151
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McHugh SM, Rogers JR, Yu H, Lin YS. Insights into How Cyclic Peptides Switch Conformations. J Chem Theory Comput 2016; 12:2480-8. [DOI: 10.1021/acs.jctc.6b00193] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean M. McHugh
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Julia R. Rogers
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Hongtao Yu
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department
of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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152
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Horses for courses: reaching outside drug-like chemical space for inhibitors of challenging drug targets. Future Med Chem 2016; 7:1093-5. [PMID: 26132520 DOI: 10.4155/fmc.15.56] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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153
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Liu H, Zeng F, Zhang M, Huang F, Wang J, Guo J, Liu C, Wang H. Emerging landscape of cell penetrating peptide in reprogramming and gene editing. J Control Release 2016; 226:124-137. [PMID: 26849918 DOI: 10.1016/j.jconrel.2016.02.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/31/2016] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
Abstract
The plasma membrane remains a major barrier for intracellular drug delivery, to overcome this issue, a variety of approaches have been developed and used to deliver therapeutic cargos. Among these approaches, cell penetrating peptide (CPP) is promising and affords widely used vector for efficient intracellular delivery of cargos. Moreover, the latter findings including iPS reprogramming and direct transdifferentiation as well as gene editing have gradually become hot research topic; because their application in tissue engineering and disease modeling have great potential to advance innovation in precision medicine. Since the beginning, research on these approaches is mainly based on virus transduction system, while, under the consideration for obviating the risk of mutagenic insertion and enables more accurate controlling, CPP-based efficient virus-free delivery strategy has been used recently. In this review, we summarize the existing CPP-based delivery system, emerging landscape of CPP application in stem cell manipulation and reprogramming, along with CPP contributions to gene editing techniques.
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Affiliation(s)
- Huiting Liu
- Medical School, China Three Gorges University, Yichang 443002, China; Department of Nuclear Medicine, Chongqing Three Gorges Central Hospital, Wanzhou 404000, China
| | - Fanhui Zeng
- The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China
| | - Ming Zhang
- Medical School, China Three Gorges University, Yichang 443002, China
| | - Fajun Huang
- School of Medical Science, Hubei University for Nationalities, Enshi 445000, China
| | - Jiajun Wang
- Medical School, China Three Gorges University, Yichang 443002, China; School of Medical Science, Hubei University for Nationalities, Enshi 445000, China.
| | - Jingjing Guo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Changbai Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China.
| | - Hu Wang
- Medical School, China Three Gorges University, Yichang 443002, China; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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154
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Meanwell NA. Improving Drug Design: An Update on Recent Applications of Efficiency Metrics, Strategies for Replacing Problematic Elements, and Compounds in Nontraditional Drug Space. Chem Res Toxicol 2016; 29:564-616. [DOI: 10.1021/acs.chemrestox.6b00043] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research & Development, Wallingford, Connecticut 06492, United States
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155
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Henning RK, Varghese JO, Das S, Nag A, Tang G, Tang K, Sutherland AM, Heath JR. Degradation of Akt using protein-catalyzed capture agents. J Pept Sci 2016; 22:196-200. [PMID: 26880702 DOI: 10.1002/psc.2858] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 12/22/2022]
Abstract
Abnormal signaling of the protein kinase Akt has been shown to contribute to human diseases such as diabetes and cancer, but Akt has proven to be a challenging target for drugging. Using iterative in situ click chemistry, we recently developed multiple protein-catalyzed capture (PCC) agents that allosterically modulate Akt enzymatic activity in a protein-based assay. Here, we utilize similar PCCs to exploit endogenous protein degradation pathways. We use the modularity of the anti-Akt PCCs to prepare proteolysis targeting chimeric molecules that are shown to promote the rapid degradation of Akt in live cancer cells. These novel proteolysis targeting chimeric molecules demonstrate that the epitope targeting selectivity of PCCs can be coupled with non-traditional drugging moieties to inhibit challenging targets.
