1
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Rosado-Quiñones AM, Colón-Lorenzo EE, Pala ZR, Bosch J, Kudyba K, Kudyba H, Leed SE, Roncal N, Baerga-Ortiz A, Roche-Lima A, Gerena Y, Fidock DA, Roth A, Vega-Rodríguez J, Serrano AE. Novel hydrazone compounds with broad-spectrum antiplasmodial activity and synergistic interactions with antimalarial drugs. Antimicrob Agents Chemother 2024:e0164323. [PMID: 38639491 DOI: 10.1128/aac.01643-23] [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: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
The development of novel antiplasmodial compounds with broad-spectrum activity against different stages of Plasmodium parasites is crucial to prevent malaria disease and parasite transmission. This study evaluated the antiplasmodial activity of seven novel hydrazone compounds (referred to as CB compounds: CB-27, CB-41, CB-50, CB-53, CB-58, CB-59, and CB-61) against multiple stages of Plasmodium parasites. All CB compounds inhibited blood stage proliferation of drug-resistant or sensitive strains of Plasmodium falciparum in the low micromolar to nanomolar range. Interestingly, CB-41 exhibited prophylactic activity against hypnozoites and liver schizonts in Plasmodium cynomolgi, a primate model for Plasmodium vivax. Four CB compounds (CB-27, CB-41, CB-53, and CB-61) inhibited P. falciparum oocyst formation in mosquitoes, and five CB compounds (CB-27, CB-41, CB-53, CB-58, and CB-61) hindered the in vitro development of Plasmodium berghei ookinetes. The CB compounds did not inhibit the activation of P. berghei female and male gametocytes in vitro. Isobologram assays demonstrated synergistic interactions between CB-61 and the FDA-approved antimalarial drugs, clindamycin and halofantrine. Testing of six CB compounds showed no inhibition of Plasmodium glutathione S-transferase as a putative target and no cytotoxicity in HepG2 liver cells. CB compounds are promising candidates for further development as antimalarial drugs against multidrug-resistant parasites, which could also prevent malaria transmission.
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Affiliation(s)
- Angélica M Rosado-Quiñones
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Emilee E Colón-Lorenzo
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Zarna Rajeshkumar Pala
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Jürgen Bosch
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
- InterRayBio, LLC, Cleveland, Ohio, USA
| | - Karl Kudyba
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Heather Kudyba
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Susan E Leed
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Norma Roncal
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Abel Baerga-Ortiz
- Department of Biochemistry, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Abiel Roche-Lima
- RCMI Program, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Yamil Gerena
- Department of Pharmacology and Toxicology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York, USA
| | - Alison Roth
- Department of Drug Discovery, Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Joel Vega-Rodríguez
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Adelfa E Serrano
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
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2
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Kattar SD, Gulati A, Margrey KA, Keylor MH, Ardolino M, Yan X, Johnson R, Palte RL, McMinn SE, Nogle L, Su J, Xiao D, Piesvaux J, Lee S, Hegde LG, Woodhouse JD, Faltus R, Moy LY, Xiong T, Ciaccio PJ, Pearson K, Patel M, Otte KM, Leyns CEG, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Discovery of MK-1468: A Potent, Kinome-Selective, Brain-Penetrant Amidoisoquinoline LRRK2 Inhibitor for the Potential Treatment of Parkinson's Disease. J Med Chem 2023; 66:14912-14927. [PMID: 37861679 DOI: 10.1021/acs.jmedchem.3c01486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Genetic mutation of the leucine-rich repeat kinase 2 (LRRK2) protein has been associated with Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder that is devoid of efficacious disease-modifying therapies. Herein, we describe the invention of an amidoisoquinoline (IQ)-derived LRRK2 inhibitor lead chemical series. Knowledge-, structure-, and property-based drug design in concert with rigorous application of in silico calculations and presynthesis predictions enabled the prioritization of molecules with favorable CNS "drug-like" physicochemical properties. This resulted in the discovery of compound 8, which was profiled extensively before human ether-a-go-go (hERG) ion channel inhibition halted its progression. Strategic reduction of lipophilicity and basicity resulted in attenuation of hERG ion channel inhibition while maintaining a favorable CNS efflux transporter profile. Further structure- and property-based optimizations resulted in the discovery of preclinical candidate MK-1468. This exquisitely selective LRRK2 inhibitor has a projected human dose of 48 mg BID and a preclinical safety profile that supported advancement toward GLP toxicology studies.
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Affiliation(s)
- Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dong Xiao
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Susi Lee
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kara Pearson
- Merck & Co., Inc., 770 Sumneytown Pike., West Point, Pennsylvania 19486, United States
| | - Mayankbhai Patel
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cheryl E G Leyns
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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3
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Hong E, Carmanov E, Shi A, Chung PS, Rao AP, Forrester K, Beringer PM. Application of Physiologically Based Pharmacokinetic Modeling to Predict Drug-Drug Interactions between Elexacaftor/Tezacaftor/Ivacaftor and Tacrolimus in Lung Transplant Recipients. Pharmaceutics 2023; 15:pharmaceutics15051438. [PMID: 37242680 DOI: 10.3390/pharmaceutics15051438] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 04/28/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Elexacaftor/tezacaftor/ivacaftor (ETI) treatment has potential benefits in lung transplant recipients, including improvements in extrapulmonary manifestations, such as gastrointestinal and sinus disease; however, ivacaftor is an inhibitor of cytochrome P450 3A (CYP3A) and may, therefore, pose a risk for elevated systemic exposure to tacrolimus. The aim of this investigation is to determine the impact of ETI on tacrolimus exposure and devise an appropriate dosing regimen to manage the risk of this drug-drug interaction (DDI). The CYP3A-mediated DDI of ivacaftor-tacrolimus was evaluated using a physiologically based pharmacokinetic (PBPK) modeling approach, incorporating CYP3A4 inhibition parameters of ivacaftor and in vitro enzyme kinetic parameters of tacrolimus. To further support the findings in PBPK modeling, we present a case series of lung transplant patients who received both ETI and tacrolimus. We predicted a 2.36-fold increase in tacrolimus exposure when co-administered with ivacaftor, which would require a 50% dose reduction of tacrolimus upon initiation of ETI treatment to avoid the risk of elevated systemic exposure. Clinical cases (N = 13) indicate a median 32% (IQR: -14.30, 63.80) increase in the dose-normalized tacrolimus trough level (trough concentration/weight-normalized daily dose) after starting ETI. These results indicate that the concomitant administration of tacrolimus and ETI may lead to a clinically significant DDI, requiring the dose adjustment of tacrolimus.
