1
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Logan KM, Kaplan W, Simov V, Zhou H, Li D, Torres L, Morriello GJ, Acton JJ, Pio B, Chen YH, Keylor MH, Johnson R, Kattar SD, Chau R, Yan X, Ardolino M, Zarate C, Otte KM, Palte RL, Xiong T, McMinn SE, Lin S, Neelamkavil SF, Liu P, Su J, Hegde LG, Woodhouse JD, Moy LY, Ciaccio PJ, Piesvaux J, Zebisch M, Henry C, Barker J, Wood HB, Kennedy ME, DiMauro EF, Fell MJ, Fuller PH. Discovery and Optimization of N-Heteroaryl Indazole LRRK2 Inhibitors. J Med Chem 2024; 67:16807-16819. [PMID: 39231262 DOI: 10.1021/acs.jmedchem.4c01627] [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: 09/06/2024]
Abstract
Inhibition of leucine-rich repeat kinase 2 is a genetically supported mechanism for the treatment of Parkinson's disease. We previously disclosed the discovery of an indazole series lead that demonstrated both safety and translational risks. The safety risks were hypothesized to be of unknown origin, so structural diversity in subsequent chemical matter was prioritized. The translational risks were identified due to a low brain Kpu,u in nonhuman primate studies, which raised concern over the use of an established peripheral biomarker as a surrogate for central target engagement. Given these challenges, the team sought to leverage structure- and property-based drug design and expanded efflux transporter profiling to identify structurally distinct leads with enhanced CNS drug-likeness. Herein, we describe the discovery of a "reinvented" indazole series with improved physicochemical properties and efflux transporter profiles while maintaining excellent potency and off-target kinase selectivity, which resulted in advanced lead, compound 23.
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Affiliation(s)
- Kaitlyn M Logan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Will Kaplan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Hua Zhou
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derun Li
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Luis Torres
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - John J Acton
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Barbara Pio
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Yi-Heng Chen
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Mitchell H Keylor
- 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
| | - Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan Chau
- 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
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cayetana Zarate
- 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
| | - Rachel L Palte
- 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
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Shishi Lin
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | | | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- 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
| | - Lily Y Moy
- 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
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthias Zebisch
- Evotec (U.K.) Ltd., 90 Park Drive, Milton Park, Abingdon OX14 4RZ, Oxfordshire, U.K
| | - Clare Henry
- Evotec (U.K.) Ltd., 90 Park Drive, Milton Park, Abingdon OX14 4RZ, Oxfordshire, U.K
| | - John Barker
- Evotec (U.K.) Ltd., 90 Park Drive, Milton Park, Abingdon OX14 4RZ, Oxfordshire, U.K
| | - Harold B Wood
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, 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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2
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Castagna D, Gourdet B, Hjerpe R, MacFaul P, Novak A, Revol G, Rochette E, Jordan A. To homeostasis and beyond! Recent advances in the medicinal chemistry of heterobifunctional derivatives. PROGRESS IN MEDICINAL CHEMISTRY 2024; 63:61-160. [PMID: 39370242 DOI: 10.1016/bs.pmch.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
The field of induced proximity therapeutics has expanded dramatically over the past 3 years, and heterobifunctional derivatives continue to form a significant component of the activities in this field. Here, we review recent advances in the field from the perspective of the medicinal chemist, with a particular focus upon informative case studies, alongside a review of emerging topics such as Direct-To-Biology (D2B) methodology and utilities for heterobifunctional compounds beyond E3 ligase mediated degradation. We also include a critical evaluation of the latest thinking around the optimisation of physicochemical and pharmacokinetic attributes of these beyond Role of Five molecules, to deliver appropriate therapeutic exposure in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | - Allan Jordan
- Sygnature Discovery, Nottingham, United Kingdom; Sygnature Discovery, Macclesfield, United Kingdom.
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3
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Wang YT, Price E, Feng M, Hulen J, Doktor S, Stresser DM, Maes EM, Ji QC, Jenkins GJ. High-Throughput SFC-MS/MS Method to Measure EPSA and Predict Human Permeability. J Med Chem 2024; 67:13765-13777. [PMID: 38976596 DOI: 10.1021/acs.jmedchem.4c00571] [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: 07/10/2024]
Abstract
Permeability is a key factor driving the absorption of orally administered drugs. In early discovery, the efficient evaluation of permeability, particularly for compounds violating Lipinski's Rule of 5, remains challenging. Addressing this, we established a high-throughput method to measure the experimental polar surface area (HT-EPSA) as an in vitro surrogate to measure permeability. Compared to earlier methods, HT-EPSA significantly reduces data acquisition time with enhanced sensitivity, selectivity, and data quality. In the effort of translating EPSA to human in vitro and in vivo passive permeability, we demonstrated the application of EPSA for predicting Caco-2 cell and human intestinal permeability, showing improvements over topological polar surface area and the parallel artificial membrane permeability assay for rank-ordering permeability in a proteolysis targeting chimera case study. The HT-EPSA method is expected to be highly beneficial in guiding early stage compound rank-ordering, faster decision-making, and in predicting in vitro and/or in vivo human intestinal permeability.
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Affiliation(s)
- Yue-Ting Wang
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Edward Price
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Mei Feng
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jason Hulen
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stella Doktor
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - David M Stresser
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Estelle M Maes
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Qin C Ji
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Gary J Jenkins
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
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4
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Hayhow TG, Williamson B, Lawson M, Cureton N, Braybrooke EL, Campbell A, Carbajo RJ, Cheraghchi-Bashi A, Chiarparin E, Diène CR, Fallan C, Fisher DI, Goldberg FW, Hopcroft L, Hopcroft P, Jackson A, Kettle JG, Klinowska T, Künzel U, Lamont G, Lewis HJ, Maglennon G, Martin S, Gutierrez PM, Morrow CJ, Nikolaou M, Nissink JWM, O'Shea P, Polanski R, Schade M, Scott JS, Smith A, Weber J, Wilson J, Yang B, Crafter C. Metabolism-driven in vitro/in vivo disconnect of an oral ERɑ VHL-PROTAC. Commun Biol 2024; 7:563. [PMID: 38740899 DOI: 10.1038/s42003-024-06238-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Targeting the estrogen receptor alpha (ERα) pathway is validated in the clinic as an effective means to treat ER+ breast cancers. Here we present the development of a VHL-targeting and orally bioavailable proteolysis-targeting chimera (PROTAC) degrader of ERα. In vitro studies with this PROTAC demonstrate excellent ERα degradation and ER antagonism in ER+ breast cancer cell lines. However, upon dosing the compound in vivo we observe an in vitro-in vivo disconnect. ERα degradation is lower in vivo than expected based on the in vitro data. Investigation into potential causes for the reduced maximal degradation reveals that metabolic instability of the PROTAC linker generates metabolites that compete for binding to ERα with the full PROTAC, limiting degradation. This observation highlights the requirement for metabolically stable PROTACs to ensure maximal efficacy and thus optimisation of the linker should be a key consideration when designing PROTACs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bin Yang
- Oncology R&D, AstraZeneca, Waltham, MA, USA
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5
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Weiss D, Baylon JL, Evans ED, Paiva A, Everlof G, Cutrone J, Broccatelli F. Balanced Permeability Index: A Multiparameter Index for Improved In Vitro Permeability. ACS Med Chem Lett 2024; 15:457-462. [PMID: 38628792 PMCID: PMC11017404 DOI: 10.1021/acsmedchemlett.3c00542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
The optimization of passive permeability is a key objective for orally available small molecule drug candidates. For drugs targeting the central nervous system (CNS), minimizing P-gp-mediated efflux is an additional important target for optimization. The physicochemical properties most strongly associated with high passive permeability and lower P-gp efflux are size, polarity, and lipophilicity. In this study, a new metric called the Balanced Permeability Index (BPI) was developed that combines these three properties. The BPI was found to be more effective than any single property in classifying molecules based on their permeability and efflux across a diverse range of chemicals and assays. BPI is easy to understand, allowing researchers to make decisions about which properties to prioritize during the drug development process.
