1
|
Nippa DF, Atz K, Hohler R, Müller AT, Marx A, Bartelmus C, Wuitschik G, Marzuoli I, Jost V, Wolfard J, Binder M, Stepan AF, Konrad DB, Grether U, Martin RE, Schneider G. Enabling late-stage drug diversification by high-throughput experimentation with geometric deep learning. Nat Chem 2024; 16:239-248. [PMID: 37996732 PMCID: PMC10849962 DOI: 10.1038/s41557-023-01360-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Late-stage functionalization is an economical approach to optimize the properties of drug candidates. However, the chemical complexity of drug molecules often makes late-stage diversification challenging. To address this problem, a late-stage functionalization platform based on geometric deep learning and high-throughput reaction screening was developed. Considering borylation as a critical step in late-stage functionalization, the computational model predicted reaction yields for diverse reaction conditions with a mean absolute error margin of 4-5%, while the reactivity of novel reactions with known and unknown substrates was classified with a balanced accuracy of 92% and 67%, respectively. The regioselectivity of the major products was accurately captured with a classifier F-score of 67%. When applied to 23 diverse commercial drug molecules, the platform successfully identified numerous opportunities for structural diversification. The influence of steric and electronic information on model performance was quantified, and a comprehensive simple user-friendly reaction format was introduced that proved to be a key enabler for seamlessly integrating deep learning and high-throughput experimentation for late-stage functionalization.
Collapse
Affiliation(s)
- David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kenneth Atz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Remo Hohler
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Alex T Müller
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andreas Marx
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christian Bartelmus
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Georg Wuitschik
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Irene Marzuoli
- Process Chemistry and Catalysis (PCC), F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Vera Jost
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Jens Wolfard
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Martin Binder
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Antonia F Stepan
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - David B Konrad
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- ETH Singapore SEC Ltd, Singapore, Singapore.
| |
Collapse
|
2
|
Shim SY. Late-Stage C-H Activation of Drug (Derivative) Molecules with Pd(ll) Catalysis. Chemistry 2023; 29:e202302620. [PMID: 37846586 DOI: 10.1002/chem.202302620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/18/2023]
Abstract
This review comprehensively analyses representative examples of Pd(II)-catalyzed late-stage C-H activation reactions and demonstrates their efficacy in converting C-H bonds at multiple positions within drug (derivative) molecules into diverse functional groups. These transformative reactions hold immense potential in medicinal chemistry, enabling the efficient and selective functionalization of specific sites within drug molecules, thereby enhancing their pharmacological activity and expanding the scope of potential drug candidates. Although notable articles have focused on late-stage C-H functionalization reactions of drug-like molecules using transition-metal catalysts, reviews specifically focusing on late-stage C-H functionalization reactions of drug (derivative) molecules using Pd(II) catalysts are required owing to their prominence as the most widely utilized metal catalysts for C-H activation and their ability to introduce a myriad of functional groups at specific C-H bonds. The utilization of Pd-catalyzed C-H activation methodologies demonstrates impressive success in introducing various functional groups, such as cyano (CN), fluorine (F), chlorine (Cl), aromatic rings, olefin, alkyl, alkyne, and hydroxyl groups, to drug (derivative) molecules with high regioselectivity and functional-group tolerance. These breakthroughs in late-stage C-H activation reactions serve as invaluable tools for drug discovery and development, thereby offering strategic options to optimize drug candidates and drive the exploration of innovative therapeutic solutions.
Collapse
Affiliation(s)
- Su Yong Shim
- Infectious Diseases Therapeutic Research Center Division of Medicinal Chemistry and Pharmacology Korea Research Institute of Chemical Technology (KRICT) KRICT School, University of Science and Technology, Daejeon, 34114, Republic of Korea
| |
Collapse
|
3
|
Talaty NN, Johnson RW, Sawicki J, Nacham O, Djuric SW. Recent Developments in Mass Spectrometry to Support Next-Generation Synthesis and Screening. ACS Med Chem Lett 2023; 14:711-718. [PMID: 37312853 PMCID: PMC10258828 DOI: 10.1021/acsmedchemlett.3c00040] [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: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
The complexity of new therapeutics continues to increase and the timeline for the discovery of these therapeutics continues to shrink. This creates demand for new analytical techniques to facilitate quicker discovery and development of novel drugs. Mass spectrometry is one of the most prolific analytical techniques that has been applied across the entire drug discovery pipeline. New mass spectrometers and the associated methods for sampling have been introduced at a rate that keeps pace with new chemistries, therapeutic types, and screening practices used by modern drug hunters. This microperspective covers application and implementation of new mass spectrometry workflows that enable current and future efforts in screening and synthesis for drug discovery.