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Affiliation(s)
- Eunjin Hong
- Department of Clinical Pharmacy, Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave, Los Angeles, CA 90033, USA
| | - Eugeniu Carmanov
- Department of Clinical Pharmacy, Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave, Los Angeles, CA 90033, USA
| | - Alan Shi
- Department of Clinical Pharmacy, Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave, Los Angeles, CA 90033, USA
| | - Peter S Chung
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, 1975 Zonal Ave, Los Angeles, CA 90033, USA
- USC Anton Yelchin CF Clinic, 1510 San Pablo St, Los Angeles, CA 90033, USA
| | - Adupa P Rao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, 1975 Zonal Ave, Los Angeles, CA 90033, USA
- USC Anton Yelchin CF Clinic, 1510 San Pablo St, Los Angeles, CA 90033, USA
| | - Kevin Forrester
- Department of Clinical Pharmacy, Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave, Los Angeles, CA 90033, USA
| | - Paul M Beringer
- Department of Clinical Pharmacy, Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave, Los Angeles, CA 90033, USA
- USC Anton Yelchin CF Clinic, 1510 San Pablo St, Los Angeles, CA 90033, USA
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4
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Building a Human Physiologically Based Pharmacokinetic Model for Aflatoxin B1 to Simulate Interactions with Drugs. Pharmaceutics 2023; 15:pharmaceutics15030894. [PMID: 36986755 PMCID: PMC10053806 DOI: 10.3390/pharmaceutics15030894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Mycotoxins such as aflatoxin B1 (AFB1) are secondary fungal metabolites present in food commodities and part of one’s daily exposure, especially in certain regions, e.g., sub-Saharan Africa. AFB1 is mostly metabolised by cytochrome P450 (CYP) enzymes, namely, CYP1A2 and CYP3A4. As a consequence of chronic exposure, it is interesting to check for interactions with drugs taken concomitantly. A physiologically based pharmacokinetic (PBPK) model was developed based on the literature and in-house-generated in vitro data to characterise the pharmacokinetics (PK) of AFB1. The substrate file was used in different populations (Chinese, North European Caucasian and Black South African), provided by SimCYP® software (v21), to evaluate the impact of populations on AFB1 PK. The model’s performance was verified against published human in vivo PK parameters, with AUC ratios and Cmax ratios being within the 0.5–2.0-fold range. Effects on AFB1 PK were observed with commonly prescribed drugs in South Africa, leading to clearance ratios of 0.54 to 4.13. The simulations revealed that CYP3A4/CYP1A2 inducer/inhibitor drugs might have an impact on AFB1 metabolism, altering exposure to carcinogenic metabolites. AFB1 did not have effects on the PK of drugs at representative exposure concentrations. Therefore, chronic AFB1 exposure is unlikely to impact the PK of drugs taken concomitantly.
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5
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McNair D. Artificial Intelligence and Machine Learning for Lead-to-Candidate Decision-Making and Beyond. Annu Rev Pharmacol Toxicol 2023; 63:77-97. [PMID: 35679624 DOI: 10.1146/annurev-pharmtox-051921-023255] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The use of artificial intelligence (AI) and machine learning (ML) in pharmaceutical research and development has to date focused on research: target identification; docking-, fragment-, and motif-based generation of compound libraries; modeling of synthesis feasibility; rank-ordering likely hits according to structural and chemometric similarity to compounds having known activity and affinity to the target(s); optimizing a smaller library for synthesis and high-throughput screening; and combining evidence from screening to support hit-to-lead decisions. Applying AI/ML methods to lead optimization and lead-to-candidate (L2C) decision-making has shown slower progress, especially regarding predicting absorption, distribution, metabolism, excretion, and toxicology properties. The present review surveys reasons why this is so, reports progress that has occurred in recent years, and summarizes some of the issues that remain. Effective AI/ML tools to derisk L2C and later phases of development are important to accelerate the pharmaceutical development process, ameliorate escalating development costs, and achieve greater success rates.
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Affiliation(s)
- Douglas McNair
- Global Health, Integrated Development, Bill & Melinda Gates Foundation, Seattle, Washington, USA;
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6
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Matias M, Santos AO, Silvestre S, Alves G. Fighting Epilepsy with Nanomedicines-Is This the Right Weapon? Pharmaceutics 2023; 15:pharmaceutics15020306. [PMID: 36839629 PMCID: PMC9959131 DOI: 10.3390/pharmaceutics15020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Epilepsy is a chronic and complex condition and is one of the most common neurological diseases, affecting about 50 million people worldwide. Pharmacological therapy has been, and is likely to remain, the main treatment approach for this disease. Although a large number of new antiseizure drugs (ASDs) has been introduced into the market in the last few years, many patients suffer from uncontrolled seizures, demanding the development of more effective therapies. Nanomedicines have emerged as a promising approach to deliver drugs to the brain, potentiating their therapeutic index. Moreover, nanomedicine has applied the knowledge of nanoscience, not only in disease treatment but also in prevention and diagnosis. In the current review, the general features and therapeutic management of epilepsy will be addressed, as well as the main barriers to overcome to obtain better antiseizure therapies. Furthermore, the role of nanomedicines as a valuable tool to selectively deliver drugs will be discussed, considering the ability of nanocarriers to deal with the less favourable physical-chemical properties of some ASDs, enhance their brain penetration, reduce the adverse effects, and circumvent the concerning drug resistance.
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Affiliation(s)
- Mariana Matias
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- Correspondence: (M.M.); (A.O.S.); Tel.: +351-275-329-002 (M.M.); +351-275-329-079 (A.O.S.)
| | - Adriana O. Santos
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- Correspondence: (M.M.); (A.O.S.); Tel.: +351-275-329-002 (M.M.); +351-275-329-079 (A.O.S.)
| | - Samuel Silvestre
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
- CNC—Centre for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Gilberto Alves
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
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7
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Candito DA, Simov V, Gulati A, Kattar S, Chau RW, Lapointe BT, Methot JL, DeMong DE, Graham TH, Kurukulasuriya R, Keylor MH, Tong L, Morriello GJ, Acton JJ, Pio B, Liu W, Scott JD, Ardolino MJ, Martinot TA, Maddess ML, Yan X, Gunaydin H, Palte RL, McMinn SE, Nogle L, Yu H, Minnihan EC, Lesburg CA, Liu P, Su J, Hegde LG, Moy LY, Woodhouse JD, Faltus R, Xiong T, Ciaccio P, Piesvaux JA, Otte KM, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Neelamkavil S, Wood HB, Fuller PH, Ellis JM. Discovery and Optimization of Potent, Selective, and Brain-Penetrant 1-Heteroaryl-1 H-Indazole LRRK2 Kinase Inhibitors for the Treatment of Parkinson's Disease. J Med Chem 2022; 65:16801-16817. [PMID: 36475697 DOI: 10.1021/acs.jmedchem.2c01605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of leucine-rich repeat kinase 2 (LRRK2) kinase activity represents a genetically supported, chemically tractable, and potentially disease-modifying mechanism to treat Parkinson's disease. Herein, we describe the optimization of a novel series of potent, selective, central nervous system (CNS)-penetrant 1-heteroaryl-1H-indazole type I (ATP competitive) LRRK2 inhibitors. Type I ATP-competitive kinase physicochemical properties were integrated with CNS drug-like properties through a combination of structure-based drug design and parallel medicinal chemistry enabled by sp3-sp2 cross-coupling technologies. This resulted in the discovery of a unique sp3-rich spirocarbonitrile motif that imparted extraordinary potency, pharmacokinetics, and favorable CNS drug-like properties. The lead compound, 25, demonstrated exceptional on-target potency in human peripheral blood mononuclear cells, excellent off-target kinase selectivity, and good brain exposure in rat, culminating in a low projected human dose and a pre-clinical safety profile that warranted advancement toward pre-clinical candidate enabling studies.