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Affiliation(s)
- Dahlia
R. Weiss
- Bristol-Myers
Squibb Company, Redwood
City, California 94063, United States
| | - Javier L. Baylon
- Bristol-Myers
Squibb Company, San Diego, California 92121, United States
| | - Ethan D. Evans
- Bristol-Myers
Squibb Company, Redwood
City, California 94063, United States
| | - Anthony Paiva
- Bristol-Myers
Squibb Company, Lawrence Township, New Jersey 08648, United States
| | - Gerry Everlof
- Bristol-Myers
Squibb Company, Lawrence Township, New Jersey 08648, United States
| | - Jingfang Cutrone
- Bristol-Myers
Squibb Company, Lawrence Township, New Jersey 08648, United States
| | - Fabio Broccatelli
- Bristol-Myers
Squibb Company, San Diego, California 92121, United States
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6
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Price E, Weinheimer M, Rivkin A, Jenkins G, Nijsen M, Cox PB, DeGoey D. Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape. J Med Chem 2024; 67:5683-5698. [PMID: 38498697 DOI: 10.1021/acs.jmedchem.3c02332] [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: 03/20/2024]
Abstract
Developing orally bioavailable drugs demands an understanding of absorption in early drug development. Traditional methods and physicochemical properties optimize absorption for rule of five (Ro5) compounds; beyond rule of five (bRo5) drugs necessitate advanced tools like the experimental measure of exposed polarity (EPSA) and the AbbVie multiparametric score (AB-MPS). Analyzing AB-MPS and EPSA against ∼1000 compounds with human absorption data and ∼10,000 AbbVie tool compounds (∼1000 proteolysis targeting chimeras or PROTACs, ∼7000 Ro5s, and ∼2000 bRo5s) revealed new patterns of physicochemical trends. We introduced a high-throughput "polarity reduction" descriptor: ETR, the EPSA-to-topological polar surface area (TPSA) ratio, highlights unique bRo5 and PROTAC subsets for specialized drug design strategies for effective absorption. Our methods and guidelines refine drug design by providing innovative in vitro approaches, enhancing physicochemical property optimization, and enabling accurate predictions of intestinal absorption in the complex bRo5 domain.
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Affiliation(s)
- Edward Price
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Manuel Weinheimer
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alexey Rivkin
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gary Jenkins
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Marjoleen Nijsen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - David DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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7
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Shurtleff VW, Layton ME, Parish CA, Perkins JJ, Schreier JD, Wang Y, Adam GC, Alvarez N, Bahmanjah S, Bahnck-Teets CM, Boyce CW, Burlein C, Cabalu TD, Campbell BT, Carroll SS, Chang W, de Lera Ruiz M, Dolgov E, Fay JF, Fox NG, Goh SL, Hartingh TJ, Hurzy DM, Kelly MJ, Klein DJ, Klingler FM, Krishnamurthy H, Kudalkar S, Mayhood TW, McKenna PM, Murray EM, Nahas D, Nawrat CC, Park S, Qian D, Roecker AJ, Sharma V, Shipe WD, Su J, Taggart RV, Truong Q, Wu Y, Zhou X, Zhuang N, Perlin DS, Olsen DB, Howe JA, McCauley JA. Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic. J Med Chem 2024; 67:3935-3958. [PMID: 38365209 DOI: 10.1021/acs.jmedchem.3c02248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.
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Affiliation(s)
| | - Mark E Layton
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Craig A Parish
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - James J Perkins
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John D Schreier
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yunyi Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Gregory C Adam
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | | | | | - Tamara D Cabalu
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Brian T Campbell
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Steven S Carroll
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Wonsuk Chang
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Enriko Dolgov
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - John F Fay
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nicholas G Fox
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shih Lin Goh
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Danielle M Hurzy
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Michael J Kelly
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J Klein
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | | | - Shalley Kudalkar
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Philip M McKenna
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Edward M Murray
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Debbie Nahas
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | - Vijeta Sharma
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - William D Shipe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jing Su
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Robert V Taggart
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Quang Truong
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yin Wu
- Viva Biotech Ltd., Shanghai 201318, China
| | - Xiaoyan Zhou
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - David B Olsen
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A Howe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A McCauley
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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8
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Poongavanam V, Wieske LHE, Peintner S, Erdélyi M, Kihlberg J. Molecular chameleons in drug discovery. Nat Rev Chem 2024; 8:45-60. [PMID: 38123688 DOI: 10.1038/s41570-023-00563-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.
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Affiliation(s)
| | | | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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9
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Asano D, Takakusa H, Nakai D. Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs. Pharmaceutics 2023; 16:47. [PMID: 38258058 PMCID: PMC10820198 DOI: 10.3390/pharmaceutics16010047] [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: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
To meet unmet medical needs, middle-to-large molecules, including peptides and oligonucleotides, have emerged as new therapeutic modalities. Owing to their middle-to-large molecular sizes, middle-to-large molecules are not suitable for oral absorption, but there are high expectations around orally bioavailable macromolecular drugs, since oral administration is the most convenient dosing route. Therefore, extensive efforts have been made to create bioavailable middle-to-large molecules or develop absorption enhancement technology, from which some successes have recently been reported. For example, Rybelsus® tablets and Mycapssa® capsules, both of which contain absorption enhancers, were approved as oral medications for type 2 diabetes and acromegaly, respectively. The oral administration of Rybelsus and Mycapssa exposes their pharmacologically active peptides with molecular weights greater than 1000, namely, semaglutide and octreotide, respectively, into systemic circulation. Although these two medications represent major achievements in the development of orally absorbable peptide formulations, the oral bioavailability of peptides after taking Rybelsus and Mycapssa is still only around 1%. In this article, we review the approaches and recent advances of orally bioavailable middle-to-large molecules and discuss challenges for improving their oral absorption.
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Affiliation(s)
- Daigo Asano
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan; (H.T.); (D.N.)
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10
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Tang X, Kokot J, Waibl F, Fernández-Quintero ML, Kamenik AS, Liedl KR. Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity. J Chem Inf Model 2023; 63:7107-7123. [PMID: 37943023 PMCID: PMC10685455 DOI: 10.1021/acs.jcim.3c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.
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Affiliation(s)
- Xuechen Tang
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Janik Kokot
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Franz Waibl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, 8093 Zürich, Switzerland
| | | | - Anna S. Kamenik
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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11
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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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12
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Saw YL, Boughton JR, Wroniuk FL, Mostafa ME, Pellegrinelli PJ, Calvez SA, Kaplitz AS, Perez LJ, Edwards JL, Grinias JP. Use of N-(4-aminophenyl)piperidine derivatization to improve organic acid detection with supercritical fluid chromatography-mass spectrometry. J Sep Sci 2023; 46:e2300343. [PMID: 37603367 DOI: 10.1002/jssc.202300343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023]
Abstract
The analysis of organic acids in complex mixtures by LC-MS can often prove challenging, especially due to the poor sensitivity of negative ionization mode required for detection of these compounds in their native (i.e., underivatized or untagged) form. These compounds have also been difficult to measure using supercritical fluid chromatography (SFC)-MS, a technique of growing importance for metabolomic analysis, with similar limitations based on negative ionization. In this report, the use of a high proton affinity N-(4-aminophenyl)piperidine derivatization tag is explored for the improvement of organic acid detection by SFC-MS. Four organic acids (lactic, succinic, malic, and citric acids) with varying numbers of carboxylate groups were derivatized with N-(4-aminophenyl)piperidine to achieve detection limits down to 0.5 ppb, with overall improvements in detection limit ranging from 25-to-2100-fold. The effect of the derivatization group on sensitivity, which increased by at least 200-fold for compounds that were detectable in their native form, and mass spectrometric detection are also described. Preliminary investigations into the separation of these derivatized compounds identified multiple stationary phases that could be used for complete separation of all four compounds by SFC. This derivatization technique provides an improved approach for the analysis of organic acids by SFC-MS, especially for those that are undetectable in their native form.
