magyar Tudósok krt. 2, Hungary; Department of Applied Chemistry, Faculty of Food Science, Szent István University of Budapest, H-1118 Budapest XI., Villányi út 29-43, Hungary
| | - Sandra Šegan
- Institute of Chemistry, Technology and Metallurgy, Njegoševa 12, 11000 Belgrade, Serbia
| | - Károly Héberger
- Plasma Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest XI., Magyar Tudósok krt. 2, Hungary.
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45
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Patlewicz G, Fitzpatrick JM. Current and Future Perspectives on the Development, Evaluation, and Application of in Silico Approaches for Predicting Toxicity. Chem Res Toxicol 2016; 29:438-51. [PMID: 26686752 DOI: 10.1021/acs.chemrestox.5b00388] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Exploiting non-testing approaches to predict toxicity early in the drug discovery development cycle is a helpful component in minimizing expensive drug failures due to toxicity being identified in late development or even during clinical trials. Changes in regulations in the industrial chemicals and cosmetics sectors in recent years have prompted a significant number of advances in the development, application, and assessment of non-testing approaches, such as (Q)SARs. Many efforts have also been undertaken to establish guiding principles for performing read-across within category and analogue approaches. This review offers a perspective, as taken from these sectors, of the current status of non-testing approaches, their evolution in light of the advances in high-throughput approaches and constructs such as adverse outcome pathways, and their potential relevance for drug discovery. It also proposes a workflow for how non-testing approaches could be practically integrated within testing and assessment strategies.
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Affiliation(s)
- Grace Patlewicz
- National Center for Computational Toxicology (NCCT), U.S. Environmental Protection Agency , Research Triangle Park, North Carolina 27711, United States
| | - Jeremy M Fitzpatrick
- National Center for Computational Toxicology (NCCT), U.S. Environmental Protection Agency , Research Triangle Park, North Carolina 27711, United States
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46
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Wenlock MC. Profiling the estimated plasma concentrations of 215 marketed oral drugs. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00583c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human pharmacokinetic parameters of 215 marketed oral drugs have been collated and their estimated plasma concentrations (following repeat dosing) profiled against time using a one-compartment model.
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Abstract
Predictive toxicology plays a critical role in reducing the failure rate of new drugs in pharmaceutical research and development. Despite recent gains in our understanding of drug-induced toxicity, however, it is urgent that the utility and limitations of our current predictive tools be determined in order to identify gaps in our understanding of mechanistic and chemical toxicology. Using recently published computational regression analyses of in vitro and in vivo toxicology data, it will be demonstrated that significant gaps remain in early safety screening paradigms. More strategic analyses of these data sets will allow for a better understanding of their domain of applicability and help identify those compounds that cause significant in vivo toxicity but which are currently mis-predicted by in silico and in vitro models. These ‘outliers’ and falsely predicted compounds are metaphorical lighthouses that shine light on existing toxicological knowledge gaps, and it is essential that these compounds are investigated if attrition is to be reduced significantly in the future. As such, the modern computational toxicologist is more productively engaged in understanding these gaps and driving investigative toxicology towards addressing them.
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Affiliation(s)
- RT Naven
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Andover, MA, USA
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48
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Ryan E, Morrow BJ, Hemley CF, Pinson JA, Charman SA, Chiu FCK, Foitzik RC. Evidence for the in Vitro Bioactivation of Aminopyrazole Derivatives: Trapping Reactive Aminopyrazole Intermediates Using Glutathione Ethyl Ester in Human Liver Microsomes. Chem Res Toxicol 2015; 28:1747-52. [DOI: 10.1021/acs.chemrestox.5b00202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | - Benjamin J. Morrow
- Cancer Therapeutics CRC, 343
Royal Parade, Parkville, Victoria 3052 Australia
| | - Catherine F. Hemley
- Cancer Therapeutics CRC, 343
Royal Parade, Parkville, Victoria 3052 Australia
| | - Jo-Anne Pinson
- Cancer Therapeutics CRC, 343
Royal Parade, Parkville, Victoria 3052 Australia
| | | | | | - Richard C. Foitzik
- Cancer Therapeutics CRC, 343
Royal Parade, Parkville, Victoria 3052 Australia
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Abstract
In recent decades, in silico absorption, distribution, metabolism, excretion (ADME), and toxicity (T) modelling as a tool for rational drug design has received considerable attention from pharmaceutical scientists, and various ADME/T-related prediction models have been reported. The high-throughput and low-cost nature of these models permits a more streamlined drug development process in which the identification of hits or their structural optimization can be guided based on a parallel investigation of bioavailability and safety, along with activity. However, the effectiveness of these tools is highly dependent on their capacity to cope with needs at different stages, e.g. their use in candidate selection has been limited due to their lack of the required predictability. For some events or endpoints involving more complex mechanisms, the current in silico approaches still need further improvement. In this review, we will briefly introduce the development of in silico models for some physicochemical parameters, ADME properties and toxicity evaluation, with an emphasis on the modelling approaches thereof, their application in drug discovery, and the potential merits or deficiencies of these models. Finally, the outlook for future ADME/T modelling based on big data analysis and systems sciences will be discussed.
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50
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Zhuang C, Sheng C, Shin WS, Wu Y, Li J, Yao J, Dong G, Zhang W, Sham YY, Miao Z, Zhang W. A novel drug discovery strategy: mechanistic investigation of an enantiomeric antitumor agent targeting dual p53 and NF-κB pathways. Oncotarget 2015; 5:10830-9. [PMID: 25350970 PMCID: PMC4279413 DOI: 10.18632/oncotarget.2521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/24/2014] [Indexed: 01/02/2023] Open
Abstract
The p53 and nuclear factor κB (NF-κB) pathways play crucial roles in human cancer development. Simultaneous targeting of both pathways is an attractive therapeutic strategy against cancer. In this study, we report an antitumor molecule that bears a pyrrolo[3,4-c]pyrazole scaffold and functions as an enantiomeric inhibitor against both the p53-MDM2 interaction and the NF-κB activation. It is a first-in-class enantiomeric inhibitor with dual efficacy for cancer therapy. Synergistic effect was observed in vitro and in vivo. Docking and molecular dynamics simulation studies further provided insights into the nature of stereoselectivity.
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Affiliation(s)
- Chunlin Zhuang
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China. Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Woo Shik Shin
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, 55455, Minnesota
| | - Yuelin Wu
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Jin Li
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Jianzhong Yao
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Guoqiang Dong
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Wen Zhang
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Yuk Yin Sham
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, 55455, Minnesota
| | - Zhenyuan Miao
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Wannian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, People's Republic of China
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