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Affiliation(s)
- David A Candito
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Solomon Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ryan W Chau
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Blair T Lapointe
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Joey L Methot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Duane E DeMong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Thomas H Graham
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ravi Kurukulasuriya
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ling Tong
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Weiguo Liu
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Jack D Scott
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Theodore A Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew L Maddess
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hakan Gunaydin
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Hongshi Yu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ellen C Minnihan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Paul Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Jennifer A Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey07033, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
| | - J Michael Ellis
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts02115, United States
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8
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Kim MC, Lee YJ. Analysis of Time-Dependent Pharmacokinetics Using In Vitro-In Vivo Extrapolation and Physiologically Based Pharmacokinetic Modeling. Pharmaceutics 2022; 14:pharmaceutics14122562. [PMID: 36559055 PMCID: PMC9780873 DOI: 10.3390/pharmaceutics14122562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022] Open
Abstract
SCR430, a sorafenib derivative, is an investigational drug exhibiting anti-tumor action. This study aimed to have a mechanistic understanding of SCR430's time-dependent pharmacokinetics (TDPK) through an ex vivo study combined with an in vitro-in vivo extrapolation (IVIVE) and physiologically based pharmacokinetic (PBPK) modeling. A non-compartmental pharmacokinetic analysis was performed after intravenous SCR430 administration in female Sprague-Dawley rats for a control group (no treatment), a vehicle group (vehicle only, 14 days, PO), and a repeated-dosing group (SCR430, 30 mg/kg/day, 14 days, PO). In addition, hepatic uptake and metabolism modulation were investigated using isolated hepatocytes from each group of rats. The minimal PBPK model based on IVIVE was constructed to explain SCR430's TDPK. Repeated SCR430 administration decreased the systemic exposure by 4.4-fold, which was explained by increased hepatic clearance (4.7-fold). The ex vivo study using isolated hepatocytes from each group suggested that the increased hepatic uptake (9.4-fold), not the metabolic activity, contributes to the increased hepatic clearance. The minimal PBPK modeling based on an ex vivo study could explain the decreased plasma levels after the repeated doses. The current study demonstrates the TDPK after repeated dosing by hepatic uptake induction, not hepatic metabolism, as well as the effectiveness of an ex vivo approach combined with IVIVE and PBPK modeling to investigate the TDPK.
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Affiliation(s)
- Min-Chang Kim
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemungu, Seoul 02453, Republic of Korea
- Division of Biopharmaceutics, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Young-Joo Lee
- Division of Biopharmaceutics, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Integrated Drug Development and Natural Products, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
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9
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 37118182 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 360] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations. ![]()
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J V Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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10
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Hopkins BT, Bame E, Bell N, Bohnert T, Bowden-Verhoek JK, Bui M, Cancilla MT, Conlon P, Cullen P, Erlanson DA, Fan J, Fuchs-Knotts T, Hansen S, Heumann S, Jenkins TJ, Gua C, Liu Y, Liu Y, Lulla M, Marcotte D, Marx I, McDowell B, Mertsching E, Negrou E, Romanowski MJ, Scott D, Silvian L, Yang W, Zhong M. Utilizing structure based drug design and metabolic soft spot identification to optimize the in vitro potency and in vivo pharmacokinetic properties leading to the discovery of novel reversible Bruton's tyrosine kinase inhibitors. Bioorg Med Chem 2021; 44:116275. [PMID: 34314938 DOI: 10.1016/j.bmc.2021.116275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
Bruton's tyrosine kinase (BTK) is an essential node on the BCR signaling in B cells, which are clinically validated to play a critical role in B-cell lymphomas and various auto-immune diseases such as Multiple Sclerosis (MS), Pemphigus, and rheumatoid arthritis (RA). Although non-selective irreversible BTK inhibitors have been approved for oncology, due to the emergence of drug resistance in B-cell lymphoma associated with covalent inhibitor, there an unmet medical need to identify reversible, selective, potent BTK inhibitor as viable therapeutics for patients. Herein, we describe the identification of Hits and subsequence optimization to improve the physicochemical properties, potency and kinome selectivity leading to the discovery of a novel class of BTK inhibitors. Utilizing Met ID and structure base design inhibitors were synthesized with increased in vivo metabolic stability and oral exposure in rodents suitable for advancing to lead optimization.
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Affiliation(s)
| | - Eris Bame
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Noah Bell
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Tonika Bohnert
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | | | - Minna Bui
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Mark T Cancilla
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Patrick Conlon
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Patrick Cullen
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Junfa Fan
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Tarra Fuchs-Knotts
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Stig Hansen
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Stacey Heumann
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | | | - Chuck Gua
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Ying Liu
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - YuTing Liu
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Mukush Lulla
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | | | - Isaac Marx
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Bob McDowell
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | | | - Ella Negrou
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Michael J Romanowski
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Daniel Scott
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Laura Silvian
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, USA
| | - Wenjin Yang
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | - Min Zhong
- Sunesis Pharmaceuticals, Inc. 395 Oyster Point Boulevard, South San Francisco, CA 94080, USA
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11
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Gulati A, Yeung CS, Lapointe B, Kattar SD, Gunaydin H, Scott JD, Childers KK, Methot JL, Simov V, Kurukulasuriya R, Pio B, Morriello GJ, Liu P, Tang H, Neelamkavil S, Wood HB, Rada VL, Ardolino MJ, Yan XC, Palte R, Otte K, Faltus R, Woodhouse J, Hegde LG, Ciaccio P, Minnihan EC, DiMauro EF, Fell MJ, Fuller PH, Ellis JM. Optimization of brain-penetrant picolinamide derived leucine-rich repeat kinase 2 (LRRK2) inhibitors. RSC Med Chem 2021; 12:1164-1173. [PMID: 34355182 DOI: 10.1039/d1md00097g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
The discovery of potent, kinome selective, brain penetrant LRRK2 inhibitors is the focus of extensive research seeking new, disease-modifying treatments for Parkinson's disease (PD). Herein, we describe the discovery and evolution of a picolinamide-derived lead series. Our initial optimization efforts aimed at improving the potency and CLK2 off-target selectivity of compound 1 by modifying the heteroaryl C-H hinge and linker regions. This resulted in compound 12 which advanced deep into our research operating plan (ROP) before heteroaryl aniline metabolite 14 was characterized as Ames mutagenic, halting its progression. Strategic modifications to our ROP were made to enable early de-risking of putative aniline metabolites or hydrolysis products for mutagenicity in Ames. This led to the discovery of 3,5-diaminopyridine 15 and 4,6-diaminopyrimidine 16 as low risk for mutagenicity (defined by a 3-strain Ames negative result). Analysis of key matched molecular pairs 17 and 18 led to the prioritization of the 3,5-diaminopyridine sub-series for further optimization due to enhanced rodent brain penetration. These efforts culminated in the discovery of ethyl trifluoromethyl pyrazole 23 with excellent LRRK2 potency and expanded selectivity versus off-target CLK2.