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Affiliation(s)
- Yih Ling Saw
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - John R Boughton
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Faith L Wroniuk
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | | | - Peter J Pellegrinelli
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Samantha A Calvez
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Alexander S Kaplitz
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Lark J Perez
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - James L Edwards
- Department of Chemistry, Saint Louis University, St. Louis, Missouri, USA
| | - James P Grinias
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
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13
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Young RJ. Today's drug discovery and the shadow of the rule of 5. Expert Opin Drug Discov 2023; 18:965-972. [PMID: 37378429 DOI: 10.1080/17460441.2023.2228199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION The rule of 5 developed by Lipinski et al., a landmark and prescient piece of scholarship, focused the minds of drug hunters by systematically characterizing the physical make-up of drug molecules for the first time, noting many sub-optimal compounds identified by high-throughput screening practices. Its profound influence on thinking and practices, whilst providing benefit, perhaps etched the guidelines too strongly in the minds of some drug hunters who applied the bounds too literally without understanding the implications of the underlying statistics. AREAS COVERED This opinion is based on recent key developments that take thinking, measurements, and standards beyond those first set out, particularly the influences of molecular weight and the understanding, measurement, and calculation of lipophilicity. EXPERT OPINION Techniques and technologies for physicochemical estimations set new standards. It is timely to celebrate the significance and influence of the rule of 5, whilst taking thinking to new levels with better characterizations. The shadow of the rule of 5 may be long, but it is not dark, as new measurements, predictions and principles emerge as guiding lights in the design and prioritization of higher-quality molecules redefining the meaning of beyond the rule of 5.
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Affiliation(s)
- Robert J Young
- Blue Burgundy (Drug Discovery Consultancy) Ltd, Bedford, UK
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14
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Whitehurst BC, Bauer MR, Edfeldt F, Gunnarsson A, Margreitter C, Rawlins PB, Storer RI. Design and Evaluation of a Low Hydrogen Bond Donor Count Fragment Screening Set to Aid Hit Generation of PROTACs Intended for Oral Delivery. J Med Chem 2023. [PMID: 37224440 DOI: 10.1021/acs.jmedchem.3c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The development of orally bioavailable PROTACs presents a significant challenge due to the inflated physicochemical properties of such heterobifunctional molecules. Molecules occupying this "beyond rule of five" space often demonstrate limited oral bioavailability due to the compounding effects of elevated molecular weight and hydrogen bond donor count (among other properties), but it is possible to achieve sufficient oral bioavailability through physicochemical optimization. Herein, we disclose the design and evaluation of a low hydrogen bond donor count (≤1 HBD) fragment screening set to aid hit generation of PROTACs intended for an oral route of delivery. We demonstrate that application of this library can enhance fragment screens against PROTAC proteins of interest and ubiquitin ligases, yielding fragment hits containing ≤1 HBD suitable for optimizing toward orally bioavailable PROTACs.
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Affiliation(s)
- Benjamin C Whitehurst
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Fredrik Edfeldt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Anders Gunnarsson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Christian Margreitter
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Philip B Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
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15
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Jurica EA, Wu X, Williams KN, Haque LE, Rampulla RA, Mathur A, Zhou M, Cao G, Cai H, Wang T, Liu H, Xu C, Kunselman LK, Antrilli TM, Hicks MB, Sun Q, Dierks EA, Apedo A, Moore DB, Foster KA, Cvijic ME, Panemangalore R, Khandelwal P, Wilkes JJ, Zinker BA, Robertson DG, Janovitz EB, Galella M, Li YX, Li J, Ramar T, Jalagam PR, Jayaram R, Whaley JM, Barrish JC, Robl JA, Ewing WR, Ellsworth BA. Optimization of Physicochemical Properties of Pyrrolidine GPR40 AgoPAMs Results in a Differentiated Profile with Improved Pharmacokinetics and Reduced Off-Target Activities. Bioorg Med Chem 2023; 85:117273. [PMID: 37030194 DOI: 10.1016/j.bmc.2023.117273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
GPR40 AgoPAMs are highly effective antidiabetic agents that have a dual mechanism of action, stimulating both glucose-dependent insulin and GLP-1 secretion. The early lipophilic, aromatic pyrrolidine and dihydropyrazole GPR40 AgoPAMs from our laboratory were highly efficacious in lowering plasma glucose levels in rodents but possessed off-target activities and triggered rebound hyperglycemia in rats at high doses. A focus on increasing molecular complexity through saturation and chirality in combination with reducing polarity for the pyrrolidine AgoPAM chemotype resulted in the discovery of compound 46, which shows significantly reduced off-target activities as well as improved aqueous solubility, rapid absorption, and linear PK. In vivo, compound 46 significantly lowers plasma glucose levels in rats during an oral glucose challenge yet does not demonstrate the reactive hyperglycemia effect at high doses that was observed with earlier GPR40 AgoPAMs.
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Affiliation(s)
- Elizabeth A Jurica
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States.
| | - Ximao Wu
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Kristin N Williams
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Lauren E Haque
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Richard A Rampulla
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Arvind Mathur
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Min Zhou
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Gary Cao
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Hong Cai
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Tao Wang
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Heng Liu
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Carrie Xu
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Lori K Kunselman
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Thomas M Antrilli
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Michael B Hicks
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Qin Sun
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Elizabeth A Dierks
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Atsu Apedo
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Douglas B Moore
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Kimberly A Foster
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Mary Ellen Cvijic
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Reshma Panemangalore
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Purnima Khandelwal
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Jason J Wilkes
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Bradley A Zinker
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Donald G Robertson
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Evan B Janovitz
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Michael Galella
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Yi-Xin Li
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Julia Li
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Thangeswaran Ramar
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Prasada Rao Jalagam
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Ramya Jayaram
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Jean M Whaley
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Joel C Barrish
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Jeffrey A Robl
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - William R Ewing
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
| | - Bruce A Ellsworth
- Research and Development, Bristol Myers Squibb, Co., P.O. Box 4000, Princeton, NJ 08543-4000, United States
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16
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Lei Z, Chang W, Guo H, Feng J, Zhang Z. A Brief Review on the Synthesis of the N-CF3 Motif in Heterocycles. Molecules 2023; 28:molecules28073012. [PMID: 37049775 PMCID: PMC10095997 DOI: 10.3390/molecules28073012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The trifluoromethyl group is widely recognized for its significant role in the fields of medicinal chemistry and material science due to its unique electronic and steric properties that can alter various physiochemical properties of the parent molecule, such as lipophilicity, acidity, and hydrogen bonding capabilities. Compared to the well-established C-trifluoromethylation, N-trifluoromethylation has received lesser attention. Considering the extensive contribution of nitrogen to drug molecules, it is predicted that constructing N-trifluoromethyl (N-CF3) motifs will be of great significance in pharmaceutical and agrochemical industries. This review is mainly concerned with the synthesis of heterocycles containing this motif. In three-membered heterocycles containing the N-CF3 motif, the existing literature mostly demonstrated the synthetic strategy, as it does for four- and larger-membered heterocycles. Certain structures, such as oxaziridines, could serve as an oxidant or building blocks in organic synthesis. In five-membered heterocycles, it has been reported that N-CF3 azoles showed a higher lipophilicity and a latent increased metabolic stability and Caco-2-permeability compared with their N-CH3 counterparts, illustrating the potential of the N-CF3 motif. Various N-CF3 analogues of drugs or bioactive molecules, such as sildenafil analogue, have been obtained. In general, the N-CF3 motif is developing and has great potential in bioactive molecules or materials. Give the recent development in this motif, it is foreseeable that its synthesis methods and applications will become more and more extensive. In this paper, we present an overview of the synthesis of N-CF3 heterocycles, categorized on the basis of the number of rings (three-, four-, five-, six- and larger-membered heterocycles), and focus on the five-membered heterocycles containing the N-CF3 group.
