1
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Poulin P. Which Unbound Fraction Should We Use in the Well-Stirred Model for More Accurately Predicting Hepatic Clearance of Drugs for Humans? J Pharm Sci 2025:103827. [PMID: 40414348 DOI: 10.1016/j.xphs.2025.103827] [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: 03/05/2025] [Revised: 05/07/2025] [Accepted: 05/07/2025] [Indexed: 05/27/2025]
Abstract
As the hepatic clearance (CLH) of drugs becomes independent of hepatic blood flow rate, CLH depends primarily on intrinsic clearance (CLint). Incubations of microsomes or hepatocytes are commonly used to generate CLint. Therefore, CLint estimates corrected for binding to the in vitro systems and scaled to whole liver, are applied to a well-stirred liver model to obtain CLH predictions for drugs. In other words, CLint is extrapolated with the ratio of unbound fraction between the plasma (fup) and incubation medium (fuinc). However, this binding correction resulted to an important underprediction bias of CLH. Therefore, the approach considering fup and fuinc needs to be better understood for more precisely scaling CLint. The objective of this study was to explain the underprediction bias of CLH based on physicochemical properties of drugs. Analysis-ready datasets have been collected so that evaluation of the data generates a mechanistic understanding of the impact of unbound fraction on the prediction of CLH of human for 128 drugs. Experimental values of fuinc for liver are quantifying solely the binding to lipids in microsomes or hepatocytes in the absence of plasma proteins in the incubations. However, the experimental values of fup for plasma can estimate the binding to lipids and plasma proteins. Therefore, drugs binding primarily to lipids in the liver and plasma showed a less pronounced underprediction bias of CLH by using the ratios of fup/fuinc in the well-stirred model. In contrast, drugs binding primarily to the plasma proteins in the liver and plasma showed a larger underprediction bias of CLH. Furthermore, for the ionized drugs, values of fup and fuinc are not covering the pH gradient effect between plasma and hepatocytes, which also impacted the CLH predictions. For these reasons, a mechanistic approach was proposed to replace the conventional fup value with an adjusted fup (fu-adjusted) that accounts for differences in proteins/lipids binding and pH gradient effect between the liver and plasma. Hence, replacing fup with fu-adjusted did provide a universal and mechanisms-based approach removing the underprediction bias for all datasets of drugs. Overall, this study indicates which drug properties generated the largest underprediction bias of CLH and suggests that the Poulin et al. method referring to fu-adjusted could be the most proper unbound fraction to reduce that bias with the well-stirred model.
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Affiliation(s)
- Patrick Poulin
- Consultant Patrick Poulin Inc., Québec City, Québec, Canada; School of Public Health, Université de Montréal, Montréal, Québec, Canada.
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2
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Yao Y, Simes ML, Ying W, Zhao Q, Winkler A, Shukla S, Gray F, Nikolaidis C, Hewett G, Grembecka J, Cierpicki T. Development of PRC1 Inhibitors Employing Fragment-Based Approach and NMR-Guided Optimization. J Med Chem 2025; 68:1382-1396. [PMID: 39746899 PMCID: PMC11969575 DOI: 10.1021/acs.jmedchem.4c01955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
Polycomb Repressive Complex 1 (PRC1) is associated with transcriptional silencing, and its dysregulation plays an important role in various cancers. Well-characterized PRC1 inhibitors can facilitate the exploration of PRC1 inhibition as therapeutic agents. By employing an NMR-based fragment screening approach, we have previously identified a very weak millimolar ligand RB-1, which directly binds to RING1B-BMI1. Then, we reported a low-micromolar PRC1 inhibitor, RB-3, which is active in leukemic cells, showing inhibition of H2A ubiquitylation and modulation of target genes. Here, we describe details of the optimization campaign of RB-1 into potent PRC1 inhibitors by guiding the SAR employing two NMR approaches and a probe-based biochemical assay. These efforts, combined with medicinal chemistry optimization, resulted in the development of RB-3 and slightly improved RB-4. We have demonstrated that RB-4 binds to both RING1A and RING1B proteins and inhibits the activity of RING1B-BMI1 and RING1B-PCGF1, representing both canonical and noncanonical PRC1 complexes.
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Affiliation(s)
- Yiwu Yao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Miranda L Simes
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Weijiang Ying
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Qingjie Zhao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alyssa Winkler
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shirish Shukla
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Felicia Gray
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Caroline Nikolaidis
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Geoff Hewett
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Feng Q, De Chavez D, Kihlberg J, Poongavanam V. A membrane permeability database for nonpeptidic macrocycles. Sci Data 2025; 12:10. [PMID: 39753569 PMCID: PMC11698989 DOI: 10.1038/s41597-024-04302-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 12/13/2024] [Indexed: 01/06/2025] Open
Abstract
The process of developing new drugs is arduous and costly, particularly for targets classified as "difficult-to-drug." Macrocycles show a particular ability to modulate difficult-to-drug targets, including protein-protein interactions, while still allowing oral administration. However, the determination of membrane permeability, critical for reaching intracellular targets and for oral bioavailability, is laborious and expensive. In silico methods are a cost-effective alternative, enabling predictions prior to compound synthesis. Here, we present a comprehensive online database ( https://swemacrocycledb.com/ ), housing 5638 membrane permeability datapoints for 4216 nonpeptidic macrocycles, curated from the literature, patents, and bioactivity repositories. In addition, we present a new descriptor, the "amide ratio" (AR), that quantifies the peptidic nature of macrocyclic compounds, enabling the classification of peptidic, semipeptidic, and nonpeptidic macrocycles. Overall, this resource fills a gap among existing databases, offering valuable insights into the membrane permeability of nonpeptidic and semipeptidic macrocycles, and facilitating predictions for drug discovery projects.