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Affiliation(s)
- Anmol Gulati
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Charles S Yeung
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Blair Lapointe
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Solomon D Kattar
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Hakan Gunaydin
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Jack D Scott
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Kaleen K Childers
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Joey L Methot
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Vladimir Simov
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Ravi Kurukulasuriya
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Barbara Pio
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Greg J Morriello
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Ping Liu
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Haiqun Tang
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | | | - Harold B Wood
- Merck & Co., Inc. 2015 Galloping Hill Road Kenilworth New Jersey 07033 USA
| | - Vanessa L Rada
- Merck & Co., Inc. 770 Sumneytown Pike West Point Pennsylvania 19486 USA
| | - Michael J Ardolino
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Xin Cindy Yan
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Rachel Palte
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Karin Otte
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Robert Faltus
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Janice Woodhouse
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Laxminarayan G Hegde
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Paul Ciaccio
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Ellen C Minnihan
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Erin F DiMauro
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Matthew J Fell
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - Peter H Fuller
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
| | - J Michael Ellis
- Merck & Co., Inc. 33 Avenue Louis Pasteur Boston Massachusetts 02115 USA +1 617 992 2472 +1 617 992 3113
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12
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Pennington LD, Muegge I. Holistic drug design for multiparameter optimization in modern small molecule drug discovery. Bioorg Med Chem Lett 2021; 41:128003. [DOI: 10.1016/j.bmcl.2021.128003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 01/28/2023]
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13
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Benet LZ, Sodhi JK, Makrygiorgos G, Mesbah A. There is Only One Valid Definition of Clearance: Critical Examination of Clearance Concepts Reveals the Potential for Errors in Clinical Drug Dosing Decisions. AAPS JOURNAL 2021; 23:67. [PMID: 33973074 PMCID: PMC8110503 DOI: 10.1208/s12248-021-00591-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 04/07/2021] [Indexed: 11/30/2022]
Abstract
Drug dosing decisions in clinical medicine and in introducing a drug to market for the past 60 years are based on the pharmacokinetic/clinical pharmacology concept of clearance. We used chemical reaction engineering models to demonstrate the limitations of presently employed clearance measurements based upon systemic blood concentration in reflecting organ clearance. The belief for the last 49 years that in vivo clearance is independent of the mechanistic model for organ clearance is incorrect. There is only one valid definition of clearance. Defining organ clearance solely on the basis of systemic blood concentrations can lead to drug dosing errors when drug effect sites reside either in an eliminating organ exhibiting incremental clearance or in a non-eliminating organ where intraorgan concentration is governed by transporter actions. Attempts to predict clearance are presently hampered by the lack of recognition that what we are trying to predict is a well-stirred model clearance.
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Affiliation(s)
- Leslie Z Benet
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, California, 94143-0912, USA.
| | - Jasleen K Sodhi
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, California, 94143-0912, USA
| | - George Makrygiorgos
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, 94720-1462, USA
| | - Ali Mesbah
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, 94720-1462, USA.
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14
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Chen EP, Bondi RW, Michalski PJ. Model-based Target Pharmacology Assessment (mTPA): An Approach Using PBPK/PD Modeling and Machine Learning to Design Medicinal Chemistry and DMPK Strategies in Early Drug Discovery. J Med Chem 2021; 64:3185-3196. [PMID: 33719432 DOI: 10.1021/acs.jmedchem.0c02033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The optimal pharmacokinetic (PK) required for a drug candidate to elicit efficacy is highly dependent on the targeted pharmacology, a relationship that is often not well characterized during early phases of drug discovery. Generic assumptions around PK and potency risk misguiding screening and compound design toward nonoptimal absorption, distribution, metabolism, and excretion (ADME) or molecular properties and ultimately may increase attrition as well as hit-to-lead and lead optimization timelines. The present work introduces model-based target pharmacology assessment (mTPA), a computational approach combining physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) modeling, sensitivity analysis, and machine learning (ML) to elucidate the optimal combination of PK, potency, and ADME specific for the targeted pharmacology. Examples using frequently encountered PK/PD relationships are presented to illustrate its application, and the utility and benefits of deploying such an approach to guide early discovery efforts are discussed.
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Affiliation(s)
- Emile P Chen
- Systems Modeling and Translational Biology, Computational Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Robert W Bondi
- Systems Modeling and Translational Biology, Computational Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Paul J Michalski
- Systems Modeling and Translational Biology, Computational Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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15
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16
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Benet LZ, Sodhi JK. Investigating the Theoretical Basis for In Vitro-In Vivo Extrapolation (IVIVE) in Predicting Drug Metabolic Clearance and Proposing Future Experimental Pathways. AAPS JOURNAL 2020; 22:120. [PMID: 32914238 DOI: 10.1208/s12248-020-00501-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/13/2020] [Indexed: 02/04/2023]
Abstract
Extensive studies have been conducted to predict in vivo metabolic clearance from in vitro human liver metabolism parameters (i.e., in vitro-in vivo extrapolation (IVIVE)) with little success. Here, deriving IVIVE from first principles, we show that the product of fraction unbound in the blood and the predicted in vivo intrinsic clearance determined from hepatocyte or microsomal incubations is the lower boundary condition for in vivo hepatic clearance and the prerequisite for IVIVE predictions to be valid, regardless of extraction ratio. For 60-80% of drugs evaluated here, this product is markedly less than the in vivo measured clearance, a result that violates the lower boundary of the predictive relationship. This can only be explained by (a) suboptimal in vitro metabolic stability assay conditions, (b) significant error in the assumption that in vitro intrinsic clearance determinations will predict in vivo intrinsic clearance simply by scaling-up the amount of enzyme (in vitro incubation to in vivo liver), and/or (c) the methods of determining fraction unbound are incorrect. We further suggest that widely employed organ blood flow values underpredict the effective blood flow within the organ by approximately 2.5-fold, thus impacting IVIVE of high clearance compounds. We propose future pathways that should be investigated in terms of the relationship to experimentally measured clearance values, rather than model-dependent intrinsic clearance. IVIVE outcome can be improved by estimating the ratio of unbound drug concentration in the liver tissue to the liver plasma, examining the assumption of the free drug theory (i.e., there are no transporter effects at the blood cell membrane) and the finding that the upper limit of organ clearance may be greater than blood flow entering the organ.