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17
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Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
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18
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O' Donovan DH, De Fusco C, Kuhnke L, Reichel A. Trends in Molecular Properties, Bioavailability, and Permeability across the Bayer Compound Collection. J Med Chem 2023; 66:2347-2360. [PMID: 36752336 DOI: 10.1021/acs.jmedchem.2c01577] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
For oral drugs, medicinal chemists aim to design compounds with high oral bioavailability, of which permeability is a key determinant. Taking advantage of >2000 compounds tested in rat bioavailability studies and >20,000 compounds tested in Caco2 assays at Bayer, we have examined the molecular properties governing bioavailability and permeability. In addition to classical parameters such as logD and molecular weight, we also investigated the relationship between calculated pKa and permeability. We find that neutral compounds retain permeability up to a molecular weight limit of 700, while stronger acids and bases are restricted to weights of 400-500. We also investigate trends for common properties such as hydrogen bond donors and acceptors, polar surface area, aromatic ring count, and rotatable bonds, including compounds which exceed Lipinski's rule of five (Ro5). These property-structure relationships are combined to provide design guidelines for bioavailable drugs in both traditional and "beyond rule of 5" (bRo5) chemical space.
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Affiliation(s)
| | | | - Lara Kuhnke
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
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19
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Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader. Pharmaceutics 2023; 15:pharmaceutics15010272. [PMID: 36678900 PMCID: PMC9861353 DOI: 10.3390/pharmaceutics15010272] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Chameleonicity (the capacity of a molecule to adapt its conformations to the environment) may help to identify orally bioavailable drugs in the beyond-Rule-of-5 chemical space. Computational methods to predict the chameleonic behaviour of degraders have not yet been reported and the identification of molecular chameleons still relies on experimental evidence. Therefore, there is a need to tune predictions with experimental data. Here, we employ PROTAC-1 (a passively cell-permeable degrader), for which NMR and physicochemical data prove the chameleonic behaviour, to benchmark the capacity of two conformational sampling algorithms and selection schemes. To characterize the conformational ensembles in both polar and nonpolar environments, we compute three molecular properties proven to be essential for cell permeability: conformer shape (radius of gyration), polarity (3D PSA), and the number of intramolecular hydrogen bonds. Energetic criteria were also considered. Infographics monitored the simultaneous variation of those properties in computed and NMR conformers. Overall, we provide key points for tuning conformational sampling tools to reproduce PROTAC-1 chameleonicity according to NMR evidence. This study is expected to improve the design of PROTAC drugs and the development of computational sustainable strategies to exploit the potential of new modalities in drug discovery.
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20
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Erckes V, Steuer C. A story of peptides, lipophilicity and chromatography - back and forth in time. RSC Med Chem 2022; 13:676-687. [PMID: 35800203 PMCID: PMC9215158 DOI: 10.1039/d2md00027j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/18/2022] [Indexed: 11/25/2022] Open
Abstract
Peptides, as part of the beyond the rule of 5 (bRo5) chemical space, represent a unique class of pharmaceutical compounds. Because of their exceptional position in the chemical space between traditional small molecules (molecular weight (MW) < 500 Da) and large therapeutic proteins (MW > 5000 Da), peptides became promising candidates for targeting challenging binding sites, including even targets traditionally considered as undruggable - e.g. intracellular protein-protein interactions. However, basic knowledge about physicochemical properties that are important for a drug to be membrane permeable is missing but would enhance the drug discovery process of bRo5 molecules. Consequently, there is a demand for quick and simple lipophilicity determination methods for peptides. In comparison to the traditional lipophilicity determination methods via shake flask and in silico prediction, chromatography-based methods could have multiple benefits such as the requirement of low analyte amount, insensitivity to impurities and high throughput. Herein we elucidate the role of peptide lipophilicity and different lipophilicity values. Further, we summarize peptide analysis via common chromatographic techniques, in specific reversed phase liquid chromatography, hydrophilic interaction liquid chromatography and supercritical fluid chromatography and their role in drug discovery and development process.
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Affiliation(s)
- Vanessa Erckes
- Pharmaceutical Analytics, Institute of Pharmaceutical Sciences, Federal Institute of Technology Zurich 8093 Zurich Switzerland
| | - Christian Steuer
- Pharmaceutical Analytics, Institute of Pharmaceutical Sciences, Federal Institute of Technology Zurich 8093 Zurich Switzerland
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21
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Ecker AK, Levorse DA, Victor DA, Mitcheltree MJ. Bioisostere Effects on the EPSA of Common Permeability-Limiting Groups. ACS Med Chem Lett 2022; 13:964-971. [DOI: 10.1021/acsmedchemlett.2c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Andrew K. Ecker
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115-5727, United States
| | - Dorothy A. Levorse
- Department of Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Daniel A. Victor
- Department of Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew J. Mitcheltree
- Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115-5727, United States
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22
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Optimization of cyclic peptide property using chromatographic capacity factor on permeability of passive cell membrane and human induced pluripotent stem cell-derived intestinal membrane. J Pharm Sci 2022; 111:1879-1886. [DOI: 10.1016/j.xphs.2022.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/21/2022]
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23
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Underwood T, Hindley S, Knaggs A, White C. Synthetic chemistry screening for robust analysis and purification from discovery through to development. SEP SCI TECHNOL 2022. [DOI: 10.1016/b978-0-323-88487-7.00003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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24
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Keylor MH, Gulati A, Kattar SD, Johnson RE, Chau RW, Margrey KA, Ardolino MJ, Zarate C, Poremba KE, Simov V, Morriello GJ, Acton JJ, Pio B, Yan X, Palte RL, McMinn SE, Nogle L, Lesburg CA, Adpressa D, Lin S, Neelamkavil S, Liu P, Su J, Hegde LG, Woodhouse JD, Faltus R, Xiong T, Ciaccio PJ, Piesvaux J, Otte KM, Wood HB, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Structure-Guided Discovery of Aminoquinazolines as Brain-Penetrant and Selective LRRK2 Inhibitors. J Med Chem 2021; 65:838-856. [PMID: 34967623 DOI: 10.1021/acs.jmedchem.1c01968] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The leucine-rich repeat kinase 2 (LRRK2) protein has been genetically and functionally linked to Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder whose current therapies are limited in scope and efficacy. In this report, we describe a rigorous hit-to-lead optimization campaign supported by structural enablement, which culminated in the discovery of brain-penetrant, candidate-quality molecules as represented by compounds 22 and 24. These compounds exhibit remarkable selectivity against the kinome and offer good oral bioavailability and low projected human doses. Furthermore, they showcase the implementation of stereochemical design elements that serve to enable a potency- and selectivity-enhancing increase in polarity and hydrogen bond donor (HBD) count while maintaining a central nervous system-friendly profile typified by low levels of transporter-mediated efflux and encouraging brain penetration in preclinical models.