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Affiliation(s)
- Qiushi Feng
- Department of Chemistry-BMC, Uppsala University, SE-75123, Uppsala, Sweden
| | - Danjo De Chavez
- Department of Chemistry-BMC, Uppsala University, SE-75123, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry-BMC, Uppsala University, SE-75123, Uppsala, Sweden.
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4
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Stringer R, Kaster T. Predicting the Intravenous Pharmacokinetics of Covalent Drugs in Animals and Humans. J Med Chem 2024. [PMID: 39018425 DOI: 10.1021/acs.jmedchem.4c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
30 covalent drugs were used to assess clearance (CL) prediction reliability in animals and humans. In animals, marked CL underprediction was observed using cryopreserved hepatocytes or liver microsomes (LMs) supplemented for cytochrome P450 activity. Improved quantitative performance was observed by combining metabolic stability data from LMs and liver S9 fractions, the latter supplemented with reduced glutathione for glutathione transferase activity. While human LMs provided reliable human CL predictions, prediction statistics were improved further by incorporating S9 stability data. CL predictions with allometric scaling were less robust compared to in vitro drug metabolism methods; the best results were obtained using the fu-corrected intercept model. Human volume of distribution (Vd) was well predicted using allometric scaling of animal pharmacokinetic data; the most reliable results were achieved using simple allometric scaling of unbound Vd values. These results provide a quantitative framework to guide appropriate method selection for human PK prediction with covalent drugs.
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Affiliation(s)
- Rowan Stringer
- Novartis Biomedical Research, Basel CH-4002, Switzerland
| | - Tobias Kaster
- Novartis Biomedical Research, Basel CH-4002, Switzerland
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5
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Yan Z, Ma L, Hwang N, Huang J, Kenny JR, Hop CECA. Using the Dynamic Well-Stirred Model to Extrapolate Hepatic Clearance of Organic Anion-Transporting Polypeptide Transporter Substrates without Assuming Albumin-Mediated Hepatic Drug Uptake. Drug Metab Dispos 2024; 52:548-554. [PMID: 38604729 DOI: 10.1124/dmd.124.001645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/13/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Extrapolating in vivo hepatic clearance from in vitro uptake data is a known challenge, especially for organic anion-transporting polypeptide transporter (OATP) substrates, and the well-stirred model (WSM) commonly yields systematic underpredictions for those anionic drugs, hypothetically due to "albumin-mediated hepatic drug uptake". In the present study, we demonstrate that the WSM incorporating the dynamic free fraction (f D), a measure of drug protein binding affinity, performs reasonably well in predicting hepatic clearance of OATP substrates. For a selection of anionic drugs, including atorvastatin, fluvastatin, pravastatin, rosuvastatin, pitavastatin, cerivastatin, and repaglinide, this dynamic well-stirred model (dWSM) correctly predicts hepatic plasma clearance within 2-fold error for six out of seven OATP substrates examined. The geometric mean of clearance ratios between the predicted and the observed values falls in the range of 1.21-1.38. As expected, the WSM with unbound fraction (f u) systematically underpredicts hepatic clearance with greater than 2-fold error for five out of seven drugs, and the geometric mean of clearance ratios between the predicted and the observed values is in the range of 0.20-0.29. The results suggest that, despite its simplicity, the dWSM operates well for transporter-mediated uptake clearance, and that clearance under-prediction of OATP substrates may not necessarily be associated with the chemical class of the anionic drugs, nor is it a result of albumin-mediated hepatic drug uptake as currently hypothesized. Instead, the superior prediction power of the dWSM confirms the utility of the dynamic free fraction in clearance prediction and the importance of drug plasma binding kinetics in hepatic uptake clearance. SIGNIFICANCE STATEMENT: The traditional well-stirred model (WSM) consistently underpredicts organin anion-transporting polypeptide transporter (OATP)-mediated hepatic uptake clearance, hypothetically due to the albumin-mediated hepatic drug uptake. In this manuscript, we apply the dynamic WSM to extrapolate hepatic clearance of the OATP substrates, and our results show significant improvements in clearance prediction without assuming albumin-mediated hepatic drug uptake.