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Affiliation(s)
- Leslie Z Benet
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, 513 Parnassus Ave Rm HSE 1164, UCSF Box 0912, San Francisco, California, 94143, USA.
| | - Jasleen K Sodhi
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, 513 Parnassus Ave Rm HSE 1164, UCSF Box 0912, San Francisco, California, 94143, USA
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17
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Lombardo F, Bentzien J, Berellini G, Muegge I. In Silico Models of Human PK Parameters. Prediction of Volume of Distribution Using an Extensive Data Set and a Reduced Number of Parameters. J Pharm Sci 2020; 110:500-509. [PMID: 32891631 DOI: 10.1016/j.xphs.2020.08.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022]
Abstract
A novel, descriptor-parsimonious in silico model to predict human VDss (volume of distribution at steady-state) has been derived and thoroughly tested in a quasi-prospective regimen using an independent test set of 213 compounds. The model performs on par with a former benchmark model that relied on far more descriptors. As a result, the new random forest model relying on only six descriptors allows for interpretations that help chemists to design compounds with desired human VDss values. A comparison of in silico predictions of VDss with models using in vitro derived descriptors or in vivo scaling methods supports the strength of the in-silico approach, considering its resource- and animal-sparing nature. The strong performance of the in silico VDss models on structurally novel compounds supports the high degree of confidence that can be placed in using in silico human VDss predictions for compound design and human dose predictions.
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Affiliation(s)
- Franco Lombardo
- Drug Metabolism and Bioanalysis Group, Alkermes Inc, Waltham, MA 02451, USA.
| | - Jörg Bentzien
- Modeling and Informatics Group, Alkermes Inc, Waltham, MA 02451, USA
| | - Giuliano Berellini
- Drug Metabolism and Bioanalysis Group, Alkermes Inc, Waltham, MA 02451, USA
| | - Ingo Muegge
- Modeling and Informatics Group, Alkermes Inc, Waltham, MA 02451, USA
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18
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Wernevik J, Bergström F, Novén A, Hulthe J, Fredlund L, Addison D, Holmgren J, Strömstedt PE, Rehnström E, Lundbäck T. A Fully Integrated Assay Panel for Early Drug Metabolism and Pharmacokinetics Profiling. Assay Drug Dev Technol 2020; 18:157-179. [PMID: 32407132 PMCID: PMC7567642 DOI: 10.1089/adt.2020.970] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Evaluation and optimization of physicochemical and metabolic properties of compounds are a crucial component of the drug development process. Continuous access to this information during the design-make-test-analysis cycle enables identification of chemical entities with suitable properties for efficient project progression. In this study, we describe an integrated and automated assay panel (DMPK Wave 1) that informs weekly on lipophilicity, solubility, human plasma protein binding, and metabolic stability in rat hepatocytes and human liver microsomes. All assays are running in 96-well format with ultraperformance liquid chromatography-mass spectrometry (MS)/MS as read-out. A streamlined overall workflow has been developed by optimizing all parts of the process, including shipping of compounds between sites, use of fit-for-purpose equipment and information systems, and technology for compound requesting, data analysis, and reporting. As a result, lead times can be achieved that well match project demands across sites independently of where compounds are synthesized. This robust screening strategy is run on a weekly basis and enables optimization of structure-activity relationships in parallel with DMPK properties to allow efficient and informed decision making.
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Affiliation(s)
- Johan Wernevik
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Bergström
- DMPK, Early CVRM, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Novén
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Hulthe
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Fredlund
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Dan Addison
- Sample Management, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Jan Holmgren
- Sample Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Erika Rehnström
- Clinical Sampling & Alliances, Precision Medicine, AstraZeneca, Gothenburg, Sweden
| | - Thomas Lundbäck
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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19
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Walker PA, Ryder S, Lavado A, Dilworth C, Riley RJ. The evolution of strategies to minimise the risk of human drug-induced liver injury (DILI) in drug discovery and development. Arch Toxicol 2020; 94:2559-2585. [PMID: 32372214 PMCID: PMC7395068 DOI: 10.1007/s00204-020-02763-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/22/2020] [Indexed: 12/15/2022]
Abstract
Early identification of toxicity associated with new chemical entities (NCEs) is critical in preventing late-stage drug development attrition. Liver injury remains a leading cause of drug failures in clinical trials and post-approval withdrawals reflecting the poor translation between traditional preclinical animal models and human clinical outcomes. For this reason, preclinical strategies have evolved over recent years to incorporate more sophisticated human in vitro cell-based models with multi-parametric endpoints. This review aims to highlight the evolution of the strategies adopted to improve human hepatotoxicity prediction in drug discovery and compares/contrasts these with recent activities in our lab. The key role of human exposure and hepatic drug uptake transporters (e.g. OATPs, OAT2) is also elaborated.
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Affiliation(s)
- Paul A Walker
- Cyprotex Discovery Ltd., No.24 Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
| | - Stephanie Ryder
- Cyprotex Discovery Ltd., No.24 Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Andrea Lavado
- Cyprotex Discovery Ltd., No.24 Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Clive Dilworth
- Cyprotex Discovery Ltd., No.24 Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.,Alderley Park Accelerator, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Robert J Riley
- Cyprotex Discovery Ltd., No.24 Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
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20
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Colón-Lorenzo EE, Colón-López DD, Vega-Rodríguez J, Dupin A, Fidock DA, Baerga-Ortiz A, Ortiz JG, Bosch J, Serrano AE. Structure-Based Screening of Plasmodium berghei Glutathione S-Transferase Identifies CB-27 as a Novel Antiplasmodial Compound. Front Pharmacol 2020; 11:246. [PMID: 32256353 PMCID: PMC7090221 DOI: 10.3389/fphar.2020.00246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/24/2020] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum parasites are increasingly drug-resistant, requiring the search for novel antimalarials with distinct modes of action. Enzymes in the glutathione pathway, including glutathione S-transferase (GST), show promise as novel antimalarial targets. This study aims to better understand the biological function of Plasmodium GST, assess its potential as a drug target, and identify novel antiplasmodial compounds using the rodent model P. berghei. By using reverse genetics, we provided evidence that GST is essential for survival of P. berghei intra-erythrocytic stages and is a valid target for drug development. A structural model of the P. berghei glutathione S-transferase (PbGST) protein was generated and used in a structure-based screening of 900,000 compounds from the ChemBridge Hit2Lead library. Forty compounds were identified as potential inhibitors and analyzed in parasite in vitro drug susceptibility assays. One compound, CB-27, exhibited antiplasmodial activity with an EC50 of 0.5 μM toward P. berghei and 0.9 μM toward P. falciparum multidrug-resistant Dd2 clone B2 parasites. Moreover, CB-27 showed a concentration-dependent inhibition of the PbGST enzyme without inhibiting the human ortholog. A shape similarity screening using CB-27 as query resulted in the identification of 24 novel chemical scaffolds, with six of them showing antiplasmodial activity ranging from EC50 of 0.6-4.9 μM. Pharmacokinetic and toxicity predictions suggest that the lead compounds have drug-likeness properties. The antiplasmodial potency, the absence of hemolytic activity, and the predicted drug-likeness properties position these compounds for lead optimization and further development as antimalarials.