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Affiliation(s)
- Mitchell H Keylor
- 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
| | - Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca E Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan W Chau
- 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
| | - Michael J Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cayetana Zarate
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kelsey E Poremba
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Vladimir Simov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Gregori J Morriello
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - John J Acton
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Barbara Pio
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xin Yan
- 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
| | - Charles A Lesburg
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Donovon Adpressa
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Shishi Lin
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Santhosh Neelamkavil
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ping Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, 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
| | - 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
| | - Jennifer Piesvaux
- 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
| | - Harold B Wood
- Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, 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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25
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David L, Wenlock M, Barton P, Ritzén A. Prediction of Chameleonic Efficiency. ChemMedChem 2021; 16:2669-2685. [PMID: 34240561 DOI: 10.1002/cmdc.202100306] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/29/2021] [Indexed: 11/09/2022]
Abstract
Chameleonic properties, i. e., the capacity of a molecule to hide polarity in non-polar environments and expose it in water, help achieving sufficient permeability and solubility for drug molecules with high MW. We present models of experimental measures of polarity for a set of 24 FDA approved drugs (MW 405-1113) and one PROTAC (MW 1034). Conformational ensembles in aqueous and non-polar environments were generated using molecular dynamics. A linear regression model that predicts chromatographic apparent polarity (EPSA) with a mean unsigned error of 10 Å2 was derived based on separate terms for donor, acceptor, and total molecular SASA. A good correlation (R2 =0.92) with an experimental measure of hydrogen bond donor potential, Δlog Poct-tol , was found for the mean hydrogen bond donor SASA of the conformational ensemble scaled with Abraham's A hydrogen bond acidity. Two quantitative measures of chameleonic behaviour, the chameleonic efficiency indices, are introduced. We envision that the methods presented herein will be useful to triage designed molecules and prioritize those with the best chance of achieving acceptable permeability and solubility.
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Affiliation(s)
- Laurent David
- Computational Chemistry, H. Lundbeck A/S, Ottiliavej 9, 2300, Valby, Copenhagen, Denmark
| | - Mark Wenlock
- Physical Chemistry, Cyprotex Discovery Limited, Alderley Park, Nether Alderley, Cheshire, SK10 4TG, UK
| | - Patrick Barton
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.,DMPK, UCB Celltech, Branch of UCB Pharma S.A., 208 Bath Road, Slough, Berkshire, SL1 3WE, UK
| | - Andreas Ritzén
- Drug Design, LEO Pharma A/S, Industriparken 55, 2550, Ballerup, Denmark.,Monte Rosa Therapeutics AG, Aeschenvorstadt 36, CH 4057, Basel, Switzerland
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26
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Leeson PD, Bento AP, Gaulton A, Hersey A, Manners EJ, Radoux CJ, Leach AR. Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies. J Med Chem 2021; 64:7210-7230. [PMID: 33983732 PMCID: PMC7610969 DOI: 10.1021/acs.jmedchem.1c00416] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Physicochemical descriptors commonly used to define "drug-likeness" and ligand efficiency measures are assessed for their ability to differentiate marketed drugs from compounds reported to bind to their efficacious target or targets. Using ChEMBL version 26, a data set of 643 drugs acting on 271 targets was assembled, comprising 1104 drug-target pairs having ≥100 published compounds per target. Taking into account changes in their physicochemical properties over time, drugs are analyzed according to their target class, therapy area, and route of administration. Recent drugs, approved in 2010-2020, display no overall differences in molecular weight, lipophilicity, hydrogen bonding, or polar surface area from their target comparator compounds. Drugs are differentiated from target comparators by higher potency, ligand efficiency (LE), lipophilic ligand efficiency (LLE), and lower carboaromaticity. Overall, 96% of drugs have LE or LLE values, or both, greater than the median values of their target comparator compounds.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd, The Malt House, Main Street, Congerstone, Nuneaton, Warkwickshire CV13 6LZ, United Kingdom
| | - A Patricia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anne Hersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Emma J Manners
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Chris J Radoux
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
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27
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Golosov AA, Flyer AN, Amin J, Babu C, Gampe C, Li J, Liu E, Nakajima K, Nettleton D, Patel TJ, Reid PC, Yang L, Monovich LG. Design of Thioether Cyclic Peptide Scaffolds with Passive Permeability and Oral Exposure. J Med Chem 2021; 64:2622-2633. [PMID: 33629858 DOI: 10.1021/acs.jmedchem.0c01505] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Advances in the design of permeable peptides and in the synthesis of large arrays of macrocyclic peptides with diverse amino acids have evolved on parallel but independent tracks. Less precedent combines their respective attributes, thereby limiting the potential to identify permeable peptide ligands for key targets. Herein, we present novel 6-, 7-, and 8-mer cyclic peptides (MW 774-1076 g·mol-1) with passive permeability and oral exposure that feature the amino acids and thioether ring-closing common to large array formats, including DNA- and RNA-templated synthesis. Each oral peptide herein, selected from virtual libraries of partially N-methylated peptides using in silico methods, reflects the subset consistent with low energy conformations, low desolvation penalties, and passive permeability. We envision that, by retaining the backbone N-methylation pattern and consequent bias toward permeability, one can generate large peptide arrays with sufficient side chain diversity to identify permeability-biased ligands to a variety of protein targets.
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Affiliation(s)
- Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alec N Flyer
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jakal Amin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charles Babu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christian Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jingzhou Li
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eugene Liu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Katsumasa Nakajima
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - David Nettleton
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tajesh J Patel
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Patrick C Reid
- PeptiDream, Inc., 3-25-23 Tonomachi, Kawasaki-Ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Lihua Yang
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lauren G Monovich
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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28
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Caron G, Kihlberg J, Goetz G, Ratkova E, Poongavanam V, Ermondi G. Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space. ACS Med Chem Lett 2021; 12:13-23. [PMID: 33488959 PMCID: PMC7812602 DOI: 10.1021/acsmedchemlett.0c00581] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
An increasing number of drug discovery programs concern compounds in the beyond rule of 5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent results show that common paradigms of property-based drug design need revision to be applied to larger and more flexible compounds. A virtual event entitled "Solubility, permeability and physico-chemical properties in the bRo5 chemical space" was organized to provide preliminary guidance on how to make the discovery of oral drugs in the bRo5 space more effective. The four speakers emphasized the importance of the bRo5 space as a source of new oral drugs and provided examples of experimental and computational methods specifically tailored for design and optimization in this chemical space.
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Affiliation(s)
- Giulia Caron
- Molecular
Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy
| | - Jan Kihlberg
- Department
of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Gilles Goetz
- Hit
Discovery and Optimization, Discovery Sciences, WWRD, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ekaterina Ratkova
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Giuseppe Ermondi
- Molecular
Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy
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29
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Schiesser S, Chepliaka H, Kollback J, Quennesson T, Czechtizky W, Cox RJ. N-Trifluoromethyl Amines and Azoles: An Underexplored Functional Group in the Medicinal Chemist’s Toolbox. J Med Chem 2020; 63:13076-13089. [DOI: 10.1021/acs.jmedchem.0c01457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Hanna Chepliaka
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandstrasse 5−13, 81377 Munich, Germany
| | - Johanna Kollback
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
- Department of Chemistry and Molecular Biology, Göteborgs universitet, Kemigården 4, 41296 Gothenburg, Sweden
| | - Thibaut Quennesson
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
- Université de Lille, Institut Pasteur de Lille, INSERM U1177 − Drugs and Molecules for Living Systems, 59000 Lille, France
| | - Werngard Czechtizky
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Rhona J. Cox
- Department of Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
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30
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Pyridyl-Ala Modified Cyclic Hexapeptides: In-Vitro and In-Vivo Profiling for Oral Bioavailability. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
We and others have been aiming at modifications to maintain or to enhance solubility while enabling permeability for cyclic hexapeptides. Especially, the 2-pyridyl-Ala modification was investigated, since in this case, the pyridyl-nitrogen is able to form an H-bond to the NH of the same residue. The hypothesis of a backbone side-chain interaction was demonstrated by NMR experiments, and further results obtained on a variety of pyridyl-Ala derivatives, studied systematically in the context of permeability, are presented in this contribution. Thus, this study sheds some more light on the pyridyl-Ala modification, which had been reported earlier. In addition to the in vitro profiling, the extent of oral bioavailability was assessed in rats. In principle, the pyridyl-Ala residue can be considered as an amino acid supporting oral uptake.