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Affiliation(s)
- Zhengyin Yan
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California
| | - Li Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California
| | - Nicky Hwang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California
| | - Julie Huang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California
| | - Jane R Kenny
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California
| | - Cornelis E C A Hop
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California
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6
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Manevski N, Umehara K, Parrott N. Drug Design and Success of Prospective Mouse In Vitro-In Vivo Extrapolation (IVIVE) for Predictions of Plasma Clearance (CL p) from Hepatocyte Intrinsic Clearance (CL int). Mol Pharm 2023. [PMID: 37235687 DOI: 10.1021/acs.molpharmaceut.2c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hepatocyte intrinsic clearance (CLint) and methods of in vitro-in vivo extrapolation (IVIVE) are often used to predict plasma clearance (CLp) in drug discovery. While the prediction success of this approach is dependent on the chemotype, specific molecular properties and drug design features that govern these outcomes are poorly understood. To address this challenge, we investigated the success of prospective mouse CLp IVIVE across 2142 chemically diverse compounds. Dilution scaling, which assumes that the free fraction in hepatocyte incubations (fu,inc) is governed by binding to the 10% of serum in the incubation medium, was used as our default CLp IVIVE approach. Results show that predictions of CLp are better for smaller (molecular weight (MW) < 500 Da), less polar (total polar surface area (TPSA) < 100 Å2, hydrogen bond donor (HBD) ≤1, hydrogen bond acceptor (HBA) ≤ 6), lipophilic (log D > 3), and neutral compounds, with low HBD count playing the key role. If compounds are classified according to their chemical space, predictions were good for compounds resembling central nervous system (CNS) drugs [average absolute fold error (AAFE) of 2.05, average fold error (AFE) of 0.90], moderate for classical druglike compounds (according to Lipinski, Veber, and Ghose guidelines; AAFE of 2.55; AFE of 0.68), and poor for nonclassical "beyond the rule of 5" compounds (AAFE of 3.31; AFE of 0.41). From the perspective of measured druglike properties, predictions of CLp were better for compounds with moderate-to-high hepatocyte CLint (>10 μL/min/106 cells), high passive cellular permeability (Papp > 100 nm/s), and moderate observed CLp (5-50 mL/min/kg). Influences of plasma protein binding (fu,p) and P-glycoprotein (Pgp) apical efflux ratio (AP-ER) were less pronounced. If the extended clearance classification system (ECCS) is applied, predictions were good for class 2 (Papp > 50 nm/s; neutral or basic; AAFE of 2.35; AFE of 0.70) and acceptable for class 1A compounds (AAFE of 2.98; AFE of 0.70). Classes 1B, 3 A/B, and 4 showed poor outcomes (AAFE > 3.80; AFE < 0.60). Functional groups trending toward weaker CLp IVIVE were esters, carbamates, sulfonamides, carboxylic acids, ketones, primary and secondary amines, primary alcohols, oxetanes, and compounds liable to aldehyde oxidase metabolism, likely due to multifactorial reasons. Multivariate analysis showed that multiple properties are relevant, combining together to define the overall success of CLp IVIVE. Our results indicate that the current practice of prospective CLp IVIVE is suitable only for CNS-like compounds and well-behaved classical druglike space (e.g., high permeability or ECCS class 2) without challenging functional groups. Unfortunately, based on existing mouse data, prospective CLp IVIVE for complex and nonclassical chemotypes is poor and hardly better than random guessing. This is likely due to complexities such as extrahepatic metabolism and transporter-mediated disposition which are poorly captured by this methodology. With small-molecule drug discovery increasingly evolving toward nonclassical and complex chemotypes, existing CLp IVIVE methodology will require improvement. While empirical correction factors may bridge the gap in the near future, improved and new in vitro assays, data integration models, and machine learning (ML) methods are increasingly needed to address this challenge and reduce the number of nonclinical pharmacokinetic (PK) studies.
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Affiliation(s)
- Nenad Manevski
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Kenichi Umehara
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Neil Parrott
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, 4070 Basel, Switzerland
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7
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Tess D, Chang GC, Keefer C, Carlo A, Jones R, Di L. In Vitro-In Vivo Extrapolation and Scaling Factors for Clearance of Human and Preclinical Species with Liver Microsomes and Hepatocytes. AAPS J 2023; 25:40. [PMID: 37052732 DOI: 10.1208/s12248-023-00800-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/03/2023] [Indexed: 04/14/2023] Open
Abstract
In vitro-in vivo extrapolation ((IVIVE) and empirical scaling factors (SF) of human intrinsic clearance (CLint) were developed using one of the largest dataset of 455 compounds with data from human liver microsomes (HLM) and human hepatocytes (HHEP). For extended clearance classification system (ECCS) class 2/4 compounds, linear SFs (SFlin) are approximately 1, suggesting enzyme activities in HLM and HHEP are similar to those in vivo under physiological conditions. For ECCS class 1A/1B compounds, a unified set of SFs was developed for CLint. These SFs contain both SFlin and an exponential SF (SFβ) of fraction unbound in plasma (fu,p). The unified SFs for class 1A/1B eliminate the need to identify the transporters involved prior to clearance prediction. The underlying mechanisms of these SFs are not entirely clear at this point, but they serve practical purposes to reduce biases and increase prediction accuracy. Similar SFs have also been developed for preclinical species. For HLM-HHEP disconnect (HLM > HHEP) ECCS class 2/4 compounds that are mainly metabolized by cytochrome P450s/FMO, HLM significantly overpredicted in vivo CLint, while HHEP slightly underpredicted and geometric mean of HLM and HHEP slightly overpredicted in vivo CLint. This observation is different than in rats, where rat liver microsomal CLint correlates well with in vivo CLint for compounds demonstrating permeability-limited metabolism. The good CLint IVIVE developed using HLM and HHEP helps build confidence for prospective predictions of human clearance and supports the continued utilization of these assays to guide structure-activity relationships to improve metabolic stability.
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Affiliation(s)
- David Tess
- Modeling and Simulation, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - George C Chang
- Modeling and Simulation, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Christopher Keefer
- Modeling and Simulation, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Anthony Carlo
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Rhys Jones
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, La Jolla, CA, USA
| | - Li Di
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, CT, 06340, USA.