Collapse
Affiliation(s)
- Nari N. Talaty
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Robert W. Johnson
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James Sawicki
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Omprakash Nacham
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stevan W. Djuric
- Discovery
Chemistry and Technology Consulting LLC, New Bern, North Carolina 28562, United States
| |
Collapse
|
4
|
Castellino NJ, Montgomery AP, Danon JJ, Kassiou M. Late-stage Functionalization for Improving Drug-like Molecular Properties. Chem Rev 2023. [PMID: 37285604 DOI: 10.1021/acs.chemrev.2c00797] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The development of late-stage functionalization (LSF) methodologies, particularly C-H functionalization, has revolutionized the field of organic synthesis. Over the past decade, medicinal chemists have begun to implement LSF strategies into their drug discovery programs, allowing for the drug discovery process to become more efficient. Most reported applications of late-stage C-H functionalization of drugs and drug-like molecules have been to rapidly diversify screening libraries to explore structure-activity relationships. However, there has been a growing trend toward the use of LSF methodologies as an efficient tool for improving drug-like molecular properties of promising drug candidates. In this review, we have comprehensively reviewed recent progress in this emerging area. Particular emphasis is placed on case studies where multiple LSF techniques were implemented to generate a library of novel analogues with improved drug-like properties. We have critically analyzed the current scope of LSF strategies to improve drug-like properties and commented on how we believe LSF can transform drug discovery in the future. Overall, we aim to provide a comprehensive survey of LSF techniques as tools for efficiently improving drug-like molecular properties, anticipating its continued uptake in drug discovery programs.
Collapse
Affiliation(s)
| | | | - Jonathan J Danon
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
5
|
Gillam EMJ, Kramlinger VM. Opportunities for Accelerating Drug Discovery and Development by Using Engineered Drug-Metabolizing Enzymes. Drug Metab Dispos 2023; 51:392-402. [PMID: 36460479 DOI: 10.1124/dmd.121.000743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
The study of drug metabolism is fundamental to drug discovery and development (DDD) since by mediating the clearance of most drugs, metabolic enzymes influence their bioavailability and duration of action. Biotransformation can also produce pharmacologically active or toxic products, which complicates the evaluation of the therapeutic benefit versus liability of potential drugs but also provides opportunities to explore the chemical space around a lead. The structures and relative abundance of metabolites are determined by the substrate and reaction specificity of biotransformation enzymes and their catalytic efficiency. Preclinical drug biotransformation studies are done to quantify in vitro intrinsic clearance to estimate likely in vivo pharmacokinetic parameters, to predict an appropriate dose, and to anticipate interindividual variability in response, including from drug-drug interactions. Such studies need to be done rapidly and cheaply, but native enzymes, especially in microsomes or hepatocytes, do not always produce the full complement of metabolites seen in extrahepatic tissues or preclinical test species. Furthermore, yields of metabolites are usually limiting. Engineered recombinant enzymes can make DDD more comprehensive and systematic. Additionally, as renewable, sustainable, and scalable resources, they can also be used for elegant chemoenzymatic, synthetic approaches to optimize or synthesize candidates as well as metabolites. Here, we will explore how these new tools can be used to enhance the speed and efficiency of DDD pipelines and provide a perspective on what will be possible in the future. The focus will be on cytochrome P450 enzymes to illustrate paradigms that can be extended in due course to other drug-metabolizing enzymes. SIGNIFICANCE STATEMENT: Protein engineering can generate enhanced versions of drug-metabolizing enzymes that are more stable, better suited to industrial conditions, and have altered catalytic activities, including catalyzing non-natural reactions on structurally complex lead candidates. When applied to drugs in development, libraries of engineered cytochrome P450 enzymes can accelerate the identification of active or toxic metabolites, help elucidate structure activity relationships, and, when combined with other synthetic approaches, provide access to novel structures by regio- and stereoselective functionalization of lead compounds.