Graphic Abstract
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31
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Tinworth CP, Young RJ. Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data. J Med Chem 2020; 63:10091-10108. [PMID: 32324397 DOI: 10.1021/acs.jmedchem.9b01596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rule of 5 was designed to estimate the likelihood of poor absorption or permeation, noting the impact of poor solubility. This Perspective explores the impact of various physicochemical descriptors and contemporary lipophilicity measurements on permeability and solubility, showing that the distribution coefficient log D7.4 (rather than log P) is the most impactful parameter. Molecular weight, almost invariably the defining characteristic of "beyond the rule of 5" compounds, has little impact on solubility when log D7.4 measurements and aromaticity are considered. Predicting permeation is more complex, given passive and carrier transport mechanisms; however, notable patterns of behavior are apparent, giving insight even "beyond the rule of 5". Recommended best practices should involve using the facts (measurements) and the patterns they reveal to establish informative principles rather than fastidious rules.
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Affiliation(s)
- Christopher P Tinworth
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Young
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.,Blue Burgundy Ltd., Bedford, Bedfordshire MK45 2AD, U.K
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32
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Updating the portfolio of physicochemical descriptors related to permeability in the beyond the rule of 5 chemical space. Eur J Pharm Sci 2020; 146:105274. [PMID: 32088315 DOI: 10.1016/j.ejps.2020.105274] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 02/08/2023]
Abstract
Beyond rule of 5 (bRo5) molecules are attracting significant interest in modern drug discovery mostly because many novel targets require large and more flexible structures. The main aim of this paper is the identification of ad hoc bRo5 physicochemical descriptors of ionization, lipophilicity, polarity and chameleonicity and their measurement. We used different methods to collect ionization (pKa measures and log k'80 PLRP-S trends), lipophilicity (in octanol/water, in apolar systems and in biomimetic environments), polarity (Δlog Poct-tol, EPSA and Δlog KWIAM) and chameleonicity (ChameLogD) descriptors for 26 bRo5 drugs. A second aim was to check the relationship between physicochemical descriptors and permeability for a subset of compounds for which solid permeability values are reported in the literature. Results showed that the physicochemical profile in the bRo5 chemical space is often experimentally accessible, albeit more tools are required to overcome limitations of individual methods. For the investigated compounds, permeability is governed by Δlog Poct-tol and preliminary data support that chameleonicity could also have an impact.
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33
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Caron G, Digiesi V, Solaro S, Ermondi G. Flexibility in early drug discovery: focus on the beyond-Rule-of-5 chemical space. Drug Discov Today 2020; 25:621-627. [PMID: 31991117 DOI: 10.1016/j.drudis.2020.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/02/2023]
Abstract
Large and flexible compounds are of interest in pharmaceutical programs aimed at challenging protein targets that cannot be modulated by Rule of Five (Ro5)-compliant small molecules. Given their particular structural features, early drug discovery is now in charge of identifying which molecular descriptors should be used in the often called beyond-Rule-of-5 (bRo5) chemical space. Here, we focus on flexibility descriptors. First, we discuss the concept of flexibility and then focus on the number of rotatable bonds (NRot), the most common in silico descriptor. After identifying the pros and cons of NRot, we discuss how Kier's index Φ can replace NRot, and the limits of 3D descriptors. Finally, we show how a misuse of NRot and Φ can result in incorrect interpretations of the impact of flexibility in the bRo5 space and how flexibility has potential in the prospective design of orally bioavailable bRo5 drug candidates.
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Affiliation(s)
- Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy
| | - Vito Digiesi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy
| | - Sara Solaro
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Quarello 15, 10135, Torino, Italy.
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34
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Ciura K, Dziomba S. Application of separation methods for in vitro prediction of blood-brain barrier permeability-The state of the art. J Pharm Biomed Anal 2019; 177:112891. [PMID: 31568968 DOI: 10.1016/j.jpba.2019.112891] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 02/03/2023]
Abstract
Despite many efforts, drug discovery pipeline is still a highly inefficient process. Nowadays, when combinatorial chemistry enables to synthesize hundreds of new drugs candidates, methods for rapid assessment of biopharmaceutical parameters of new compounds are highly desired. Over one-third of drugs candidates is rejected because of unsatisfactory pharmacokinetic properties. In the drug discovery process, the blood-brain barrier (BBB) permeability plays a critical role for central nervous system active drugs candidates as well as non-central nervous system active drugs. For this reason, knowledge on the BBB permeability of compounds is essential in the development of new medicines. The review was focused on the application of different separation methods for BBB permeability assessment. Both chromatographic and electrophoretic methods were described. In the article, the advantages and limitations of well-established chromatographic methods like immobilized artificial membrane chromatography or micellar liquid chromatography, and less common techniques were discussed. Special attention was devoted to methods were microemulsion is used as mobile or pseudostationary phases.
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Affiliation(s)
- Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416, Gdansk, Poland.
| | - Szymon Dziomba
- Department of Toxicology, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416, Gdansk, Poland
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35
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Nyanguile O. Peptide Antiviral Strategies as an Alternative to Treat Lower Respiratory Viral Infections. Front Immunol 2019; 10:1366. [PMID: 31293570 PMCID: PMC6598224 DOI: 10.3389/fimmu.2019.01366] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/29/2019] [Indexed: 01/24/2023] Open
Abstract
Lower respiratory infection caused by human pathogens such as influenza and respiratory syncytial virus (RSV) is a significant healthcare burden that must be addressed. The preferred options to achieve this goal are usually to develop vaccines for prophylaxis and to develop antiviral small molecules to treat infected patients with convenient, orally administrable drugs. However, developing a vaccine against RSV poses special challenges with the diminished immune system of infants and the elderly, and finding a universal flu vaccine is difficult because the product must target a large array of viral strains. On the other hand, the use of small-molecule antivirals can result in the emergence of resistant viruses as it has well-been reported for HIV, influenza, and hepatitis C virus (HCV). This paper reviews peptide antiviral strategies as an alternative to address these challenges. The discovery of influenza and RSV peptidic fusion inhibitors will be discussed and compared to small molecules in view of escape mutations. The importance of constraining peptides into macrocycles to improve both their inhibitory activity and pharmacological properties will be highlighted.
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Affiliation(s)
- Origène Nyanguile
- HES-SO Valais-Wallis, Institute of Life Technologies, Sion, Switzerland
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36
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Fitch WL, Khojasteh C, Aliagas I, Johnson K. Using LC Retention Times in Organic Structure Determination: Drug Metabolite Identification. Drug Metab Lett 2019; 12:93-100. [PMID: 30070179 PMCID: PMC6350196 DOI: 10.2174/1872312812666180802093347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/13/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
Abstract
Background: There is a continued need for improvements in the efficiency of metabolite structure elucidation. Objective: We propose to take LC Retention Time (RT) into consideration during the process of structure determination. Methods: Herein, we develop a simple methodology that employs a Chromatographic Hydrophobicity Index (CHI) framework for standardizing LC conditions and introduce and utilize the concept of a pre-dictable CHI change upon Phase 1 biotransformation (CHIbt). Through the analysis of literature exam-ples, we offer a Quantitative Structure-Retention Relationship (QSRR) for several types of biotransfor-mation (especially hydroxylation) using physicochemical properties (clogP, hydrogen bonding). Results: The CHI system for retention indexing is shown to be practical and simple to implement. A da-tabase of CHIbt values has been created from re-incubation of 3 compounds and from analysis of an addi-tional 17 datasets from the literature. Application of this database is illustrated. Conclusion: In our experience, this simple methodology allows complementing the discovery efforts that saves resources for in-depth characterization using NMR.