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8
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Futatsugi K, Cabral S, Kung DW, Huard K, Lee E, Boehm M, Bauman J, Clark RW, Coffey SB, Crowley C, Dechert-Schmitt AM, Dowling MS, Dullea R, Gosset JR, Kalgutkar AS, Kou K, Li Q, Lian Y, Loria PM, Londregan AT, Niosi M, Orozco C, Pettersen JC, Pfefferkorn JA, Polivkova J, Ross TT, Sharma R, Stock IA, Tesz G, Wisniewska H, Goodwin B, Price DA. Discovery of Ervogastat (PF-06865571): A Potent and Selective Inhibitor of Diacylglycerol Acyltransferase 2 for the Treatment of Non-alcoholic Steatohepatitis. J Med Chem 2022; 65:15000-15013. [PMID: 36322383 DOI: 10.1021/acs.jmedchem.2c01200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Discovery efforts leading to the identification of ervogastat (PF-06865571), a systemically acting diacylglycerol acyltransferase (DGAT2) inhibitor that has advanced into clinical trials for the treatment of non-alcoholic steatohepatitis (NASH) with liver fibrosis, are described herein. Ervogastat is a first-in-class DGAT2 inhibitor that addressed potential development risks of the prototype liver-targeted DGAT2 inhibitor PF-06427878. Key design elements that culminated in the discovery of ervogastat are (1) replacement of the metabolically labile motif with a 3,5-disubstituted pyridine system, which addressed potential safety risks arising from a cytochrome P450-mediated O-dearylation of PF-06427878 to a reactive quinone metabolite precursor, and (2) modifications of the amide group to a 3-THF group, guided by metabolite identification studies coupled with property-based drug design.
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Affiliation(s)
- Kentaro Futatsugi
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Shawn Cabral
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Daniel W Kung
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kim Huard
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Esther Lee
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Markus Boehm
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jonathan Bauman
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ronald W Clark
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Steven B Coffey
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Collin Crowley
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | | | - Matthew S Dowling
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert Dullea
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - James R Gosset
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Amit S Kalgutkar
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Kou Kou
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Qifang Li
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Yajing Lian
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Paula M Loria
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Allyn T Londregan
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark Niosi
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christine Orozco
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - John C Pettersen
- Pfizer Inc. Drug Safety R&D, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeffrey A Pfefferkorn
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jana Polivkova
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Trenton T Ross
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Raman Sharma
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ingrid A Stock
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory Tesz
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Hanna Wisniewska
- Pfizer Inc. Medicine Design, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Bryan Goodwin
- Pfizer Inc. Internal Medicine Research Unit, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - David A Price
- Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States
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9
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Mizutare T, Sanoh S, Kanazu T, Ohta S, Kotake Y. Improved Predictability of Hepatic Clearance with Optimal pH for Acyl-Glucuronidation in Liver Microsomes. J Pharm Sci 2022; 111:3165-3173. [PMID: 35995204 DOI: 10.1016/j.xphs.2022.08.015] [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: 05/16/2022] [Revised: 07/30/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]
Abstract
The purpose of this study was to investigate the optimal pH for acyl-glucuronidation formation with carboxylic acid-containing compounds in human and rat liver microsomes to improve the predictability of their hepatic clearance. The optimal pH for acyl-glucuronidation of all 17 compounds was around pH 6.0 in human and rat liver microsomes. Correlation analysis was done with the predicted in vitro intrinsic clearance (CLint,in vitro) and in vivo intrinsic clearance (CLint,in vivo) calculated from available reported data of total clearance (CLtot) of 11 compounds in humans. For 8 of the 11 compounds, under the pH 6.0 condition, the CLint,in vitro were within 1/3 to 3-fold error of the observed CLint,in vivo whereas, the error was within 1/3 to 3-fold of the observed CLint,in vivo for only 3 of the 11 under the pH 7.4 condition. The intracellular pH in human and rat hepatocytes decreased in the presence of a carboxylic acid-containing compound. These findings suggest that acyl-glucuronidation in liver microsomes at pH 6.0 is closer to physiological conditions in the presence of carboxylic acid compounds, and thus, use of this pH condition is important for physiological interpretation and predictability of intrinsic clearance.
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Affiliation(s)
- Tohru Mizutare
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Laboratory for Drug Discovery and Development, Shionogi & Co., Ltd., Osaka, Japan.
| | - Seigo Sanoh
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan.