Collapse
Affiliation(s)
- Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Australia (E.M.J.G.) and Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (V.M.K.)
| | - Valerie M Kramlinger
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Australia (E.M.J.G.) and Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (V.M.K.)
| |
Collapse
|
6
|
Cecere G, Guasch L, Olivares-Morales AM, Umehara K, Stepan AF. LipMetE (Lipophilic Metabolism Efficiency) as a Simple Guide for Half-Life and Dosing Regimen Prediction of Oral Drugs. ACS Med Chem Lett 2022; 13:1444-1451. [PMID: 36105329 PMCID: PMC9465707 DOI: 10.1021/acsmedchemlett.2c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
The in vivo half-life is a key property of every drug molecule, as it determines dosing regimens, peak-to-trough ratios and often dose. However, half-life optimization can be challenging due to its multifactorial nature, with in vitro metabolic turnover, plasma protein binding and volume of distribution all impacting half-life. We here propose that the medicinal chemistry design parameter Lipophilic Metabolism Efficiency (LipMetE) can greatly simplify half-life optimization of neutral and basic compounds. Using mathematical transformations, examples from preclinical GABAA projects and clinical compounds with human pharmacokinetic data, we show that LipMetE is directly proportional to the logarithm of half-life. As the design parameter LipMetE can be swiftly calculated using the readily available parameters LogD, intrinsic clearance and fraction unbound in human liver microsomes or hepatocytes, this approach enables rational half-life optimization from the early stages of drug discovery projects.
Collapse
Affiliation(s)
- Giuseppe Cecere
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Laura Guasch
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Andres M. Olivares-Morales
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Kenichi Umehara
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Antonia F. Stepan
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| |
Collapse
|
7
|
Charlton SN, Hayes MA. Oxygenating Biocatalysts for Hydroxyl Functionalisation in Drug Discovery and Development. ChemMedChem 2022; 17:e202200115. [PMID: 35385205 PMCID: PMC9323455 DOI: 10.1002/cmdc.202200115] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/05/2022] [Indexed: 11/12/2022]
Abstract
C-H oxyfunctionalisation remains a distinct challenge for synthetic organic chemists. Oxygenases and peroxygenases (grouped here as "oxygenating biocatalysts") catalyse the oxidation of a substrate with molecular oxygen or hydrogen peroxide as oxidant. The application of oxygenating biocatalysts in organic synthesis has dramatically increased over the last decade, producing complex compounds with potential uses in the pharmaceutical industry. This review will focus on hydroxyl functionalisation using oxygenating biocatalysts as a tool for drug discovery and development. Established oxygenating biocatalysts, such as cytochrome P450s and flavin-dependent monooxygenases, have widely been adopted for this purpose, but can suffer from low activity, instability or limited substrate scope. Therefore, emerging oxygenating biocatalysts which offer an alternative will also be covered, as well as considering the ways in which these hydroxylation biotransformations can be applied in drug discovery and development, such as late-stage functionalisation (LSF) and in biocatalytic cascades.
Collapse
Affiliation(s)
- Sacha N. Charlton
- School of ChemistryUniversity of Bristol, Cantock's CloseBristolBS8 1TSUK
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery SciencesBiopharmaceuticals R&DAstraZenecaGothenburgSweden
| |
Collapse
|
8
|
Fessner ND, Badenhorst CPS, Bornscheuer UT. Enzyme Kits to Facilitate the Integration of Biocatalysis into Organic Chemistry – First Aid for Synthetic Chemists. ChemCatChem 2022. [DOI: 10.1002/cctc.202200156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nico D. Fessner
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Christoffel P. S. Badenhorst
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Uwe T. Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| |
Collapse
|
9
|
Guo J, Li F, Cheng F, Ma L, Liu X, Durairaj P, Zhang G, Tang D, Long X, Zhang W, Du L, Zhang X, Li S. Bacterial Biosynthetic P450 Enzyme PikC D50N: A Potential Biocatalyst for the Preparation of Human Drug Metabolites. J Org Chem 2021; 86:14563-14571. [PMID: 34662127 DOI: 10.1021/acs.joc.1c01407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human drug metabolites (HDMs) are important chemicals widely used in drug-related studies. However, acquiring these enzyme-derived and regio-/stereo-selectively modified compounds through chemical approaches is complicated. PikC is a biosynthetic P450 enzyme involved in pikromycin biosynthesis from the bacterium Streptomyces venezuelae. Here, we identify the mutant PikCD50N as a potential biocatalyst, with a broad substrate scope, diversified product profile, and high catalytic efficiency, for preparation of HDMs. Remarkably, PikCD50N can mediate the drug-metabolizing reactions using the low-cost H2O2 as a direct electron and oxygen donor.
