51
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Whitty A, Viarengo LA, Zhong M. Progress towards the broad use of non-peptide synthetic macrocycles in drug discovery. Org Biomol Chem 2018; 15:7729-7735. [PMID: 28876025 DOI: 10.1039/c7ob00056a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We discuss progress towards addressing three key questions pertaining to the design of screening libraries of synthetic non-peptidic macrocycles (MCs) for drug discovery: What structural and physicochemical properties of MCs maximize the likelihood of achieving strong and specific binding to protein targets? What features render a protein target suitable for binding MCs, and can this information be used to identify suitable targets for inhibition by MCs? What properties of synthetic MCs confer good pharmaceutical properties, and particularly good aqueous solubility coupled with passive membrane permeability? We additionally discuss how the criteria that define a meaningful MC screening hit are linked to the size of the screening library and the synthetic methodology employed in its preparation.
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Affiliation(s)
- Adrian Whitty
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.
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52
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Sawyer TK, Partridge AW, Kaan HYK, Juang YC, Lim S, Johannes C, Yuen TY, Verma C, Kannan S, Aronica P, Tan YS, Sherborne B, Ha S, Hochman J, Chen S, Surdi L, Peier A, Sauvagnat B, Dandliker PJ, Brown CJ, Ng S, Ferrer F, Lane DP. Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges. Bioorg Med Chem 2018; 26:2807-2815. [PMID: 29598901 DOI: 10.1016/j.bmc.2018.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022]
Abstract
Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.
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53
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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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54
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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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55
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Abstract
The generation of conformations for small molecules is a problem of continuing interest in cheminformatics and computational drug discovery. This review will present an overview of methods used to sample conformational space, focusing on those methods designed for organic molecules commonly of interest in drug discovery. Different approaches to both the sampling of conformational space and the scoring of conformational stability will be compared and contrasted, with an emphasis on those methods suitable for conformer sampling of large numbers of drug-like molecules. Particular attention will be devoted to the appropriate utilization of information from experimental solid-state structures in validating and evaluating the performance of these tools. The review will conclude with some areas worthy of further investigation.
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Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
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56
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In Silico Prediction of hPXR Activators Using Structure-Based Pharmacophore Modeling. J Pharm Sci 2017; 106:1752-1759. [DOI: 10.1016/j.xphs.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/21/2017] [Accepted: 03/06/2017] [Indexed: 11/30/2022]
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57
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Price DA, Eng H, Farley KA, Goetz GH, Huang Y, Jiao Z, Kalgutkar AS, Kablaoui NM, Khunte B, Liras S, Limberakis C, Mathiowetz AM, Ruggeri RB, Quan JM, Yang Z. Comparative pharmacokinetic profile of cyclosporine (CsA) with a decapeptide and a linear analogue. Org Biomol Chem 2017; 15:2501-2506. [PMID: 28266673 DOI: 10.1039/c7ob00096k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The synthesis and in vivo pharmacokinetic profile of an analogue of cyclosporine is disclosed. An acyclic congener was also profiled in in vitro assays to compare cell permeability. The compounds possess similar calculated and measured molecular descriptors however have different behaviors in an RRCK assay to assess cell permeability.
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Affiliation(s)
- David A Price
- Pfizer Inc. Medicine Design, 610 Main Street, Cambridge, Massachusetts, 02155 USA.
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58
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Pye CR, Hewitt WM, Schwochert J, Haddad TD, Townsend CE, Etienne L, Lao Y, Limberakis C, Furukawa A, Mathiowetz AM, Price DA, Liras S, Lokey RS. Nonclassical Size Dependence of Permeation Defines Bounds for Passive Adsorption of Large Drug Molecules. J Med Chem 2017; 60:1665-1672. [PMID: 28059508 DOI: 10.1021/acs.jmedchem.6b01483] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Macrocyclic peptides are considered large enough to inhibit "undruggable" targets, but the design of passively cell-permeable molecules in this space remains a challenge due to the poorly understood role of molecular size on passive membrane permeability. Using split-pool combinatorial synthesis, we constructed a library of cyclic, per-N-methlyated peptides spanning a wide range of calculated lipohilicities (0 < AlogP < 8) and molecular weights (∼800 Da < MW < ∼1200 Da). Analysis by the parallel artificial membrane permeability assay revealed a steep drop-off in apparent passive permeability with increasing size in stark disagreement with current permeation models. This observation, corroborated by a set of natural products, helps define criteria for achieving permeability in larger molecular size regimes and suggests an operational cutoff, beyond which passive permeability is constrained by a sharply increasing penalty on membrane permeation.