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Affiliation(s)
- William L Fitch
- Department of Gastroenterology and Hepatology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, United States
| | - Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics 1 DNA Way MS 412a, Genentech Inc., South San Francisco, CA 94080, United States
| | - Ignacio Aliagas
- Discovery Chemistry, 1 DNA Way, Genentech Inc., South San Francisco, CA 94080, United States
| | - Kevin Johnson
- Department of Drug Metabolism and Pharmacokinetics 1 DNA Way MS 412a, Genentech Inc., South San Francisco, CA 94080, United States
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37
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Russo G, Barbato F, Grumetto L, Philippe L, Lynen F, Goetz GH. Entry of therapeutics into the brain: Influence of exposed polarity calculated in silico and measured in vitro by supercritical fluid chromatography. Int J Pharm 2019; 560:294-305. [DOI: 10.1016/j.ijpharm.2019.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/18/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022]
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38
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Caron G, Kihlberg J, Ermondi G. Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry. Med Res Rev 2019; 39:1707-1729. [PMID: 30659634 DOI: 10.1002/med.21562] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/18/2018] [Accepted: 12/19/2019] [Indexed: 12/14/2022]
Abstract
Recent literature shows that intramolecular hydrogen bond (IMHB) formation can positively impact upon the triad of permeability, solubility, and potency of drugs and candidates. IMHB modulation can be applied to compounds in any chemical space as a means for discovering drug candidates with both acceptable potency and absorption, distribution, metabolism, and excretion-Tox profiles. Integrating IMHB formation in design of drugs is, therefore, an exciting and timely challenge for modern medicinal chemistry. In this review, we first provide some background about IMHBs from the medicinal chemist's point of view and highlight some IMHB-associated misconceptions. Second, we propose a classification of IMHBs for drug discovery purposes, review the most common in silico tactics to include IMHBs in lead optimization and list some experimental physicochemical descriptors, which quantify the propensity of compounds to form IMHBs. By focusing on the compounds size and the number of IMHBs that can potentially be formed, we also outline the major difficulties encountered when designing compounds based on the inclusion of IMHBs. Finally, we discuss recent case studies illustrating the application of IMHB to optimize cell permeability and physicochemical properties of small molecules, cyclic peptides and macrocycles.
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Affiliation(s)
- Giulia Caron
- Molecular Biotechnology and Health Sciences Department, University of Torino, Torino, Italy
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, University of Torino, Torino, Italy
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39
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Abstract
The neurohypophyseal hormone oxytocin (OT) and related modulators of the oxytocin receptor (OTR) have been the subject of intensive research for nearly seven decades. Despite having rather poor drug-like properties, OT is used as a treatment for labor induction, postpartum hemorrhage, and lactation support. The potential use of OT in the treatment of central nervous system (CNS)-related diseases has recently renewed interest in the pharmacology of OT. Oxytocin is one of the most extensively studied cyclic peptides and since the elucidation of its structure in 1953 thousands of peptidic OT analogs with antagonistic and agonistic properties have been synthesized and biologically evaluated. Among them are atosiban, a mixed oxytocin receptor (OTR)/vasopressin 1a receptor (V1aR) antagonist used as a tocolytic agent approved (in certain countries), and carbetocin, a longer acting OTR agonist on the market for the treatment of postpartum hemorrhage. Many other OT analogs with improved pharmacological properties (e.g., barusiban, Antag III) have been identified. These peptides have been tested in clinical trials and/or used as pharmacological tools. In this chapter, the modifications of the OT molecule that led to the discovery of these compounds are reviewed.
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40
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Abstract
One of the most exciting facets of cyclic peptides is that they have the potential to be orally bioavailable, despite having physical properties well beyond the traditional "Rule-of-5" chemistry space (Lipinski et al., Adv Drug Deliv Rev. 23(1): 3-25, 1997). An important component of meeting this challenge is to design cyclic peptides with good intestinal permeability. Here we discuss the design principles for intestinal permeability that have been developed in recent year. These principles can be subdivided into three regimes: physical property guidelines, design strategies for the macrocyclic ring, and design strategies for side chains. The most important overall aims are to minimize solvent-exposed polarity while keeping size, flexibility, and lipophilicity within favorable ranges, thereby allowing peptide chemists to achieve intestinal permeability in addition to other important properties for their compounds, such as solubility and binding affinity. Here we describe a variety of design strategies that have been developed to help peptide chemists in this endeavor.
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41
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Determining molecular properties with differential mobility spectrometry and machine learning. Nat Commun 2018; 9:5096. [PMID: 30504922 PMCID: PMC6269546 DOI: 10.1038/s41467-018-07616-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 11/06/2018] [Indexed: 01/30/2023] Open
Abstract
The fast and accurate determination of molecular properties is highly desirable for many facets of chemical research, particularly in drug discovery where pre-clinical assays play an important role in paring down large sets of drug candidates. Here, we present the use of supervised machine learning to treat differential mobility spectrometry - mass spectrometry data for ten topological classes of drug candidates. We demonstrate that the gas-phase clustering behavior probed in our experiments can be used to predict the candidates' condensed phase molecular properties, such as cell permeability, solubility, polar surface area, and water/octanol distribution coefficient. All of these measurements are performed in minutes and require mere nanograms of each drug examined. Moreover, by tuning gas temperature within the differential mobility spectrometer, one can fine tune the extent of ion-solvent clustering to separate subtly different molecular geometries and to discriminate molecules of very similar physicochemical properties.
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42
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Caron G, Vallaro M, Ermondi G. Log P as a tool in intramolecular hydrogen bond considerations. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 27:65-70. [PMID: 30103865 DOI: 10.1016/j.ddtec.2018.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/01/2018] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Intramolecular hydrogen bonding (IMHB) considerations are gaining relevance in drug discovery and a molecular descriptor which can predict very early the capacity of a compound to form IMHB is needed to speed up the optimization process of drug candidates. Although log Poct is largely used for optimization purposes, in this paper we firstly use the Block Relevance (BR) analysis to theoretically show how log Poct is not a convenient choice to assess IMHB properties of candidates. Then we discuss the limits of log Poct and introduce Δlog Poct-tol, i.e. the difference between log Poct and log Ptol (the logarithm of the partition coefficient in the toluene/water system). Finally, we provided some examples also including bRo5 protease inhibitors, to clarify how to interpret Δlog Poct-tol values.
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Affiliation(s)
- Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy.
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
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43
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Poongavanam V, Doak BC, Kihlberg J. Opportunities and guidelines for discovery of orally absorbed drugs in beyond rule of 5 space. Curr Opin Chem Biol 2018; 44:23-29. [DOI: 10.1016/j.cbpa.2018.05.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/09/2018] [Indexed: 12/11/2022]
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44
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Ermondi G, Vallaro M, Caron G. Learning how to use IAM chromatography for predicting permeability. Eur J Pharm Sci 2018; 114:385-390. [PMID: 29305983 DOI: 10.1016/j.ejps.2018.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/15/2017] [Accepted: 01/01/2018] [Indexed: 10/18/2022]
Abstract
The interest for IAM (Immobilized Artificial Membranes) chromatography in the prediction of drug permeability is increasing. Here we firstly set-up a dataset of 253 molecules including neutral and ionized drugs and few organic compounds for which we either measured or retrieved from the literature IAM.PC.DD2 log KwIAM data. Then we applied block relevance (BR) analysis to extract from PLS models the relative contribution of intermolecular forces governing log KwIAM and Δlog KwIAM (a combined descriptor calculated from log KwIAM). Finally, the relationship between log KwIAM, Δlog KwIAM and passive permeability determined in both PAMPA and MDCK-LE systems was looked for. Models provided the basis for a rational application of IAM chromatography in permeability prediction.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy.
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy.
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy.
