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Dunyak BM, Gestwicki JE. Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds. J Med Chem 2016; 59:9622-9644. [PMID: 27409354 DOI: 10.1021/acs.jmedchem.6b00411] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptidyl-proline isomerases (PPIases) are a chaperone superfamily comprising the FK506-binding proteins (FKBPs), cyclophilins, and parvulins. PPIases catalyze the cis/trans isomerization of proline, acting as a regulatory switch during folding, activation, and/or degradation of many proteins. These "clients" include proteins with key roles in cancer, neurodegeneration, and psychiatric disorders, suggesting that PPIase inhibitors could be important therapeutics. However, the active site of PPIases is shallow, solvent-exposed, and well conserved between family members, making selective inhibitor design challenging. Despite these hurdles, macrocyclic natural products, including FK506, rapamycin, and cyclosporin, bind PPIases with nanomolar or better affinity. De novo attempts to derive new classes of inhibitors have been somewhat less successful, often showcasing the "undruggable" features of PPIases. Interestingly, the most potent of these next-generation molecules tend to integrate features of the natural products, including macrocyclization or proline mimicry strategies. Here, we review recent developments and ongoing challenges in the inhibition of PPIases, with a focus on how natural products might inform the creation of potent and selective inhibitors.
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Affiliation(s)
- Bryan M Dunyak
- Department of Biological Chemistry, University of Michigan Medical School , 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States.,Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
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Delcamp JH, Brucks AP, White MC. A General and Highly Selective Chelate-Controlled Intermolecular Oxidative Heck Reaction. J Am Chem Soc 2008; 130:11270-1. [DOI: 10.1021/ja804120r] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jared H. Delcamp
- University of Illinois Urbana−Champaign, 600 S. Mathews, Urbana, Illinois 61801
| | | | - M. Christina White
- University of Illinois Urbana−Champaign, 600 S. Mathews, Urbana, Illinois 61801
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Stebbins JL, Zhang Z, Chen J, Wu B, Emdadi A, Williams ME, Cashman J, Pellecchia M. Nuclear Magnetic Resonance Fragment-Based Identification of Novel FKBP12 Inhibitors. J Med Chem 2007; 50:6607-17. [DOI: 10.1021/jm0707424] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John L. Stebbins
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - Ziming Zhang
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - Jinhua Chen
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - Bainan Wu
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - Aras Emdadi
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - Megan E. Williams
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - John Cashman
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
| | - Maurizio Pellecchia
- Infectious and Inflammatory Disease Center, Cancer Center, Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, University of California at San Diego, Division of Biological Sciences, 9500 Gilman Drive, La Jolla, California 92093, and Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, California 92121
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Andrade CKZ, Silva WA, Maia ER. Computational approach for the design of AP1867 analogs: aiming at new synthetic routes for potential immunosuppressant agents. J Biomol Struct Dyn 2007; 25:35-48. [PMID: 17676936 DOI: 10.1080/07391102.2007.10507153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Molecular modelling and synthetic arguments are valuable tools for the design of potential immunosuppressant agents. In this paper, eight proline-based compounds related to the AP1867 structure are studied and at least one of them is found to be a structurally good candidate for the inhibition of FKBP protein. Theoretical calculations were carried out to locate the most energetically favorable chemical substituent group relative to a core skeleton group on interaction with the FKBP binding cavity. Connolly accessible surface calculations have complemented the molecular mechanics and dynamics approaches. Calculated results were also analyzed on the basis of hydrogen bond interactions, relative energies of interaction, root-mean square deviations of amino acid residues of the crystallized protein, and orientation of the substituent groups within the active site. The results show a significant reduction in the relative interaction energies and very good shape complementarities between our final analog compound and the FKBP binding pocket.
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Affiliation(s)
- Carlos Kleber Z Andrade
- Laboratorio de Quimica Metodologica e Organica Sintetica (LaQMOS), Instituto de Quimica, Universidade de Brasilia, Campus Darcy Ribeiro, C.P. 4478, Brasilia, CEP 70904-970-DF, Brazil
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Röhrig CH, Loch C, Guan JY, Siegal G, Overhand M. Fragment-Based Synthesis and SAR of Modified FKBP Ligands: Influence of Different Linking on Binding Affinity. ChemMedChem 2007; 2:1054-70. [PMID: 17541991 DOI: 10.1002/cmdc.200600296] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The viability of the fragment-based approach for lead discovery depends on reliable fragment-screening methods combined with straightforward fragment-linking- or fragment-growing-chemistry. In the present study we sought a flexible synthetic approach that would allow efficient synthesis of a variety of linkers that can subsequently be tested for biological activity. We applied this approach to fragments known to bind to FKBP12 (FK506 binding protein), a peptidyl-prolyl isomerase involved in immunosuppression and neural functioning. In our set of linked FKBP ligands, ester and thioester linkages resulted in high-affinity ligands, whereas an amide linkage decreased affinity remarkably; oxime and triazole linkages were not tolerated by the target protein's binding pocket, rendering these ligands ineffective. By investigating corresponding derivatized non-linked fragments and docking studies of linked fragments, we were able to evaluate the effect of the linker region on ligand binding affinity.
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Affiliation(s)
- Christoph H Röhrig
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Abstract
Designed peptidyl-prolyl isomerase (PPIase) inhibitors of Pin1, cyclophilin (CyP), and FK506 binding protein (FKBP) are reviewed. Emphasis is placed on the design, structure, and biological activity of the inhibitors. While CyP and FKBP inhibitors have been explored fairly thoroughly, inhibitors of the relatively new Pin1 cell cycle regulator are in their infancy. Ligands designed for Pin1 and CyP have primarily been ground state analogues: alkenes and bicyclic compounds. For FKBP, more of the focus has been on analogues of bonds at the reactive center, the prolyl amide, because of the idea that the alpha-ketoamide of FK506 is an analogue of the twisted amide in the transition state.
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Affiliation(s)
- Xiaodong J Wang
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24060, USA
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Powers JF, Brachold JM, Schelling K, Tischler AS. Potentiation of mitogenesis in adult rat chromaffin cell cultures by immunosuppressive agent FK506. Neurosci Lett 2004; 356:5-8. [PMID: 14746888 DOI: 10.1016/j.neulet.2003.10.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The immunosuppressive drugs FK506 and cyclosporin inhibit T- and B-lymphocyte proliferation and exert neuritogenic and/or cytoprotective effects on several types of neurons. While the immunosuppressive actions of both drugs are mediated in large part by inhibition of the Ca(2+)-dependent phosphatase, calcineurin, FK506 is known to exert additional effects. In the present study, FK506 is shown to potentiate mitogenic effects of the neurotrophic factor, neurturin, on normal adult rat adrenal chromaffin cells in culture. The effect is not seen with cyclosporin or with a non-immunosuppressive analog of FK506, GPI-1046. The finding of increased mitogenesis in response to FK506 may have applications to the study of normal and neoplastic neuroendocrine cells and to understanding the development of some types of tumors in transplant patients.
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Affiliation(s)
- J F Powers
- Department of Pathology, Tufts New England Medical Center and Tufts University School of Medicine, Boston, MA 02111, USA.
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