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Affiliation(s)
- Cameron R Pye
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - William M Hewitt
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Terra D Haddad
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Lyns Etienne
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Yongtong Lao
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Chris Limberakis
- World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. , Groton, Connecticut 06340, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Alan M Mathiowetz
- World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. , Cambridge, Massachusetts 02139, United States
| | - David A Price
- World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. , Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. , Cambridge, Massachusetts 02139, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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59
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Goetz GH, Shalaeva M, Caron G, Ermondi G, Philippe L. Relationship between Passive Permeability and Molecular Polarity Using Block Relevance Analysis. Mol Pharm 2017; 14:386-393. [DOI: 10.1021/acs.molpharmaceut.6b00724] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Giulia Caron
- Molecular
Biotechnology and Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular
Biotechnology and Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer Inc., Groton, Connecticut 06340, United States
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60
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Matsui K, Kido Y, Watari R, Kashima Y, Yoshida Y, Shuto S. Highly Conformationally Restricted Cyclopropane Tethers with Three-Dimensional Structural Diversity Drastically Enhance the Cell Permeability of Cyclic Peptides. Chemistry 2016; 23:3034-3041. [PMID: 27878880 DOI: 10.1002/chem.201604946] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Indexed: 12/21/2022]
Abstract
The conformation of cyclic peptides is closely related to their physicochemical and biological properties, but their rational design to obtain a conformation with the desired properties is difficult. Herein, we present a new strategy by using conformationally restricted cyclopropane tethers (CPTs) to control the conformation and improve the cell permeability of cyclic peptides regardless of the amino acid sequence. Newly designed cis- or trans-CPTs with three-dimensional structural diversity were introduced into a model cyclic peptide, and the relationship between the conformation of the cyclic peptides and their cell permeability was analyzed. Peptides containing a CPT exhibited conformational diversity due to the characteristic steric feature of cyclopropane, among which peptides containing a CPT, cis-NfCf had remarkably higher cell permeability than peptides containing other CPTs-even superior to that of cyclosporine A, a known permeable cyclic peptide.
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Affiliation(s)
- Kouhei Matsui
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka-shi, Osaka, 561-0825, Japan
| | - Yasuto Kido
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka-shi, Osaka, 561-0825, Japan
| | - Ryosuke Watari
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka-shi, Osaka, 561-0825, Japan
| | - Yousuke Kashima
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka-shi, Osaka, 561-0825, Japan
| | - Yutaka Yoshida
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka-shi, Osaka, 561-0825, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
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61
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Molecular descriptors for polarity: the need for going beyond polar surface area. Future Med Chem 2016; 8:2013-2016. [DOI: 10.4155/fmc-2016-0165] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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62
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Structural and conformational determinants of macrocycle cell permeability. Nat Chem Biol 2016; 12:1065-1074. [DOI: 10.1038/nchembio.2203] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 08/04/2016] [Indexed: 12/31/2022]
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63
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Krämer SD, Aschmann HE, Hatibovic M, Hermann KF, Neuhaus CS, Brunner C, Belli S. When barriers ignore the "rule-of-five". Adv Drug Deliv Rev 2016; 101:62-74. [PMID: 26877103 DOI: 10.1016/j.addr.2016.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/20/2022]
Abstract
Why are a few drugs with properties beyond the rule of 5 (bRo5) absorbed across the intestinal mucosa while most other bRo5 compounds are not? Are such exceptional bRo5 compounds exclusively taken up by carrier-mediated transport or are they able to permeate the lipid bilayer (passive lipoidal diffusion)? Our experimental data with liposomes indicate that tetracycline, which violates one rule of the Ro5, and rifampicin, violating three of the rules, significantly permeate a phospholipid bilayer with kinetics similar to labetalol and metoprolol, respectively. Published data from experimental work and molecular dynamics simulations suggest that the formation of intramolecular H-bonds and the possibility to adopt an elongated shape besides the presence of a significant fraction of net neutral species facilitate lipid bilayer permeation. As an alternative to lipid bilayer permeation, carrier proteins can be targeted to improve absorption, with the potential drawbacks of drug-drug interactions and non-linear pharmacokinetics.