| | - Takushi Kanazu
- Laboratory for Drug Discovery and Development, Shionogi & Co., Ltd., Osaka, Japan
| | - Shigeru Ohta
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Yaichiro Kotake
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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10
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Matsumoto S, Uehara S, Kamimura H, Cho N, Ikeda H, Maeda S, Kagiyama K, Miyata A, Suemizu H, Fukasawa K. Selection of the candidate compound at an early stage of new drug development: retrospective pharmacokinetic and metabolic evaluations of valsartan using common marmosets. Xenobiotica 2022; 52:613-624. [PMID: 36148579 DOI: 10.1080/00498254.2022.2127131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Shogo Matsumoto
- Drug & Discovery & Management Department, R&D Division, Meiji Seika Pharma Co., Ltd., Tokyo, Japan
| | - Shotaro Uehara
- Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Hidetaka Kamimura
- Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki, Japan.,Business Promotion Department, CLEA Japan, Inc., Tokyo, Japan
| | - Naoki Cho
- Drug & Discovery & Management Department, R&D Division, Meiji Seika Pharma Co., Ltd., Tokyo, Japan
| | - Hiroshi Ikeda
- Tokyo Animal & Diet Department, CLEA Japan, Inc., Tokyo, Japan
| | - Satoshi Maeda
- Yaotsu Breeding Center, CLEA Japan, Inc., Gifu, Japan
| | | | - Atsunori Miyata
- Drug & Discovery & Management Department, R&D Division, Meiji Seika Pharma Co., Ltd., Tokyo, Japan
| | - Hiroshi Suemizu
- Department of Applied Research for Laboratory Animals, Central Institute for Experimental Animals, Kawasaki, Japan
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11
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Cecere G, Guasch L, Olivares-Morales AM, Umehara K, Stepan AF. LipMetE (Lipophilic Metabolism Efficiency) as a Simple Guide for Half-Life and Dosing Regimen Prediction of Oral Drugs. ACS Med Chem Lett 2022; 13:1444-1451. [PMID: 36105329 PMCID: PMC9465707 DOI: 10.1021/acsmedchemlett.2c00183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
The in vivo half-life is a key property of every drug molecule, as it determines dosing regimens, peak-to-trough ratios and often dose. However, half-life optimization can be challenging due to its multifactorial nature, with in vitro metabolic turnover, plasma protein binding and volume of distribution all impacting half-life. We here propose that the medicinal chemistry design parameter Lipophilic Metabolism Efficiency (LipMetE) can greatly simplify half-life optimization of neutral and basic compounds. Using mathematical transformations, examples from preclinical GABAA projects and clinical compounds with human pharmacokinetic data, we show that LipMetE is directly proportional to the logarithm of half-life. As the design parameter LipMetE can be swiftly calculated using the readily available parameters LogD, intrinsic clearance and fraction unbound in human liver microsomes or hepatocytes, this approach enables rational half-life optimization from the early stages of drug discovery projects.
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Affiliation(s)
- Giuseppe Cecere
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Laura Guasch
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Andres M. Olivares-Morales
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Kenichi Umehara
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Antonia F. Stepan
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
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12
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Iwata H, Matsuo T, Mamada H, Motomura T, Matsushita M, Fujiwara T, Maeda K, Handa K. Predicting Total Drug Clearance and Volumes of Distribution Using the Machine Learning-Mediated Multimodal Method through the Imputation of Various Nonclinical Data. J Chem Inf Model 2022; 62:4057-4065. [PMID: 35993595 PMCID: PMC9472274 DOI: 10.1021/acs.jcim.2c00318] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Pharmacokinetic research plays an important role in the
development
of new drugs. Accurate predictions of human pharmacokinetic parameters
are essential for the success of clinical trials. Clearance (CL) and
volume of distribution (Vd) are important factors for evaluating pharmacokinetic
properties, and many previous studies have attempted to use computational
methods to extrapolate these values from nonclinical laboratory animal
models to human subjects. However, it is difficult to obtain sufficient,
comprehensive experimental data from these animal models, and many
studies are missing critical values. This means that studies using
nonclinical data as explanatory variables can only apply a small number
of compounds to their model training. In this study, we perform missing-value
imputation and feature selection on nonclinical data to increase the
number of training compounds and nonclinical datasets available for
these kinds of studies. We could obtain novel models for total body
clearance (CLtot) and steady-state Vd (Vdss)
(CLtot: geometric mean fold error [GMFE], 1.92; percentage
within 2-fold error, 66.5%; Vdss: GMFE, 1.64; percentage
within 2-fold error, 71.1%). These accuracies were comparable to the
conventional animal scale-up models. Then, this method differs from
animal scale-up methods because it does not require animal experiments,
which continue to become more strictly regulated as time passes.