Collapse
Affiliation(s)
- Jiawei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Fengwei Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Fangyuan Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaohui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Pradeepraj Durairaj
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Gang Zhang
- Fujian Universities and Colleges Engineering Research Center of Marine Biopharmaceutical Resources, Xiamen Medical College, Xiamen, Fujian 361023, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiangtian Long
- Tianjin Hankang Pharmaceutical Biotechnology Co. Ltd., Tianjin 300409, China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| |
Collapse
|
10
|
Shanu-Wilson J, Evans L, Wrigley S, Steele J, Atherton J, Boer J. Biotransformation: Impact and Application of Metabolism in Drug Discovery. ACS Med Chem Lett 2020; 11:2087-2107. [PMID: 33214818 DOI: 10.1021/acsmedchemlett.0c00202] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
Biotransformation has a huge impact on the efficacy and safety of drugs. Ultimately the effects of metabolism can be the lynchpin in the discovery and development cycle of a new drug. This article discusses the impact and application of biotransformation of drugs by mammalian systems, microorganisms, and recombinant enzymes, covering active and reactive metabolites, the impact of the gut microbiome on metabolism, and how insights gained from biotransformation studies can influence drug design from the combined perspectives of a CRO specializing in a range of biotransformation techniques and pharma biotransformation scientists. We include a commentary on how biology-driven approaches can complement medicinal chemistry strategies in drug optimization and the in vitro and surrogate systems available to explore and exploit biotransformation.
Collapse
Affiliation(s)
- Julia Shanu-Wilson
- Hypha Discovery Ltd., 154B Brook Drive, Milton Park, Abingdon, Oxfordshire OX14 4SD, U.K
| | - Liam Evans
- Hypha Discovery Ltd., 154B Brook Drive, Milton Park, Abingdon, Oxfordshire OX14 4SD, U.K
| | - Stephen Wrigley
- Hypha Discovery Ltd., 154B Brook Drive, Milton Park, Abingdon, Oxfordshire OX14 4SD, U.K
| | - Jonathan Steele
- Hypha Discovery Ltd., 154B Brook Drive, Milton Park, Abingdon, Oxfordshire OX14 4SD, U.K
| | - James Atherton
- Incyte Corporation, 1801 Augustine Cut-off, Wilmington, Delaware 19803, United States
| | - Jason Boer
- Incyte Corporation, 1801 Augustine Cut-off, Wilmington, Delaware 19803, United States
| |
Collapse
|
11
|
Lall MS, Bassyouni A, Bradow J, Brown M, Bundesmann M, Chen J, Ciszewski G, Hagen AE, Hyek D, Jenkinson S, Liu B, Obach RS, Pan S, Reilly U, Sach N, Smaltz DJ, Spracklin DK, Starr J, Wagenaar M, Walker GS. Late-Stage Lead Diversification Coupled with Quantitative Nuclear Magnetic Resonance Spectroscopy to Identify New Structure–Activity Relationship Vectors at Nanomole-Scale Synthesis: Application to Loratadine, a Human Histamine H1 Receptor Inverse Agonist. J Med Chem 2020; 63:7268-7292. [DOI: 10.1021/acs.jmedchem.0c00483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Manjinder S. Lall
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Asser Bassyouni
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - James Bradow
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Maria Brown
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark Bundesmann
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jinshan Chen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory Ciszewski
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anne E. Hagen
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dennis Hyek
- Spectrix Analytical Services, LLC, 410 Sackett Point Road, Bldg 20, North Haven, Connecticut 06473, United States
| | - Stephen Jenkinson
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - Bo Liu