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Affiliation(s)
- Stefanie D Krämer
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland.
| | - Hélène E Aschmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Maja Hatibovic
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Katharina F Hermann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Claudia S Neuhaus
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Cyrill Brunner
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Sara Belli
- Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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64
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Matsson P, Doak BC, Over B, Kihlberg J. Cell permeability beyond the rule of 5. Adv Drug Deliv Rev 2016; 101:42-61. [PMID: 27067608 DOI: 10.1016/j.addr.2016.03.013] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 11/17/2022]
Abstract
Drug discovery for difficult targets that have large and flat binding sites is often better suited to compounds beyond the "rule of 5" (bRo5). However, such compounds carry higher pharmacokinetic risks, such as low solubility and permeability, and increased efflux and metabolism. Interestingly, recent drug approvals and studies suggest that cell permeable and orally bioavailable drugs can be discovered far into bRo5 space. Tactics such as reduction or shielding of polarity by N-methylation, bulky side chains and intramolecular hydrogen bonds may be used to increase cell permeability in this space, but often results in decreased solubility. Conformationally flexible compounds can, however, combine high permeability and solubility, properties that are keys for cell permeability and intestinal absorption. Recent developments in computational conformational analysis will aid design of such compounds and hence prediction of cell permeability. Transporter mediated efflux occurs for most investigated drugs in bRo5 space, however it is commonly overcome by high local intestinal concentrations on oral administration. In contrast, there is little data to support significant impact of transporter-mediated intestinal absorption in bRo5 space. Current knowledge of compound properties that govern transporter effects of bRo5 drugs is limited and requires further fundamental and comprehensive studies.
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Affiliation(s)
- Pär Matsson
- Department of Pharmacy, BMC, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Bradley C Doak
- Department of Medicinal Chemistry, MIPS, Monash University, 381 Royal Parade, Parkville, Victoria, Australia
| | - Björn Over
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
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65
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Whitty A, Zhong M, Viarengo L, Beglov D, Hall DR, Vajda S. Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs. Drug Discov Today 2016; 21:712-7. [PMID: 26891978 DOI: 10.1016/j.drudis.2016.02.005] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 12/27/2022]
Abstract
Key to the pharmaceutical utility of certain macrocyclic drugs is a 'chameleonic' ability to change their conformation to expose polar groups in aqueous solution, but bury them when traversing lipid membranes. Based on analysis of the structures of 20 macrocyclic compounds that are approved oral drugs, we propose that good solubility requires a topological polar surface area (TPSA, in Å(2)) of ≥0.2×molecular weight (MW). Meanwhile, good passive membrane permeability requires a molecular (i.e., 3D) PSA in nonpolar environments of ≤140Å(2). We show that one or other of these limits is almost invariably violated for compounds with MW>600Da, suggesting that some degree of chameleonic behavior is required for most high MW oral drugs.
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Affiliation(s)
- Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA, USA.
| | - Mengqi Zhong
- Department of Chemistry, Boston University, Boston, MA, USA
| | | | - Dmitri Beglov
- Departments of Biomedical Engineering and Chemistry, Boston University, Boston, MA, USA
| | | | - Sandor Vajda
- Department of Chemistry, Boston University, Boston, MA, USA; Departments of Biomedical Engineering and Chemistry, Boston University, Boston, MA, USA.
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66
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Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products. Future Med Chem 2015; 7:2121-30. [PMID: 26067057 DOI: 10.4155/fmc.15.78] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many cyclic peptide natural products are larger and structurally more complex than conventional small molecule drugs. Although some molecules in this class are known to possess favorable pharmacokinetic properties, there have been few reports on the membrane permeabilities of cyclic peptide natural products. Here, we present the passive membrane permeabilities of 39 cyclic peptide natural products, and interpret the results using a computational permeability prediction algorithm based on their known or calculated 3D conformations. We found that the permeabilities of these compounds, measured in a parallel artificial membrane permeability assay, spanned a wide range and demonstrated the important influence of conformation on membrane permeability. These results will aid in the development of these compounds as a viable drug paradigm.
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67
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Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SSF, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett 2015; 17:2928-31. [PMID: 26046483 DOI: 10.1021/acs.orglett.5b01162] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of peptide-to-peptoid substitutions on the passive membrane permeability of an N-methylated cyclic hexapeptide is examined. In general, substitutions maintained permeability but increased conformational heterogeneity. Diversification with nonproteinogenic side chains increased permeability up to 3-fold. Additionally, the conformational impact of peptoid substitutions within a β-turn are explored. Based on these results, the strategic incorporation of peptoid residues into cyclic peptides can maintain or improve cell permeability, while increasing access to diverse side-chain functionality.