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Affiliation(s)
- Hiroaki Iwata
- Graduate School of Medicine, Kyoto University, 53 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Tatsuru Matsuo
- Fujitsu Ltd., 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki-shi, Kanagawa 211-8588, Japan
| | - Hideaki Mamada
- DMPK Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takahisa Motomura
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Mayumi Matsushita
- Fujitsu Ltd., 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki-shi, Kanagawa 211-8588, Japan
| | - Takeshi Fujiwara
- Graduate School of Medicine, Kyoto University, 53 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazuya Maeda
- Graduate School of Pharmaceutical Sciences, Department of Molecular Pharmacokinetics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koichi Handa
- Toxicology & DMPK Research Department, Teijin Institute for Bio-medical Research, Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan
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13
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Petersson C, Zhou X, Berghausen J, Cebrian D, Davies M, DeMent K, Eddershaw P, Riedmaier AE, Leblanc AF, Manveski N, Marathe P, Mavroudis PD, McDougall R, Parrott N, Reichel A, Rotter C, Tess D, Volak LP, Xiao G, Yang Z, Baker J. Current Approaches for Predicting Human PK for Small Molecule Development Candidates: Findings from the IQ Human PK Prediction Working Group Survey. AAPS J 2022; 24:85. [DOI: 10.1208/s12248-022-00735-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022] Open
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14
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Weng Y, Fonseca KR, Bi YA, Mathialagan S, Riccardi K, Tseng E, Bessire AJ, Cerny MA, Tess DA, Rodrigues AD, Kalgutkar AS, Litchfield JE, Di L, Varma MVS. Transporter-Enzyme Interplay in the Pharmacokinetics of PF-06835919, A First-in-class Ketohexokinase Inhibitor for Metabolic Disorders and Non-alcoholic Fatty Liver Disease. Drug Metab Dispos 2022; 50:DMD-AR-2022-000953. [PMID: 35779864 DOI: 10.1124/dmd.122.000953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022] Open
Abstract
Excess dietary fructose consumption promotes metabolic dysfunction thereby increasing the risk of obesity, type 2 diabetes, non-alcoholic steatohepatitis (NASH), and related comorbidities. PF-06835919, a first-in-class ketohexokinase (KHK) inhibitor, showed reversal of such metabolic disorders in preclinical models and clinical studies, and is under clinical development for the potential treatment of NASH. In this study, we evaluated the transport and metabolic pathways of PF-06835919 disposition and assessed pharmacokinetics in preclinical models. PF-06835919 showed active uptake in cultured primary human hepatocytes, and substrate activity to organic anion transporter (OAT)2 and organic anion transporting-polypeptide (OATP)1B1 in transfected cells. "SLC-phenotyping" studies in human hepatocytes suggested contribution of passive uptake, OAT2- and OATP1B-mediated transport to the overall uptake to be about 15%, 60% and 25%, respectively. PF-06835919 showed low intrinsic metabolic clearance in vitro, and was found to be metabolized via both oxidative pathways (58%) and acyl glucuronidation (42%) by CYP3A, CYP2C8, CYP2C9 and UGT2B7. Following intravenous dosing, PF-06835919 showed low clearance (0.4-1.3 mL/min/kg) and volume of distribution (0.17-0.38 L/kg) in rat, dog and monkey. Human oral pharmacokinetics are predicted within 20% error when considering transporter-enzyme interplay in a PBPK model. Finally, unbound liver-to-plasma ratio (Kpuu) measured in vitro using rat, NHP and human hepatocytes was found to be approximately 4, 25 and 10, respectively. Similarly, liver Kpuu in rat and monkey following intravenous dosing of PF-06835919 was found to be 2.5 and 15, respectively, and notably higher than the muscle and brain Kpuu, consistent with the active uptake mechanisms observed in vitro. Significance Statement This work characterizes the transport/metabolic pathways in the hepatic disposition of PF-06835919, a first-in-class KHK inhibitor for the treatment of metabolic disorders and NASH. Phenotyping studies using transfected systems, human hepatocytes and liver microsomes signifies the role of OAT2 and OATP1B1 in the hepatic uptake and multiple enzymes in the metabolism of PF-06835919. Data presented suggest hepatic transporter-enzyme interplay in determining its systemic concentrations and potential enrichment in liver, a target site for KHK inhibition.
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Affiliation(s)
- Yan Weng
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., United States
| | | | | | - Sumathy Mathialagan
- Pharmacokinetics, Pharmacodynamics, and Metabolism, Medicine Design, Pfizer Inc, United States
| | | | - Elaine Tseng
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer Global Research and Development, United States
| | | | | | | | | | - Amit S Kalgutkar
- Medicine Design, Pfizer Worldwide Research and Development, United States
| | | | - Li Di
- Pharmacokintics Dynamics and Metabolism, Pfizer Inc., United States
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15
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Ryder TF, Bergman A, King-Ahmad A, Amin NB, Lall MS, Ballard TE, Kalgutkar AS. Pharmacokinetics, Mass Balance, Metabolism, and Excretion of the Liver-Targeted Acetyl-CoA Carboxylase Inhibitor PF-05221304 (Clesacostat) in Humans. Xenobiotica 2022; 52:240-253. [PMID: 35382680 DOI: 10.1080/00498254.2022.2062487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The disposition of the hepatoselective ACC inhibitor PF-05221304 (Clesacostat) was studied after a single 50-mg oral dose of [14C]-PF-05221304 to healthy human subjects.Mass balance was achieved with 89.9% of the administered dose recovered in urine and faeces, over the 11-day study period. The total administered radioactivity excreted in faeces and urine was 81.7% and 8.2%, respectively. Unchanged PF-05221304 accounted for 35.6% of the radioactive dose in faeces, suggesting ∼64% of the administered dose was absorbed.PF-05221304 was principally metabolized via oxidative and reductive pathways involving: (a) N-dealkylation, (b) isopropyl group monohydroxylation to yield enantiomeric metabolites (M2a and M2b), (c) hydroxylation on the 3-azaspiro[5.5]undecan-8-one moiety to metabolites M5 and 519c, and (d) carbonyl group reduction to enantiomeric alcohol metabolites M3, and M4. Secondary metabolites (521a, 521b, and 533), derived from a combination of oxidation and reduction of the primary metabolites accounted for ∼14.8% of the dose. In plasma, unchanged PF-05221304 represented 96.1% circulating radioactivity. Metabolites M1, M2b, and M2a represented 1.94, 1.76, and 0.18% of circulating radioactivity, respectively.Overall, these data suggest that PF-05221304 is well absorbed in humans and eliminated largely via phase I metabolism.