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Affiliation(s)
- Ryan K Henning
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Joseph O Varghese
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Samir Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Arundhati Nag
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Grace Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Kevin Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Alexander M Sutherland
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
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156
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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: 192] [Impact Index Per Article: 21.3] [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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157
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Koay YC, Richardson NL, Zaiter SS, Kho J, Nguyen SY, Tran DH, Lee KW, Buckton LK, McAlpine SR. Hitting a Moving Target: How Does anN-Methyl Group Impact Biological Activity? ChemMedChem 2016; 11:881-92. [DOI: 10.1002/cmdc.201500572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Yen Chin Koay
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Nicole L. Richardson
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Samantha S. Zaiter
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Jessica Kho
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Sheena Y. Nguyen
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Daniel H. Tran
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Ka Wai Lee
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Laura K. Buckton
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
| | - Shelli R. McAlpine
- Department of Chemistry; University of New South Wales; Gate 2 High Street, Dalton F12 Sydney NSW 2008 Australia
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158
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Allen SE, Dokholyan NV, Bowers AA. Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications. ACS Chem Biol 2016; 11:10-24. [PMID: 26575401 DOI: 10.1021/acschembio.5b00663] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.
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Affiliation(s)
- Scott E. Allen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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159
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Horn M, Reichart F, Natividad-Tietz S, Diaz D, Neundorf I. Tuning the properties of a novel short cell-penetrating peptide by intramolecular cyclization with a triazole bridge. Chem Commun (Camb) 2016; 52:2261-4. [DOI: 10.1039/c5cc08938g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic versus linear: cyclic triazole-bridged cell-penetrating peptides are optimally arranged within the membrane, thus at the same time inducing suitable DNA complexation and successful peptide membrane insertion.
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Affiliation(s)
- M. Horn
- Department of Chemistry
- Institute of Biochemistry
- 50674 Cologne
- Germany
| | - F. Reichart
- Department of Chemistry
- Institute of Biochemistry
- 50674 Cologne
- Germany
| | | | - D. Diaz
- Department of Chemistry
- Organic Chemistry
- 50939 Cologne
- Germany
| | - I. Neundorf
- Department of Chemistry
- Institute of Biochemistry
- 50674 Cologne
- Germany
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160
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Carelli JD, Sethofer SG, Smith GA, Miller HR, Simard JL, Merrick WC, Jain RK, Ross NT, Taunton J. Ternatin and improved synthetic variants kill cancer cells by targeting the elongation factor-1A ternary complex. eLife 2015; 4. [PMID: 26651998 PMCID: PMC4786417 DOI: 10.7554/elife.10222] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023] Open
Abstract
Cyclic peptide natural products have evolved to exploit diverse protein targets, many of which control essential cellular processes. Inspired by a series of cyclic peptides with partially elucidated structures, we designed synthetic variants of ternatin, a cytotoxic and anti-adipogenic natural product whose molecular mode of action was unknown. The new ternatin variants are cytotoxic toward cancer cells, with up to 500-fold greater potency than ternatin itself. Using a ternatin photo-affinity probe, we identify the translation elongation factor-1A ternary complex (eEF1A·GTP·aminoacyl-tRNA) as a specific target and demonstrate competitive binding by the unrelated natural products, didemnin and cytotrienin. Mutations in domain III of eEF1A prevent ternatin binding and confer resistance to its cytotoxic effects, implicating the adjacent hydrophobic surface as a functional hot spot for eEF1A modulation. We conclude that the eukaryotic elongation factor-1A and its ternary complex with GTP and aminoacyl-tRNA are common targets for the evolution of cytotoxic natural products. DOI:http://dx.doi.org/10.7554/eLife.10222.001 Many plants, fungi, and bacteria have evolved to produce small molecules that have powerful effects on the cells of other living organisms, and can even kill them. These naturally produced compounds are often used as starting points for developing new drugs. One such class of compounds are the cyclic peptides, which can be relatively easily produced in the laboratory and are able to penetrate cells. Some cyclic peptides have also proved to be useful for treating cancer and immune diseases, so researchers are keen to identify others that have similar effects. One promising prospect, called ternatin, is produced by several species of fungi. In high doses, ternatin can kill mammalian cells, but it was not clear how it does so. To learn more, Carelli et al. searched a chemical database for cyclic peptides related to ternatin and identified several similar compounds that were reported to kill cancer cells. Inspired by the structures of these cyclic peptides, Carelli et al. synthesized modified versions of ternatin. One of these was 500 times more potent than ternatin, which means a much lower dose of the compound is still able to kill cancer cells. Further experiments showed that ternatin blocks the production of new proteins in cells. Specifically, ternatin binds to a complex that includes a protein called elongation factor-1A (eEF1A). Mutations in a particular region of eEF1A prevent ternatin from killing cells, suggesting a potential binding site for ternatin. The next challenge is to dissect the mechanism by which compounds binding to this site on eEF1A block protein synthesis and kill cells. A related challenge is to understand why certain cancer cells are hypersensitive to ternatin and other eEF1A inhibitors, while other cancer cells are relatively resistant. These questions are relevant to the development of eEF1A inhibitors as cancer treatments. DOI:http://dx.doi.org/10.7554/eLife.10222.002