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45
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Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Kablaoui N, Vanase-Frawley M, Sciabola S. Hybrid peptide-small molecule oxytocin analogs are potent and selective agonists of the oxytocin receptor. Bioorg Med Chem Lett 2017; 28:415-419. [PMID: 29273395 DOI: 10.1016/j.bmcl.2017.12.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
Oxytocin (OT) is a peptide hormone agonist of the oxytocin receptor (OTR) that has been proposed as a therapeutic to treat a number of social and emotional disorders in addition to its current clinical use to induce labor and treat postpartum bleeding. OT is administered intravenously and intranasally rather than orally, in part because its low passive permeability causes low oral bioavailability. Non-peptidic OTR agonists have also been reported, but none with the exquisite potency of the peptide based agonists. In this report, we describe the OTR agonist activity and exposed polarity of a set of truncated OT analogs as well as hybrid peptide-small molecule analogs of OT. Examples of both truncated analogs and peptide-small molecule hybrid analogs are potent and selective OTR agonists. Hybrid agonist 13, which is 232 Da smaller than OT, still retains subnanomolar potency, full agonist activity, and selectivity over V1a. While these compounds were designed to address the low permeability of OT and other full length analogs, we found that reduction in molecular weight and the removal or replacement of the three amino acid tail of OT did not have a significant effect on passive permeability.
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Affiliation(s)
- Natasha Kablaoui
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States; Pfizer Worldwide Research and Development, Eastern Point Rd, Groton, CT 026340, United States.
| | - Michelle Vanase-Frawley
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States; Pfizer Worldwide Research and Development, Eastern Point Rd, Groton, CT 026340, United States
| | - Simone Sciabola
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States; Pfizer Worldwide Research and Development, Eastern Point Rd, Groton, CT 026340, United States
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47
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Boehm M, Beaumont K, Jones R, Kalgutkar AS, Zhang L, Atkinson K, Bai G, Brown JA, Eng H, Goetz GH, Holder BR, Khunte B, Lazzaro S, Limberakis C, Ryu S, Shapiro MJ, Tylaska L, Yan J, Turner R, Leung SSF, Ramaseshan M, Price DA, Liras S, Jacobson MP, Earp DJ, Lokey RS, Mathiowetz AM, Menhaji-Klotz E. Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators. J Med Chem 2017; 60:9653-9663. [PMID: 29045152 DOI: 10.1021/acs.jmedchem.7b01028] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The chemokine receptor CXCR7 is an attractive target for a variety of diseases. While several small-molecule modulators of CXCR7 have been reported, peptidic macrocycles may provide advantages in terms of potency, selectivity, and reduced off-target activity. We produced a series of peptidic macrocycles that incorporate an N-linked peptoid functionality where the peptoid group enabled us to explore side-chain diversity well beyond that of natural amino acids. At the same time, theoretical calculations and experimental assays were used to track and reduce the polarity while closely monitoring the physicochemical properties. This strategy led to the discovery of macrocyclic peptide-peptoid hybrids with high CXCR7 binding affinities (Ki < 100 nM) and measurable passive permeability (Papp > 5 × 10-6 cm/s). Moreover, bioactive peptide 25 (Ki = 9 nM) achieved oral bioavailability of 18% in rats, which was commensurate with the observed plasma clearance values upon intravenous administration.
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Affiliation(s)
- Markus Boehm
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Kevin Beaumont
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Rhys Jones
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Amit S Kalgutkar
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Liying Zhang
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Karen Atkinson
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Guoyun Bai
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Janice A Brown
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Heather Eng
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Gilles H Goetz
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Brian R Holder
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Bhagyashree Khunte
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Sarah Lazzaro
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Chris Limberakis
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Sangwoo Ryu
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Laurie Tylaska
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Jiangli Yan
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Rushia Turner
- Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Siegfried S F Leung
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.,Circle Pharma , South San Francisco, California 94080, United States
| | - Mahesh Ramaseshan
- Circle Pharma , South San Francisco, California 94080, United States
| | - David A Price
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - David J Earp
- Circle Pharma , South San Francisco, California 94080, United States
| | - R Scott Lokey
- Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Alan M Mathiowetz
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Elnaz Menhaji-Klotz
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
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48
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DeGoey DA, Chen HJ, Cox PB, Wendt MD. Beyond the Rule of 5: Lessons Learned from AbbVie’s Drugs and Compound Collection. J Med Chem 2017; 61:2636-2651. [DOI: 10.1021/acs.jmedchem.7b00717] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- David A. DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Hui-Ju Chen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B. Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Michael D. Wendt
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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49
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Mizuno A, Matsui K, Shuto S. From Peptides to Peptidomimetics: A Strategy Based on the Structural Features of Cyclopropane. Chemistry 2017. [PMID: 28632330 DOI: 10.1002/chem.201702119] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptidomimetics, non-natural mimicries of bioactive peptides, comprise an important class of drug molecules. The essence of the peptidomimetic design is to mimic the key conformation assumed by the bioactive peptides upon binding to their targets. Regulation of the conformation of peptidomimetics is important not only to enhance target binding affinity and selectivity, but also to confer cell-membrane permeability for targeting protein-protein interactions in cells. The rational design of peptidomimetics with suitable three-dimensional structures is challenging, however, due to the inherent flexibility of peptides and their dynamic conformational changes upon binding to the target biomolecules. In this Minireview, a three-dimensional structural diversity-oriented strategy based on the characteristic structural features of cyclopropane to address this challenging issue in peptidomimetic chemistry is described.
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Affiliation(s)
- Akira Mizuno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Kouhei Matsui
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka, 561-0825, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
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50
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Al Bakain RZ, Al-Degs Y, Andri B, Thiébaut D, Vial J, Rivals I. Supercritical Fluid Chromatography of Drugs: Parallel Factor Analysis for Column Testing in a Wide Range of Operational Conditions. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2017; 2017:5340601. [PMID: 28695040 PMCID: PMC5485488 DOI: 10.1155/2017/5340601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 04/11/2017] [Accepted: 04/23/2017] [Indexed: 06/07/2023]
Abstract
Retention mechanisms involved in supercritical fluid chromatography (SFC) are influenced by interdependent parameters (temperature, pressure, chemistry of the mobile phase, and nature of the stationary phase), a complexity which makes the selection of a proper stationary phase for a given separation a challenging step. For the first time in SFC studies, Parallel Factor Analysis (PARAFAC) was employed to evaluate the chromatographic behavior of eight different stationary phases in a wide range of chromatographic conditions (temperature, pressure, and gradient elution composition). Design of Experiment was used to optimize experiments involving 14 pharmaceutical compounds present in biological and/or environmental samples and with dissimilar physicochemical properties. The results showed the superiority of PARAFAC for the analysis of the three-way (column × drug × condition) data array over unfolding the multiway array to matrices and performing several classical principal component analyses. Thanks to the PARAFAC components, similarity in columns' function, chromatographic trend of drugs, and correlation between separation conditions could be simply depicted: columns were grouped according to their H-bonding forces, while gradient composition was dominating for condition classification. Also, the number of drugs could be efficiently reduced for columns classification as some of them exhibited a similar behavior, as shown by hierarchical clustering based on PARAFAC components.
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Affiliation(s)
- Ramia Z. Al Bakain
- Department of Chemistry, Faculty of Science, The University of Jordan, P.O. Box 11942, Amman, Jordan
| | - Yahya Al-Degs
- Chemistry Department, The Hashemite University, P.O. Box 150459, Zarqa, Jordan
| | - Bertyl Andri
- Laboratory of Analytical Chemistry, CIRM, University of Liege (ULg), 15 Avenue Hippocrate (B36), 4000 Liege, Belgium
| | - Didier Thiébaut
- Laboratoire Sciences Analytiques, Bioanalytiques et Miniaturisation, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Jérôme Vial
- Laboratoire Sciences Analytiques, Bioanalytiques et Miniaturisation, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Isabelle Rivals
- Équipe de Statistique Appliquée, ESPCI Paris, PSL Research University, UMRS 1158, 75005 Paris, France
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