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Affiliation(s)
- Emilee E. Colón-Lorenzo
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, PR, United States
| | - Daisy D. Colón-López
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Joel Vega-Rodríguez
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, PR, United States
| | - Alice Dupin
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, United States
| | - Abel Baerga-Ortiz
- Department of Biochemistry, University of Puerto Rico School of Medicine, San Juan, PR, United States
| | - José G. Ortiz
- Department of Pharmacology and Toxicology, University of Puerto Rico School of Medicine, San Juan, PR, United States
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Division of Pediatric Pulmonology and Allergy/Immunology, Case Western Reserve University, Cleveland, OH, United States
- InterRayBio, LLC, Baltimore, MD, United States
| | - Adelfa E. Serrano
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, San Juan, PR, United States
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21
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Peters SA, Petersson C, Blaukat A, Halle JP, Dolgos H. Prediction of active human dose: learnings from 20 years of Merck KGaA experience, illustrated by case studies. Drug Discov Today 2020; 25:909-919. [PMID: 31981792 DOI: 10.1016/j.drudis.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/24/2019] [Accepted: 01/15/2020] [Indexed: 12/12/2022]
Abstract
High-quality dose predictions based on a good understanding of target engagement is one of the main translational goals in drug development. Here, we systematically evaluate active human dose predictions for 15 Merck KGaA/EMD Serono assets spanning several modalities and therapeutic areas. Using case studies, we illustrate the value of adhering to the translational best practices of having an exposure-response relationship in an appropriate animal model; having validated, translatable pharmacodynamic (PD) biomarkers measurable in Phase I populations in the right tissue; having a deeper understanding of biology; and capturing uncertainties in predictions. Given the gap in publications on the subject, we believe that the learnings from this unique diverse data set, which are generic to the industry, will trigger actions to improve future predictions.
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Affiliation(s)
- Sheila Annie Peters
- Translational Quantitative Pharmacology, Translational Medicine, Biopharma, Global R&D, Merck Healthcare, Frankfurter Str. 250, 64293 Darmstadt, Germany.
| | - Carl Petersson
- Drug Metabolism and Disposition, Discovery Technology, Biopharma, Global R&D, Merck Healthcare, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Andree Blaukat
- Translational Innovation Platform Oncology, Biopharma, Global R&D, Merck Healthcare, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Joern-Peter Halle
- Translational Innovation Platform Immuno Oncology, Biopharma, Global R&D, Merck Healthcare, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Hugues Dolgos
- Biopharmacy Center of Excellence, Servier RD, Suresnes, 92150, France
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22
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Patel D, Yang W, Lipert M, Wu T. Application and Impact of Human Dose Projection from Discovery to Early Drug Development. AAPS PharmSciTech 2020; 21:44. [PMID: 31897807 DOI: 10.1208/s12249-019-1598-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/01/2019] [Indexed: 12/31/2022] Open
Abstract
The application and impact of human dose projection (HDP) has been well recognized in the late drug development phase, with increasing appreciation earlier during discovery and early development. This commentary describes the perspective of pharmaceutical scientists on the evolving application and impact of HDP at various phases from discovery to early development, including lead generation, lead optimization, lead up to candidate nomination, and early drug development. The underlying fundamental concepts and key input parameters for HDP are briefly discussed. A broad overview of phase-specific tools and approaches commonly utilized for human dose projection in the pharmaceutical industry is provided. A discussion of phase-appropriate implementation strategies, associated limitations/assumptions and continuous refinement for HDP from discovery to early development is presented. The authors describe the phase-specific applications of human dose projection to facilitate key assessments and relative impact on decision points.
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23
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Lucas AJ, Sproston JL, Barton P, Riley RJ. Estimating human ADME properties, pharmacokinetic parameters and likely clinical dose in drug discovery. Expert Opin Drug Discov 2019; 14:1313-1327. [DOI: 10.1080/17460441.2019.1660642] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Adam J. Lucas
- Drug Metabolism and Pharmacokinetics, Evotec, Abingdon, UK
| | | | - Patrick Barton
- Drug Metabolism and Pharmacokinetics, Evotec, Abingdon, UK
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24
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Winiwarter S, Chang G, Desai P, Menzel K, Faller B, Arimoto R, Keefer C, Broccatell F. Prediction of Fraction Unbound in Microsomal and Hepatocyte Incubations: A Comparison of Methods across Industry Datasets. Mol Pharm 2019; 16:4077-4085. [PMID: 31348668 DOI: 10.1021/acs.molpharmaceut.9b00525] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fraction unbound in the incubation, fu,inc, is an important parameter to consider in the evaluation of intrinsic clearance measurements performed in vitro in hepatocytes or microsomes. Reliable estimates of fu,inc based on a compound's structure have the potential to positively impact the screening timelines in drug discovery. Previous works suggested that fu,inc is primarily driven by passive processes and can be described using physicochemical properties such as lipophilicity and the protonation state of the molecule. While models based on these principles proved predictive in relatively small datasets that included marketed drugs, their applicability domain has not been extensively explored. The work presented here from the in silico ADME discussion group (part of the International Consortium for Innovation through Quality in Pharmaceutical Development, the IQ consortium) describes the accuracy of these models in large proprietary datasets that include several thousand of compounds across chemical space. Overall, the models do well for compounds with low lipophilicity. In other words, the equations correctly predict that fu,inc is, in general, above 0.5 for compounds with a calculated logP of less than 3. When applied to lipophilic compounds, the models failed to produce quantitatively accurate predictions of fu,inc, with a high risk of underestimating binding properties. These models can, therefore, be used quantitatively for less lipophilic compounds. On the other hand, internal machine-learning models using a company's own proprietary dataset also predict compounds with higher lipophilicity reasonably well. Additionally, the data shown indicate that microsomal binding is, in general, a good proxy for hepatocyte binding.