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Affiliation(s)
- Jordan D Carelli
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Steven G Sethofer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Geoffrey A Smith
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Jillian L Simard
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, United States
| | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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161
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Parvatkar P, Kato N, Uesugi M, Sato SI, Ohkanda J. Intracellular Generation of a Diterpene-Peptide Conjugate that Inhibits 14-3-3-Mediated Interactions. J Am Chem Soc 2015; 137:15624-7. [PMID: 26632868 DOI: 10.1021/jacs.5b09817] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic agents that disrupt intracellular protein-protein interactions (PPIs) are highly desirable for elucidating signaling networks and developing new therapeutics. However, designing cell-penetrating large molecules equipped with the many functional groups necessary for binding to large interfaces remains challenging. Here, we describe a rational strategy for the intracellular oxime ligation-mediated generation of an amphipathic bivalent inhibitor composed of a peptide and diterpene natural product, fusicoccin, which binds 14-3-3 protein with submicromolar affinity. Our results demonstrate that co-treatment of cells with small module molecules, the aldehyde-containing fusicoccin 1 and the aminooxy-containing peptide 2, generates the corresponding conjugate 3 in cells, resulting in significant cytotoxicity. In contrast, chemically synthesized 3 is not cytotoxic, likely due to its inability to penetrate cells. Compound 3, but not 1 or 2, disrupts endogenous 14-3-3/cRaf interactions, suggesting that cell death is caused by inhibition of 14-3-3 activity. These results suggest that intracellular generation of large-sized molecules may serve as a new approach for modulating PPIs.
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Affiliation(s)
- Prakash Parvatkar
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nobuo Kato
- Institute of Scientific and Industrial Research, Osaka University , 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
| | - Junko Ohkanda
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
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162
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Dunyak BM, Nakamura RL, Frankel AD, Gestwicki JE. Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. ACS Chem Biol 2015; 10:2441-7. [PMID: 26322864 DOI: 10.1021/acschembio.5b00426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In drug discovery, small molecules must often discriminate between healthy and diseased cells. This feat is usually accomplished by binding to a protein that is preferentially expressed in the target cell or on its surface. However, in many cases, the expression of an individual protein may not generate sufficient cyto-selectivity. Here, we demonstrate that bispecific molecules can better discriminate between similar cell types by exploiting their simultaneous affinity for two proteins. Inspired by the natural product FK506, we designed molecules that have affinity for both FKBP12 and HIV protease. Using cell-based reporters and live virus assays, we observed that these compounds preferentially accumulated in cells that express both targets, mimicking an infected lymphocyte. Treatment with FKBP12 inhibitors reversed this partitioning, while overexpression of FKBP12 protein further promoted it. The partitioning into the target cell type could be tuned by controlling the properties of the linker and the affinities for the two proteins. These results show that bispecific molecules create significantly better potential for cyto-selectivity, which might be especially important in the development of safe and effective antivirals and anticancer compounds.
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Affiliation(s)
| | - Robert L. Nakamura
- Advanced Genetic Systems, San Francisco, California 94158, United States
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163
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Rational, computer-enabled peptide drug design: principles, methods, applications and future directions. Future Med Chem 2015; 7:2173-93. [PMID: 26510691 DOI: 10.4155/fmc.15.142] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Peptides provide promising templates for developing drugs to occupy a middle space between small molecules and antibodies and for targeting 'undruggable' intracellular protein-protein interactions. Importantly, rational or in cerebro design, especially when coupled with validated in silico tools, can be used to efficiently explore chemical space and identify islands of 'drug-like' peptides to satisfy diverse drug discovery program objectives. Here, we consider the underlying principles of and recent advances in rational, computer-enabled peptide drug design. In particular, we consider the impact of basic physicochemical properties, potency and ADME/Tox opportunities and challenges, and recently developed computational tools for enabling rational peptide drug design. Key principles and practices are spotlighted by recent case studies. We close with a hypothetical future case study.