- Spectrix Analytical Services, LLC, 410 Sackett Point Road, Bldg 20, North Haven, Connecticut 06473, United States
| | - R. Scott Obach
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Senliang Pan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Usa Reilly
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Neal Sach
- Pfizer Worldwide Research and Development, Science Center Drive, San Diego, California 92121, United States
| | - Daniel J. Smaltz
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Douglas K. Spracklin
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeremy Starr
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Melissa Wagenaar
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory S. Walker
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| |
Collapse
|
12
|
Di Nardo G, Gilardi G. Natural Compounds as Pharmaceuticals: The Key Role of Cytochromes P450 Reactivity. Trends Biochem Sci 2020; 45:511-525. [PMID: 32413326 DOI: 10.1016/j.tibs.2020.03.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/16/2022]
Abstract
The design of drugs from natural products is a re-emerging area due to the need for bioactive compounds. The exploitation of natural products and their derivatives obtained by biocatalysis is in line with the higher attention given today to new sustainable technologies that better preserve the environment (green chemistry). The research field of cytochromes P450 (CYPs) is continuously providing new enzymes and mutants that produce metabolites suitable for late-stage functionalization for new potential drugs. This review provides an overview of the exploitation of CYPs as biocatalysts in drug synthesis. Additionally, recent progress in protein and metabolic engineering is provided to show how these enzymes offer a toolbox that can be combined with other biocatalytic or chemical processes to build new platforms for the green production of new drugs.
Collapse
Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
| |
Collapse
|
13
|
Biocatalysis in drug discovery and development. Curr Opin Chem Biol 2020; 55:151-160. [DOI: 10.1016/j.cbpa.2020.01.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022]
|
14
|
An Inexpensive, Efficient Alternative to NADPH to Support Catalysis by Thermostable Cytochrome P450 Enzymes. ChemCatChem 2020. [DOI: 10.1002/cctc.201902235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
15
|
Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
Collapse
Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| |
Collapse
|
16
|
Fessner ND. P450 Monooxygenases Enable Rapid Late-Stage Diversification of Natural Products via C-H Bond Activation. ChemCatChem 2019; 11:2226-2242. [PMID: 31423290 PMCID: PMC6686969 DOI: 10.1002/cctc.201801829] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/07/2019] [Indexed: 01/07/2023]
Abstract
The biological potency of natural products has been exploited for decades. Their inherent structural complexity and natural diversity might hold the key to efficiently address the urgent need for the development of novel pharmaceuticals. At the same time, it is that very complexity, which impedes necessary chemical modifications such as structural diversification, to improve the effectiveness of the drug. For this purpose, Cytochrome P450 enzymes, which possess unique abilities to activate inert sp3-hybridised C-H bonds in a late-stage fashion, offer an attractive synthetic tool. In this review the potential of cytochrome P450 enzymes in chemoenzymatic lead diversification is illustrated discussing studies reporting late-stage functionalisations of natural products and other high-value compounds. These enzymes were proven to extend the synthetic toolbox significantly by adding to the flexibility and efficacy of synthetic strategies of natural product chemists, and scientists of other related disciplines.