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Affiliation(s)
- Susanne Winiwarter
- DMPK, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D , AstraZeneca , Gothenburg SE-43183 , Sweden
| | - George Chang
- Pfizer Inc. , Groton , Connecticut 06340 , United States
| | - Prashant Desai
- Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | | | - Rieko Arimoto
- Vertex Pharmaceuticals Inc. , Boston , Massachusetts 02210 , United States
| | | | - Fabio Broccatell
- Genentech Inc. , South San Francisco , California 94080 , United States
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25
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von Berg S, Xue Y, Collins M, Llinas A, Olsson RI, Halvarsson T, Lindskog M, Malmberg J, Jirholt J, Krutrök N, Ramnegård M, Brännström M, Lundqvist A, Lepistö M, Aagaard A, McPheat J, Hansson EL, Chen R, Xiong Y, Hansson TG, Narjes F. Discovery of Potent and Orally Bioavailable Inverse Agonists of the Retinoic Acid Receptor-Related Orphan Receptor C2. ACS Med Chem Lett 2019; 10:972-977. [PMID: 31223457 DOI: 10.1021/acsmedchemlett.9b00158] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022] Open
Abstract
The further optimization of a recently disclosed series of inverse agonists of the nuclear receptor RORC2 is described. Investigations into the left-hand side of compound 1, guided by X-ray crystal structures, led to the substitution of the 4-aryl-thiophenyl residue with the hexafluoro-2-phenyl-propan-2-ol moiety. This change resulted in to compound 28, which combined improved drug-like properties with good cell potency and a significantly lower dose, using an early dose to man prediction. Target engagement in vivo was demonstrated in the thymus of mice by a reduction in the number of double positive T cells after oral dosing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rongfeng Chen
- Pharmaron Beijing Co., Ltd., Taihe Road BDA, Beijing 100176, P. R. China
| | - Yao Xiong
- Pharmaron Beijing Co., Ltd., Taihe Road BDA, Beijing 100176, P. R. China
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26
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Bhhatarai B, Walters WP, Hop CECA, Lanza G, Ekins S. Opportunities and challenges using artificial intelligence in ADME/Tox. NATURE MATERIALS 2019; 18:418-422. [PMID: 31000801 PMCID: PMC6594826 DOI: 10.1038/s41563-019-0332-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A recent conference organized a panel of scientists representing small and big pharma companies, who work at the interface of machine learning (ML) and absorption, distribution, metabolism, excretion, and toxicology (ADME/Tox). With the recent rebirth of AI related to pharma, it is timely to present this collaborative commentary to capture the diverging opinions on the past, present and future role of AI for ADME/Tox and how it can be applied in newer areas such as nanomaterials.
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Affiliation(s)
- Barun Bhhatarai
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | | | - Sean Ekins
- Collaborations Pharmaceuticals Inc., Raleigh, NC, USA.
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27
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Bergström F, Lindmark B. Accelerated drug discovery by rapid candidate drug identification. Drug Discov Today 2019; 24:1237-1241. [PMID: 30946980 DOI: 10.1016/j.drudis.2019.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/01/2019] [Accepted: 03/28/2019] [Indexed: 01/20/2023]
Abstract
The eventual candidate drug (CD) is often already synthesized during early drug discovery but not nominated until much later. To facilitate the rapid identification of a potential CD, a thoroughly worked-out CD target profile (CDTP) with criteria acceptable for the disease target product profile (TPP) is required at the start of lead generation (LG). In addition to driving the compound property optimization, the preclinical project team has to understand the ultimate goal to be able to rapidly identify and progress a potential CD. A screening cascade with meaningful and well-balanced progression criteria based on the CDTP is required to rapidly filter out unwanted compounds and to progress a potential CD through the cascade to candidate selection.
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Affiliation(s)
- Fredrik Bergström
- Drug Metabolism and Pharmacokinetics, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
| | - Bo Lindmark
- Drug Metabolism and Pharmacokinetics, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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28
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Lemurell M, Ulander J, Emtenäs H, Winiwarter S, Broddefalk J, Swanson M, Hayes MA, Prieto Garcia L, Westin Eriksson A, Meuller J, Cassel J, Saarinen G, Yuan ZQ, Löfberg C, Karlsson S, Sundqvist M, Whatling C. Novel Chemical Series of 5-Lipoxygenase-Activating Protein Inhibitors for Treatment of Coronary Artery Disease. J Med Chem 2019; 62:4325-4349. [DOI: 10.1021/acs.jmedchem.8b02012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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29
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30
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Granberg KL, Yuan ZQ, Lindmark B, Edman K, Kajanus J, Hogner A, Malmgren M, O’Mahony G, Nordqvist A, Lindberg J, Tångefjord S, Kossenjans M, Löfberg C, Brånalt J, Liu D, Selmi N, Nikitidis G, Nordberg P, Hayen A, Aagaard A, Hansson E, Hermansson M, Ivarsson I, Jansson-Löfmark R, Karlsson U, Johansson U, William-Olsson L, Hartleib-Geschwindner J, Bamberg K. Identification of Mineralocorticoid Receptor Modulators with Low Impact on Electrolyte Homeostasis but Maintained Organ Protection. J Med Chem 2018; 62:1385-1406. [DOI: 10.1021/acs.jmedchem.8b01523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dongmei Liu
- Pharmaron Beijing Co., Ltd., No. 6 Taihe Road, BDA, Beijing 100176, P. R. China
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31
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Panteleev J, Gao H, Jia L. Recent applications of machine learning in medicinal chemistry. Bioorg Med Chem Lett 2018; 28:2807-2815. [PMID: 30122222 DOI: 10.1016/j.bmcl.2018.06.046] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/24/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
In recent decades, artificial intelligence and machine learning have played a significant role in increasing the efficiency of processes across a wide spectrum of industries. When it comes to the pharmaceutical and biotechnology sectors, numerous tools enabled by advancement of computer science have been developed and are now routinely utilized. However, there are many aspects of the drug discovery process, which can further benefit from refinement of computational methods and tools, as well as improvement of accessibility of these new technologies. In this review, examples of recent developments in machine learning application are described, which have the potential to impact different parts of the drug discovery and development flow scheme. Notably, new deep learning-based approaches across compound design and synthesis, prediction of binding, activity and ADMET properties, as well as applications of genetic algorithms are highlighted.
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Affiliation(s)
- Jane Panteleev
- Amgen Discovery Research, 360 Binney St., Cambridge, MA 02141, USA
| | - Hua Gao
- Amgen Discovery Research, 360 Binney St., Cambridge, MA 02141, USA
| | - Lei Jia
- Amgen Discovery Research, One Amgen Center Dr., Thousand Oaks, CA 91320, USA.
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32
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Gunaydin H, Altman MD, Ellis JM, Fuller P, Johnson SA, Lahue B, Lapointe B. Strategy for Extending Half-life in Drug Design and Its Significance. ACS Med Chem Lett 2018; 9:528-533. [PMID: 29937977 DOI: 10.1021/acsmedchemlett.8b00018] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/02/2018] [Indexed: 01/22/2023] Open
Abstract
Preclinical optimization of compounds toward viable drug candidates requires an integrated understanding of properties that impact predictions of the clinically efficacious dose. The importance of optimizing half-life, unbound clearance, and potency and how they impact dose predictions are discussed in this letter. Modest half-life improvements for short half-life compounds can dramatically lower the efficacious dose. The relationship between dose and half-life is nonlinear when unbound clearance is kept constant, whereas the relationship between dose and unbound clearance is linear when half-life is kept constant. Due to this difference, we show that dose is more sensitive to changes in half-life than changes in unbound clearance when half-lives are shorter than 2 h. Through matched molecular pair analyses, we also show that the strategic introduction of halogens is likely to increase half-life and lower projected human dose even though increased lipophilicity does not guarantee extended half-life.