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164
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Marelli UK, Ovadia O, Frank AO, Chatterjee J, Gilon C, Hoffman A, Kessler H. cis-Peptide Bonds: A Key for Intestinal Permeability of Peptides? Chemistry 2015; 21:15148-52. [DOI: 10.1002/chem.201501600] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Indexed: 12/12/2022]
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165
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Bockus AT, Schwochert JA, Pye CR, Townsend CE, Sok V, Bednarek MA, Lokey RS. Going Out on a Limb: Delineating The Effects of β-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues. J Med Chem 2015; 58:7409-18. [PMID: 26308180 DOI: 10.1021/acs.jmedchem.5b00919] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is well established that intramolecular hydrogen bonding and N-methylation play important roles in the passive permeability of cyclic peptides, but other structural features have been explored less intensively. Recent studies on the oral bioavailability of the cyclic heptapeptide sanguinamide A have raised the question of whether steric occlusion of polar groups via β-branching is an effective, yet untapped, tool in cyclic peptide permeability optimization. We report the structures of 17 sanguinamide A analogues designed to test the relative contributions of β-branching, N-methylation, and side chain size to passive membrane permeability and aqueous solubility. We demonstrate that β-branching has little effect on permeability compared to the effects of aliphatic carbon count and N-methylation of exposed NH groups. We highlight a new N-methylated analogue of sanguinamide A with a Leu substitution at position 2 that exhibits solvent-dependent flexibility and improved permeability over that of the natural product.
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Affiliation(s)
- Andrew T Bockus
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Joshua A Schwochert
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Cameron R Pye
- 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
| | - Vong Sok
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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166
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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: 128] [Impact Index Per Article: 12.8] [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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167
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Abstract
Recently, peptides have been validated to address intracellular targets and/or to be orally bioavailable. This review describes some of these scaffolds, offers insight in new cyclization methodologies thought to be beneficial to enhance permeability, and highlights modification on peptides thought to improve oral bioavailability. In this context, side chains and back-bone derivatization beneficial to encourage cellular uptake are presented. In addition, new methodologies supporting the assessment of permeability are discussed.
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168
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Predicting the unpredictable: Recent structure–activity studies on peptide-based macrocycles. Bioorg Chem 2015; 60:74-97. [DOI: 10.1016/j.bioorg.2015.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 11/18/2022]
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169
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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: 9.0] [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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170
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Marelli UK, Bezençon J, Puig E, Ernst B, Kessler H. Enantiomeric Cyclic Peptides with Different Caco-2 Permeability Suggest Carrier-Mediated Transport. Chemistry 2015; 21:8023-7. [DOI: 10.1002/chem.201501270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/23/2022]
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171
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Wang CK, Northfield SE, Swedberg JE, Colless B, Chaousis S, Price DA, Liras S, Craik DJ. Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability. Eur J Med Chem 2015; 97:202-13. [PMID: 25974856 DOI: 10.1016/j.ejmech.2015.04.049] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/25/2022]
Abstract
An increasing number of macrocyclic peptides that cross biological membranes are being reported, suggesting that it might be possible to develop peptides into orally bioavailable therapeutics; however, current understanding of what makes macrocyclic peptides cell permeable is still limited. Here, we synthesized 62 cyclic hexapeptides and characterized their permeability using in vitro assays commonly used to predict in vivo absorption rates, i.e. the Caco-2 and PAMPA assays. We correlated permeability with experimentally measured parameters of peptide conformation obtained using rapid methods based on chromatography and nuclear magnetic resonance spectroscopy. Based on these correlations, we propose a model describing the interplay between peptide permeability, lipophilicity and hydrogen bonding potential. Specifically, peptides with very high permeability have high lipophilicity and few solvent hydrogen bond interactions, whereas peptides with very low permeability have low lipophilicity or many solvent interactions. Our model is supported by molecular dynamics simulations of the cyclic peptides calculated in explicit solvent, providing a structural basis for the observed correlations. This prospective exploration into biomarkers of peptide permeability has the potential to unlock wider opportunities for development of peptides into drugs.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E Northfield
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Barbara Colless
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David A Price
- Worldwide Medicinal Chemistry, CVMED, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Spiros Liras
- Worldwide Medicinal Chemistry, CVMED, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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