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Affiliation(s)
- Joshua Schwochert
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Rushia Turner
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Melissa Thang
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Ray F Berkeley
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Alexandra R Ponkey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Kelsie M Rodriguez
- †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
| | - Bhagyashree Khunte
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Gilles Goetz
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Chris Limberakis
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Amit S Kalgutkar
- §Pharmacokinetics and Drug Metabolism, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Heather Eng
- ⊥Pharmacokinetics and Drug Metabolism, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Alan M Mathiowetz
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - David A Price
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - R Scott Lokey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
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68
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Bockus AT, Lexa KW, Pye CR, Kalgutkar AS, Gardner JW, Hund KCR, Hewitt WM, Schwochert JA, Glassey E, Price DA, Mathiowetz AM, Liras S, Jacobson MP, Lokey RS. Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products. J Med Chem 2015; 58:4581-9. [DOI: 10.1021/acs.jmedchem.5b00128] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrew T. Bockus
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Katrina W. Lexa
- Department
of Pharmaceutical Chemistry, University of California— San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - Cameron R. Pye
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Amit S. Kalgutkar
- Pharmacokinetics
and Drug Metabolism, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Jarret W. Gardner
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Kathryn C. R. Hund
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua A. Schwochert
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Emerson Glassey
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - David A. Price
- Worldwide
Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Alan M. Mathiowetz
- Worldwide
Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Spiros Liras
- Worldwide
Medicinal Chemistry, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Matthew P. Jacobson
- Department
of Pharmaceutical Chemistry, University of California— San Francisco, 1700 4th Street, San Francisco, California 94158, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University of California—Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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69
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Hewitt WM, Leung SSF, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS. Cell-Permeable Cyclic Peptides from Synthetic Libraries Inspired by Natural Products. J Am Chem Soc 2015; 137:715-21. [DOI: 10.1021/ja508766b] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- William M. Hewitt
- Department
of 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 94143, United States
| | - Cameron R. Pye
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Alexandra R. Ponkey
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Maria Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd., Cambridge CB21 6GH, U.K
| | - Matthew P. Jacobson
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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70
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Yang NJ, Hinner MJ. Getting across the cell membrane: an overview for small molecules, peptides, and proteins. Methods Mol Biol 2015; 1266:29-53. [PMID: 25560066 DOI: 10.1007/978-1-4939-2272-7_3] [Citation(s) in RCA: 456] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ability to efficiently access cytosolic proteins is desired in both biological research and medicine. However, targeting intracellular proteins is often challenging, because to reach the cytosol, exogenous molecules must first traverse the cell membrane. This review provides a broad overview of how certain molecules are thought to cross this barrier, and what kinds of approaches are being made to enhance the intracellular delivery of those that are impermeable. We first discuss rules that govern the passive permeability of small molecules across the lipid membrane, and mechanisms of membrane transport that have evolved in nature for certain metabolites, peptides, and proteins. Then, we introduce design strategies that have emerged in the development of small molecules and peptides with improved permeability. Finally, intracellular delivery systems that have been engineered for protein payloads are surveyed. Viewpoints from varying disciplines have been brought together to provide a cohesive overview of how the membrane barrier is being overcome.