Collapse
Affiliation(s)
- Nico D. Fessner
- Institute of Molecular BiotechnologyGraz University of Technology, NAWI GrazPetersgasse 148010GrazAustria
| |
Collapse
|
17
|
Devine PN, Howard RM, Kumar R, Thompson MP, Truppo MD, Turner NJ. Extending the application of biocatalysis to meet the challenges of drug development. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0055-1] [Citation(s) in RCA: 191] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
18
|
Salter R, Beshore DC, Colletti SL, Evans L, Gong Y, Helmy R, Liu Y, Maciolek CM, Martin G, Pajkovic N, Phipps R, Small J, Steele J, de Vries R, Williams H, Martin IJ. Microbial biotransformation – an important tool for the study of drug metabolism. Xenobiotica 2018; 49:877-886. [DOI: 10.1080/00498254.2018.1512018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rhys Salter
- Department of Preclinical Development and Safety, Janssen Research and Development LLC, Spring House, PA, USA
| | | | | | | | - Yong Gong
- Department of Preclinical Development and Safety, Janssen Research and Development LLC, Spring House, PA, USA
| | - Roy Helmy
- Department of Pharmacokinetics, Pharmacokinetics and Drug Metabolism, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yong Liu
- Department of Preclinical Development, Merck & Co., Inc., West Point, PA, USA
| | - Cheri M. Maciolek
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA
| | - Gary Martin
- Department of Global Chemistry, Merck & Co., Inc., Rahway, NJ, USA
| | - Natasa Pajkovic
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA
| | | | - James Small
- Department of Global Chemistry, Merck & Co., Inc., West Point, PA, USA
| | | | - Ronald de Vries
- Department of Preclinical Development and Safety, Janssen Pharmaceutica, Beerse, Belgium
| | | | - Iain J. Martin
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Boston, MA, USA
| |
Collapse
|
19
|
Stachel SJ, Berger R, Nomland AB, Ginnetti AT, Paone DV, Wang D, Puri V, Lange H, Drott J, Lu J, Marcus J, Dwyer MP, Suon S, Uslaner JM, Smith SM. Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor. ACS Med Chem Lett 2018; 9:815-820. [PMID: 30128073 DOI: 10.1021/acsmedchemlett.8b00214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/26/2018] [Indexed: 12/20/2022] Open
Abstract
Herein we describe the development of a series of pyrazolopyrimidinone phosphodiesterase 2A (PDE2) inhibitors using structure-guided lead identification and design. The series was derived from informed chemotype replacement based on previously identified internal leads. The initially designed compound 3, while potent on PDE2, displayed unsatisfactory selectivity against the other PDE2 isoforms. Compound 3 was subsequently optimized for improved PDE2 activity and isoform selectivity. Insights into the origins of PDE2 selectivity are described and verified using cocrystallography. An optimized lead, 4, demonstrated improved performance in both a rodent and a nonhuman primate cognition model.
Collapse
Affiliation(s)
- Shawn J. Stachel
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Richard Berger
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Ashley B. Nomland
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | | | - Daniel V. Paone
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Deping Wang
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Vanita Puri
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Henry Lange
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jason Drott
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jun Lu
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jacob Marcus
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Michael P. Dwyer
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Sokreine Suon
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jason M. Uslaner
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Sean M. Smith
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| |
Collapse
|
20
|
Brodney MA, Sharma R, Lazzaro JT, Walker GS, Scott Obach R. Harnessing biosynthesis and quantitative NMR for late stage functionalization of lead molecules: Application to the M1 positive allosteric modulator (PAM) program. Bioorg Med Chem Lett 2018; 28:2068-2073. [PMID: 29716781 DOI: 10.1016/j.bmcl.2018.04.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/15/2018] [Accepted: 04/22/2018] [Indexed: 11/19/2022]
Abstract
A facile method for late stage diversification of lead molecules for the M1 PAM program using biosynthesis is described. Liver microsomes from several species are screened to identify a high turnover system. Subsequent incubations using less than 1 mg of substrate generate nanomole quantities of drug metabolites that are purified, characterized by microcryoprobe NMR spectroscopy, and quantified to known concentrations to enable rapid biology testing. The late-stage diversification of lead compounds provides rapid SAR feedback to the medicinal chemistry design cycle.
Collapse
Affiliation(s)
- Michael A Brodney
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States.
| | - Raman Sharma
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States
| | - John T Lazzaro
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States
| | - Gregory S Walker
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States
| | - R Scott Obach
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States
| |
Collapse
|
21
|
Obach RS, Walker GS, Sharma R, Jenkinson S, Tran TP, Stepan AF. Lead Diversification at the Nanomole Scale Using Liver Microsomes and Quantitative Nuclear Magnetic Resonance Spectroscopy: Application to Phosphodiesterase 2 Inhibitors. J Med Chem 2018; 61:3626-3640. [DOI: 10.1021/acs.jmedchem.8b00116] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- R. Scott Obach
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gregory S. Walker
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Raman Sharma
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Stephen Jenkinson
- Pfizer Worldwide Research and Development, 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Tuan P. Tran
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Antonia F. Stepan
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|