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Affiliation(s)
- Tim F Ryder
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut, USA
| | - Arthur Bergman
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts, USA
| | - Amanda King-Ahmad
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut, USA
| | - Neeta B Amin
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts, USA
| | - Manjinder S Lall
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut, USA
| | - T Eric Ballard
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut, USA
| | - Amit S Kalgutkar
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts, USA
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16
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Docci L, Milani N, Ramp T, Romeo AA, Godoy P, Franyuti DO, Krähenbühl S, Gertz M, Galetin A, Parrott N, Fowler S. Exploration and application of a liver-on-a-chip device in combination with modelling and simulation for quantitative drug metabolism studies. LAB ON A CHIP 2022; 22:1187-1205. [PMID: 35107462 DOI: 10.1039/d1lc01161h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Microphysiological systems (MPS) are complex and more physiologically realistic cellular in vitro tools that aim to provide more relevant human in vitro data for quantitative prediction of clinical pharmacokinetics while also reducing the need for animal testing. The PhysioMimix liver-on-a-chip integrates medium flow with hepatocyte culture and has the potential to be adopted for in vitro studies investigating the hepatic disposition characteristics of drug candidates. The current study focusses on liver-on-a-chip system exploration for multiple drug metabolism applications. Characterization of cytochrome P450 (CYP), UDP-glucuronosyl transferase (UGT) and aldehyde oxidase (AO) activities was performed using 15 drugs and in vitro to in vivo extrapolation (IVIVE) was assessed for 12 of them. Next, the utility of the liver-on-a-chip for estimation of the fraction metabolized (fm) via specific biotransformation pathways of quinidine and diclofenac was established. Finally, the metabolite identification opportunities were also explored using efavirenz as an example drug with complex primary and secondary metabolism involving a combination of CYP, UGT and sulfotransferase enzymes. A key aspect of these investigations was the application of mathematical modelling for improved parameter calculation. Such approaches will be required for quantitative assessment of metabolism and/or transporter processes in systems where medium flow and system compartments result in non-homogeneous drug concentrations. In particular, modelling was used to explore the effect of evaporation from the medium and it was found that the intrinsic clearance (CLint) might be underestimated by up to 40% for low clearance compounds if evaporation is not accounted for. Modelling of liver-on-a-chip in vitro data also enhanced the approach to fm estimation allowing objective assessment of metabolism models of different complexity. The resultant diclofenac fm,UGT of 0.64 was highly comparable with values reported previously in the literature. The current study demonstrates the integration of mathematical modelling with experimental liver-on-a-chip studies and illustrates how this approach supports generation of high quality of data from complex in vitro cellular systems.
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Affiliation(s)
- Luca Docci
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
- Clinical Pharmacology & Toxicology, University Hospital, Schanzenstrasse 55, 4031, Basel, Switzerland
| | - Nicolò Milani
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Thomas Ramp
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Andrea A Romeo
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Patricio Godoy
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Daniela Ortiz Franyuti
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Stephan Krähenbühl
- Clinical Pharmacology & Toxicology, University Hospital, Schanzenstrasse 55, 4031, Basel, Switzerland
| | - Michael Gertz
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Aleksandra Galetin
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Neil Parrott
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Stephen Fowler
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland.
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17
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In Vitro - in Vivo Extrapolation of Hepatic Clearance in Preclinical Species. Pharm Res 2022; 39:1615-1632. [PMID: 35257289 DOI: 10.1007/s11095-022-03205-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/15/2022] [Indexed: 10/18/2022]
Abstract
Accurate prediction of human clearance is of critical importance in drug discovery. In this study, in vitro - in vivo extrapolation (IVIVE) of hepatic clearance was established using large sets of compounds for four preclinical species (mouse, rat, dog, and non-human primate) to enable better understanding of clearance mechanisms and human translation. In vitro intrinsic clearances were obtained using pooled liver microsomes (LMs) or hepatocytes (HEPs) and scaled to hepatic clearance using the parallel-tube and well-stirred models. Subsequently, IVIVE scaling factors (SFs) were derived to best predict in vivo clearance. The SFs for extended clearance classification system (ECCS) class 2/4 compounds, involving metabolic clearance, were generally small (≤ 2.6) using both LMs and HEPs with parallel-tube model, with the exception of the rodents (~ 2.4-4.6), suggesting in vitro reagents represent in vivo reasonably well. SFs for ECCS class 1A and 1B are generally higher than class 2/4 across the species, likely due to the contribution of transporter-mediated clearance that is under-represented with in vitro reagents. The parallel-tube model offered lower variability in clearance predictions over the well-stirred model. For compounds that likely demonstrate passive permeability-limited clearance in vitro, rat LM predicted in vivo clearance more accurately than HEP. This comprehensive analysis demonstrated reliable IVIVE can be achieved using LMs and HEPs. Evaluation of clearance IVIVE in preclinical species helps to better understand clearance mechanisms, establish more reliable IVIVE in human, and enhance our confidence in human clearance and PK prediction, while considering species differences in drug metabolizing enzymes and transporters.