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Affiliation(s)
- Nicole J Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139, USA,
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71
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Thansandote P, Harris RM, Dexter HL, Simpson GL, Pal S, Upton RJ, Valko K. Improving the passive permeability of macrocyclic peptides: Balancing permeability with other physicochemical properties. Bioorg Med Chem 2015; 23:322-7. [DOI: 10.1016/j.bmc.2014.11.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 12/29/2022]
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72
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Schwochert J, Pye C, Ahlbach C, Abdollahian Y, Farley K, Khunte B, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Lokey RS. Revisiting N-to-O Acyl Shift for Synthesis of Natural Product-like Cyclic Depsipeptides. Org Lett 2014; 16:6088-91. [DOI: 10.1021/ol503170b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Joshua Schwochert
- Chemistry
and Biochemistry, University of California—Santa Cruz, Santa Cruz, California 95064, United States
| | - Cameron Pye
- Chemistry
and Biochemistry, University of California—Santa Cruz, Santa Cruz, California 95064, United States
| | - Christopher Ahlbach
- Chemistry
and Biochemistry, University of California—Santa Cruz, Santa Cruz, California 95064, United States
| | - Yashar Abdollahian
- Chemistry
and Biochemistry, University of California—Santa Cruz, Santa Cruz, California 95064, United States
| | - Kathleen Farley
- Worldwide Medicinal
Chemistry, Groton Laboratories, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Bhagyashree Khunte
- Worldwide Medicinal
Chemistry, Groton Laboratories, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Chris Limberakis
- Worldwide Medicinal
Chemistry, Groton Laboratories, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Amit S. Kalgutkar
- Pharmacokinetics,
Dynamics, and Metabolism, Cambridge Laboratories, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Heather Eng
- Pharmacokinetics,
Dynamics, and Metabolism, Groton Laboratories, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Worldwide Medicinal
Chemistry, Groton Laboratories, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Alan M. Mathiowetz
- Worldwide Medicinal
Chemistry, Cambridge Laboratories, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - David A. Price
- Worldwide Medicinal
Chemistry, Cambridge Laboratories, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- Worldwide Medicinal
Chemistry, Cambridge Laboratories, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - R. Scott Lokey
- Chemistry
and Biochemistry, University of California—Santa Cruz, Santa Cruz, California 95064, United States
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73
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Goetz GH, Philippe L, Shapiro MJ. EPSA: A Novel Supercritical Fluid Chromatography Technique Enabling the Design of Permeable Cyclic Peptides. ACS Med Chem Lett 2014; 5:1167-72. [PMID: 25313332 DOI: 10.1021/ml500239m] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/04/2014] [Indexed: 12/23/2022] Open
Abstract
Most peptides are generally insufficiently permeable to be used as oral drugs. Designing peptides with improved permeability without reliable permeability monitoring is a challenge. We have developed a supercritical fluid chromatography technique for peptides, termed EPSA, which is shown here to enable improved permeability design. Through assessing the exposed polarity of a peptide, this technique can be used as a permeability surrogate.
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Affiliation(s)
- Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
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74
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Hill TA, Lohman RJ, Hoang HN, Nielsen DS, Scully CCG, Kok WM, Liu L, Lucke AJ, Stoermer MJ, Schroeder CI, Chaousis S, Colless B, Bernhardt PV, Edmonds DJ, Griffith DA, Rotter CJ, Ruggeri RB, Price DA, Liras S, Craik DJ, Fairlie DP. Cyclic Penta- and Hexaleucine Peptides without N-Methylation Are Orally Absorbed. ACS Med Chem Lett 2014; 5:1148-51. [PMID: 25313329 DOI: 10.1021/ml5002823] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/04/2014] [Indexed: 02/08/2023] Open
Abstract
Development of peptide-based drugs has been severely limited by lack of oral bioavailability with less than a handful of peptides being truly orally bioavailable, mainly cyclic peptides with N-methyl amino acids and few hydrogen bond donors. Here we report that cyclic penta- and hexa-leucine peptides, with no N-methylation and five or six amide NH protons, exhibit some degree of oral bioavailability (4-17%) approaching that of the heavily N-methylated drug cyclosporine (22%) under the same conditions. These simple cyclic peptides demonstrate that oral bioavailability is achievable for peptides that fall outside of rule-of-five guidelines without the need for N-methylation or modified amino acids.