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33
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Pike KG, Barlaam B, Cadogan E, Campbell A, Chen Y, Colclough N, Davies NL, de-Almeida C, Degorce SL, Didelot M, Dishington A, Ducray R, Durant ST, Hassall LA, Holmes J, Hughes GD, MacFaul PA, Mulholland KR, McGuire TM, Ouvry G, Pass M, Robb G, Stratton N, Wang Z, Wilson J, Zhai B, Zhao K, Al-Huniti N. The Identification of Potent, Selective, and Orally Available Inhibitors of Ataxia Telangiectasia Mutated (ATM) Kinase: The Discovery of AZD0156 (8-{6-[3-(Dimethylamino)propoxy]pyridin-3-yl}-3-methyl-1-(tetrahydro-2H-pyran-4-yl)-1,3-dihydro-2H-imidazo[4,5-c]quinolin-2-one). J Med Chem 2018; 61:3823-3841. [DOI: 10.1021/acs.jmedchem.7b01896] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kurt G. Pike
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Bernard Barlaam
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Elaine Cadogan
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Andrew Campbell
- Pharmaceutical Sciences, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | - Yingxue Chen
- Oncology, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nicola Colclough
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Nichola L. Davies
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Camila de-Almeida
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Sebastien L. Degorce
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Myriam Didelot
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Allan Dishington
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Richard Ducray
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Stephen T. Durant
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Lorraine A. Hassall
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Jane Holmes
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Gareth D. Hughes
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Philip A. MacFaul
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Keith R. Mulholland
- Chemical Development, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | - Thomas M. McGuire
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Gilles Ouvry
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Martin Pass
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Graeme Robb
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Natalie Stratton
- Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Zhenhua Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Joanne Wilson
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Baochang Zhai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Kang Zhao
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Nidal Al-Huniti
- Oncology, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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Wenlock MC. Oral drug suitability parameters. MEDCHEMCOMM 2018; 9:460-470. [PMID: 30108936 PMCID: PMC6072407 DOI: 10.1039/c7md00586e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/09/2018] [Indexed: 11/21/2022]
Abstract
Assessing the oral drug suitability of compounds as early as possible within drug discovery is an important objective. This study describes a methodology that attempts to simplify the evaluation of compounds based on their in vivo quantity levels within a mammalian body, represented using a mathematical model that imposes a time limitation on oral absorption and assumes non-instantaneous drug distribution between plasma and tissue. This simplification results in two new oral drug suitability parameters that can quantitatively relate oral dose to in vivo exposure for compounds with vastly different tendencies in terms of absorption into, and elimination from, the body. Consequently, the complexities associated with evaluating a compound's oral drug suitability are simplified to an assessment of these two new parameters. Application of this methodology at the virtual design stage is discussed, along with functionality that accounts for uncertainty related to a compound's distribution kinetics and errors associated to in silico QSAR predictions for the required input data.
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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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How to identify and eliminate compounds with a risk of high clinical dose during the early phase of lead optimisation in drug discovery. Eur J Pharm Sci 2017; 110:37-50. [DOI: 10.1016/j.ejps.2017.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 11/18/2022]
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36
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Screening of pharmacokinetic properties of fifty dihydropyrimidin(thi)one derivatives using a combo of in vitro and in silico assays. Eur J Pharm Sci 2017; 109:334-346. [DOI: 10.1016/j.ejps.2017.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/19/2022]
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Ericsson T, Fridén M, Kärrman-Mårdh C, Dainty I, Grime K. Benchmarking of Human Dose Prediction for Inhaled Medicines from Preclinical In Vivo Data. Pharm Res 2017; 34:2557-2567. [DOI: 10.1007/s11095-017-2218-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022]
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38
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Lombardo F, Desai PV, Arimoto R, Desino KE, Fischer H, Keefer CE, Petersson C, Winiwarter S, Broccatelli F. In Silico Absorption, Distribution, Metabolism, Excretion, and Pharmacokinetics (ADME-PK): Utility and Best Practices. An Industry Perspective from the International Consortium for Innovation through Quality in Pharmaceutical Development. J Med Chem 2017; 60:9097-9113. [DOI: 10.1021/acs.jmedchem.7b00487] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Franco Lombardo
- Alkermes Inc., 852 Winter Street, Waltham, Massachusetts 02451, United States
| | - Prashant V. Desai
- Computational
ADME, Drug Disposition, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rieko Arimoto
- Vertex Pharmaceuticals Inc., 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | | | - Holger Fischer
- Roche
Pharmaceutical Research and Early Development, Pharmaceutical Sciences,
Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | | | - Carl Petersson
- Discovery Drug Disposition, Biopharma, R&D Global Early Development, EMD Serono, Frankfurter Strasse 250 I Postcode D39/001, 64293 Darmstadt, Germany
| | - Susanne Winiwarter
- Drug Safety and Metabolism, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Fabio Broccatelli
- Genentech Inc., South San Francisco, California 94080, United States
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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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40
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Kratochwil NA, Meille C, Fowler S, Klammers F, Ekiciler A, Molitor B, Simon S, Walter I, McGinnis C, Walther J, Leonard B, Triyatni M, Javanbakht H, Funk C, Schuler F, Lavé T, Parrott NJ. Metabolic Profiling of Human Long-Term Liver Models and Hepatic Clearance Predictions from In Vitro Data Using Nonlinear Mixed-Effects Modeling. AAPS JOURNAL 2017; 19:534-550. [DOI: 10.1208/s12248-016-0019-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/18/2016] [Indexed: 12/15/2022]
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41
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Muegge I, Bergner A, Kriegl JM. Computer-aided drug design at Boehringer Ingelheim. J Comput Aided Mol Des 2016; 31:275-285. [DOI: 10.1007/s10822-016-9975-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/15/2016] [Indexed: 12/18/2022]
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42
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Automatically updating predictive modeling workflows support decision-making in drug design. Future Med Chem 2016; 8:1779-96. [DOI: 10.4155/fmc-2016-0070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Using predictive models for early decision-making in drug discovery has become standard practice. We suggest that model building needs to be automated with minimum input and low technical maintenance requirements. Models perform best when tailored to answering specific compound optimization related questions. If qualitative answers are required, 2-bin classification models are preferred. Integrating predictive modeling results with structural information stimulates better decision making. For in silico models supporting rapid structure–activity relationship cycles the performance deteriorates within weeks. Frequent automated updates of predictive models ensure best predictions. Consensus between multiple modeling approaches increases the prediction confidence. Combining qualified and nonqualified data optimally uses all available information. Dose predictions provide a holistic alternative to multiple individual property predictions for reaching complex decisions.
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Abstract
This study considers how the estimated in vivo free plasma concentrations for compounds tends to vary between human, dog and rat and proposes empirical-based criteria to aid drug design.
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Affiliation(s)
- M. C. Wenlock
- InSilicoLynx Ltd
- BioHub at Alderley Park
- Mereside
- Cheshire
- UK
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