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18
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Mammoliti O, Jansen K, El Bkassiny S, Palisse A, Triballeau N, Bucher D, Allart B, Jaunet A, Tricarico G, De Wachter M, Menet C, Blanc J, Letfus V, Rupčić R, Šmehil M, Poljak T, Coornaert B, Sonck K, Duys I, Waeckel L, Lecru L, Marsais F, Jagerschmidt C, Auberval M, Pujuguet P, Oste L, Borgonovi M, Wakselman E, Christophe T, Houvenaghel N, Jans M, Heckmann B, Sanière L, Brys R. Discovery and Optimization of Orally Bioavailable Phthalazone and Cinnolone Carboxylic Acid Derivatives as S1P2 Antagonists against Fibrotic Diseases. J Med Chem 2021; 64:14557-14586. [PMID: 34581584 DOI: 10.1021/acs.jmedchem.1c01066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease. Current treatments only slow down disease progression, making new therapeutic strategies compelling. Increasing evidence suggests that S1P2 antagonists could be effective agents against fibrotic diseases. Our compound collection was mined for molecules possessing substructure features associated with S1P2 activity. The weakly potent indole hit 6 evolved into a potent phthalazone series, bearing a carboxylic acid, with the aid of a homology model. Suboptimal pharmacokinetics of a benzimidazole subseries were improved by modifications targeting potential interactions with transporters, based on concepts deriving from the extended clearance classification system (ECCS). Scaffold hopping, as a part of a chemical enablement strategy, permitted the rapid exploration of the position adjacent to the carboxylic acid. Compound 38, with good pharmacokinetics and in vitro potency, was efficacious at 10 mg/kg BID in three different in vivo mouse models of fibrotic diseases in a therapeutic setting.
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Affiliation(s)
- Oscar Mammoliti
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Koen Jansen
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Adeline Palisse
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Denis Bucher
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Brigitte Allart
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Alex Jaunet
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | | | - Maxim De Wachter
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Christel Menet
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Javier Blanc
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Vatroslav Letfus
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | - Renata Rupčić
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | - Mario Šmehil
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | - Tanja Poljak
- Fidelta Ltd., Prilaz Baruna Filipovića 29, ZagrebHR-10000, Croatia
| | | | - Kathleen Sonck
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Inge Duys
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Ludovic Waeckel
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Lola Lecru
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Florence Marsais
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | | | - Marielle Auberval
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Philippe Pujuguet
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Line Oste
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Monica Borgonovi
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | | | | | | | - Mia Jans
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
| | - Bertrand Heckmann
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Laurent Sanière
- Galapagos SASU, 102 avenue Gaston Roussel, 93230 Romainville, France
| | - Reginald Brys
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium
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19
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Eng H, Bi YA, West MA, Ryu S, Yamaguchi E, Kosa RE, Tess DA, Griffith DA, Litchfield J, Kalgutkar AS, Varma MVS. Organic Anion-Transporting Polypeptide 1B1/1B3-Mediated Hepatic Uptake Determines the Pharmacokinetics of Large Lipophilic Acids: In Vitro-In Vivo Evaluation in Cynomolgus Monkey. J Pharmacol Exp Ther 2021; 377:169-180. [PMID: 33509903 DOI: 10.1124/jpet.120.000457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/25/2021] [Indexed: 12/22/2022] Open
Abstract
It is generally presumed that uptake transport mechanisms are of limited significance in hepatic clearance for lipophilic or high passive-permeability drugs. In this study, we evaluated the mechanistic role of the hepato-selective organic anion-transporting polypeptides (OATPs) 1B1/1B3 in the pharmacokinetics of compounds representing large lipophilic acid space. Intravenous pharmacokinetics of 16 compounds with molecular mass ∼400-730 Da, logP ∼3.5-8, and acid pKa <6 were obtained in cynomolgus monkey after dosing without and with a single-dose rifampicin-OATP1B1/1B3 probe inhibitor. Rifampicin (30 mg/kg oral) significantly (P < 0.05) reduced monkey clearance and/or steady-state volume of distribution (VDss) for 15 of 16 acids evaluated. Additionally, clearance of danoprevir was reduced by about 35%, although statistical significance was not reached. A significant linear relationship was noted between the clearance ratio (i.e., ratio of control to treatment groups) and VDss ratio, suggesting hepatic uptake contributes to the systemic clearance and distribution simultaneously. In vitro transport studies using primary monkey and human hepatocytes showed uptake inhibition by rifampicin (100 µM) for compounds with logP ≤6.5 but not for the very lipophilic acids (logP > 6.5), which generally showed high nonspecific binding in hepatocyte incubations. In vitro uptake clearance and fraction transported by OATP1B1/1B3 (ft,OATP1B) were found to be similar in monkey and human hepatocytes. Finally, for compounds with logP ≤6.5, good agreement was noted between in vitro ft,OATP1B and clearance ratio (as well as VDss ratio) in cynomolgus monkey. In conclusion, this study provides mechanistic evidence for the pivotal role of OATP1B-mediated hepatic uptake in the pharmacokinetics across a wide, large lipophilic acid space. SIGNIFICANCE STATEMENT: This study provides mechanistic insight into the pharmacokinetics of a broad range of large lipophilic acids. Organic anion-transporting polypeptides 1B1/1B3-mediated hepatic uptake is of key importance in the pharmacokinetics and drug-drug interactions of almost all drugs and new molecular entities in this space. Diligent in vitro and in vivo transport characterization is needed to avoid the false negatives often noted because of general limitations in the in vitro assays while handling compounds with such physicochemical attributes.
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Affiliation(s)
- Heather Eng
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Yi-An Bi
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Mark A West
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Sangwoo Ryu
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Emi Yamaguchi
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Rachel E Kosa
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - David A Tess
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - David A Griffith
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - John Litchfield
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Amit S Kalgutkar
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Manthena V S Varma
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
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