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Affiliation(s)
- Timothy A. Hill
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rink-Jan Lohman
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Huy N. Hoang
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel S. Nielsen
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conor C. G. Scully
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - W. Mei Kok
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ligong Liu
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew J. Lucke
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Martin J. Stoermer
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina I. Schroeder
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Barbara Colless
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Paul V. Bernhardt
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - David J. Edmonds
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - David A. Griffith
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - Charles J. Rotter
- Pfizer Pharmacokinetics, Dynamics, and Metabolism, Groton, Connecticut 06340, United States
| | - Roger B. Ruggeri
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - David A. Price
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - Spiros Liras
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - David J. Craik
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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75
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Doak B, Over B, Giordanetto F, Kihlberg J. Oral Druggable Space beyond the Rule of 5: Insights from Drugs and Clinical Candidates. ACTA ACUST UNITED AC 2014; 21:1115-42. [DOI: 10.1016/j.chembiol.2014.08.013] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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76
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Goetz GH, Farrell W, Shalaeva M, Sciabola S, Anderson D, Yan J, Philippe L, Shapiro MJ. High Throughput Method for the Indirect Detection of Intramolecular Hydrogen Bonding. J Med Chem 2014; 57:2920-9. [DOI: 10.1021/jm401859b] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gilles H. Goetz
- Groton Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - William Farrell
- La Jolla Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Marina Shalaeva
- Groton Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Simone Sciabola
- Neuroscience, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Dennis Anderson
- Groton Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jiangli Yan
- Groton Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Groton Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Groton Laboratories, Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340, United States
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77
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Certal V, Carry JC, Halley F, Virone-Oddos A, Thompson F, Filoche-Rommé B, El-Ahmad Y, Karlsson A, Charrier V, Delorme C, Rak A, Abecassis PY, Amara C, Vincent L, Bonnevaux H, Nicolas JP, Mathieu M, Bertrand T, Marquette JP, Michot N, Benard T, Perrin MA, Lemaitre O, Guerif S, Perron S, Monget S, Gruss-Leleu F, Doerflinger G, Guizani H, Brollo M, Delbarre L, Bertin L, Richepin P, Loyau V, Garcia-Echeverria C, Lengauer C, Schio L. Discovery and Optimization of Pyrimidone Indoline Amide PI3Kβ Inhibitors for the Treatment of Phosphatase and Tensin Homologue (PTEN)-Deficient Cancers. J Med Chem 2014; 57:903-20. [DOI: 10.1021/jm401642q] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victor Certal
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Jean-Christophe Carry
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Frank Halley
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Angela Virone-Oddos
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Fabienne Thompson
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Bruno Filoche-Rommé
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Youssef El-Ahmad
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Andreas Karlsson
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Véronique Charrier
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Cécile Delorme
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Alexey Rak
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Pierre-Yves Abecassis
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Céline Amara
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Loïc Vincent
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Hélène Bonnevaux
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Jean-Paul Nicolas
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Magali Mathieu
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Thomas Bertrand
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Jean-Pierre Marquette
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Nadine Michot
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Tsiala Benard
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Marc-Antoine Perrin
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Olivier Lemaitre
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Stephane Guerif
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Sébastien Perron
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Sylvie Monget
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Florence Gruss-Leleu
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Gilles Doerflinger
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Houlfa Guizani
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Maurice Brollo
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Laurence Delbarre
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Luc Bertin
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Patrick Richepin
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Véronique Loyau
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Carlos Garcia-Echeverria
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Christoph Lengauer
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
| | - Laurent Schio
- Oncology Drug Discovery, §Structure Design Informatics,
and Structural Biology, #Drug Disposition and Safety (DSAR), †Protein Production,⊥Pharmaceutical Sciences, ∥Analytical Sciences, Sanofi, 13, quai Jules Guesde, 94403 Vitry-sur-Seine, France
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78
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Giordanetto F, Kihlberg J. Macrocyclic drugs and clinical candidates: what can medicinal chemists learn from their properties? J Med Chem 2013; 57:278-95. [PMID: 24044773 DOI: 10.1021/jm400887j] [Citation(s) in RCA: 404] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Macrocycles are ideal in efforts to tackle "difficult" targets, but our understanding of what makes them cell permeable and orally bioavailable is limited. Analysis of approximately 100 macrocyclic drugs and clinical candidates revealed that macrocycles are predominantly used for infectious disease and in oncology and that most belong to the macrolide or cyclic peptide class. A significant number (N = 34) of these macrocycles are administered orally, revealing that oral bioavailability can be obtained at molecular weights up to and above 1 kDa and polar surface areas ranging toward 250 Å(2). Moreover, insight from a group of "de novo designed" oral macrocycles in clinical studies and understanding of how cyclosporin A and model cyclic hexapeptides cross cell membranes may unlock wider opportunities in drug discovery. However, the number of oral macrocycles is still low and it remains to be seen if they are outliers or if macrocycles will open up novel oral druggable space.
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Affiliation(s)
- Fabrizio Giordanetto
- Cardiovascular and Metabolic Disorders Research Area, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
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79
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Shalaeva M, Caron G, Abramov YA, O’Connell TN, Plummer MS, Yalamanchi G, Farley KA, Goetz GH, Philippe L, Shapiro MJ. Integrating Intramolecular Hydrogen Bonding (IMHB) Considerations in Drug Discovery Using ΔlogP As a Tool. J Med Chem 2013; 56:4870-9. [DOI: 10.1021/jm301850m] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Giulia Caron
- Molecular Biotechnology and
Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Yuriy A. Abramov
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Thomas N. O’Connell
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Mark S. Plummer
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Geeta Yalamanchi
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Kathleen A. Farley
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
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80
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