1
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Lee TK, Kassees K, Chen CY, Viswanadhapalli S, Parra K, Vadlamudi RK, Ahn JM. Structure-Activity Relationship Study of Tris-Benzamides as Estrogen Receptor Coregulator Binding Modulators. ACS Pharmacol Transl Sci 2024; 7:2023-2043. [PMID: 39022350 PMCID: PMC11249634 DOI: 10.1021/acsptsci.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
Estrogen receptor coregulator binding modulators (ERXs) are a novel class of molecules targeting the interaction between estrogen receptor α (ERα) and its coregulator proteins, which has proven to be an attractive strategy for overcoming endocrine resistance in breast cancer. We previously reported ERX-11, an orally bioavailable tris-benzamide, that demonstrated promising antitumor activity against ERα-positive breast cancer cells. To comprehend the significance of the substituents in ERX-11, we carried out structure-activity relationship studies. In addition, we introduced additional alkyl substituents at either the N- or C-terminus to improve binding affinity and biological activity. Further optimization guided by conformational restriction led to the identification of a trans-4-phenylcyclcohexyl group at the C-terminus (18h), resulting in a greater than 10-fold increase in binding affinity and cell growth inhibition potency compared to ERX-11. Tris-benzamide 18h disrupted the ERα-coregulator interaction and inhibited the ERα-mediated transcriptional activity. It demonstrated strong antiproliferative activity on ERα-positive breast cancer cells both in vitro and in vivo, offering a promising potential as a therapeutic candidate for treating ERα-positive breast cancer.
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Affiliation(s)
- Tae-Kyung Lee
- Department
of Chemistry and Biochemistry, University
of Texas at Dallas, Richardson, Texas 75080, United States
| | - Kara Kassees
- Department
of Chemistry and Biochemistry, University
of Texas at Dallas, Richardson, Texas 75080, United States
| | - Chia-Yuan Chen
- Department
of Chemistry and Biochemistry, University
of Texas at Dallas, Richardson, Texas 75080, United States
| | - Suryavathi Viswanadhapalli
- Department
of Obstetrics and Gynecology, University
of Texas Health, San Antonio, Texas 78229, United States
| | - Karla Parra
- Departments
of Urology and Pharmacology, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Ratna K. Vadlamudi
- Department
of Obstetrics and Gynecology, University
of Texas Health, San Antonio, Texas 78229, United States
| | - Jung-Mo Ahn
- Department
of Chemistry and Biochemistry, University
of Texas at Dallas, Richardson, Texas 75080, United States
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2
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Negi A, Murphy PV. Development of Mcl-1 inhibitors for cancer therapy. Eur J Med Chem 2020; 210:113038. [PMID: 33333396 DOI: 10.1016/j.ejmech.2020.113038] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022]
Abstract
The myeloid leukemia cell differentiation protein (Mcl-1) is an anti-apoptotic protein of the B-cell lymphoma 2 (Bcl-2) family, which regulates cellular apoptosis. Mcl-1 expression plays a key role in survival of cancer cells and therefore serves as a promising target in cancer therapy. Besides, its importance as a cancer target, various peptides and small-molecule inhibitors have been successfully designed and synthesized, yet no Mcl-1 inhibitor is approved for clinical use. However, recent development on the understanding of Mcl-1's role in key cellular processes in cancer and an upsurge of reports highlighting its association in various anticancer drug resistance supports the view that Mcl-1 is a key target in various cancers, especially hematological cancers. This review compiles structures of a variety of inhibitors of Mcl-1 reported to date. These include inhibitors based on a diverse range of heterocycles (e.g. indole, imidazole, thiophene, nicotinic acid, piperazine, triazine, thiazole, isoindoline), oligomers (terphenyl, quaterpyridine), polyphenol, phenalene, anthranilic acid, anthraquinone, macrocycles, natural products, and metal-based complexes. In addition, an effort has been made to summarize the structure activity relationships, based on a variety of assays, of some important classes of Mcl-1 inhibitors, giving affinities and selectivities for Mcl-1 compared to other Bcl-2 family members. A focus has been placed on categorizing the inhibitors based on their core frameworks (scaffolds) to appeal to the chemical biologist or medicinal chemist.
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Affiliation(s)
- Arvind Negi
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Paul V Murphy
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.
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3
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Wang X, Zhu G, Liang W, Zhao S, Yuan L, Zhou X, Lu L, Xu H. Design, Synthesis and Docking of Linear and Hairpin‐Like Alpha Helix Mimetics Based on Alkoxylated Oligobenzamide. ChemistrySelect 2019. [DOI: 10.1002/slct.201900171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xiang Wang
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Guanhua Zhu
- Division of Structural Biology and BiochemistrySchool of Biological SciencesNanyang Technological University
| | - Wenjie Liang
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Siqi Zhao
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Lvbing Yuan
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of Sciences
| | - Xiaohu Zhou
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Lanyuan Lu
- Division of Structural Biology and BiochemistrySchool of Biological SciencesNanyang Technological University
| | - Hai Xu
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
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4
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Nevola L, Varese M, Martín-Quirós A, Mari G, Eckelt K, Gorostiza P, Giralt E. Targeted Nanoswitchable Inhibitors of Protein-Protein Interactions Involved in Apoptosis. ChemMedChem 2018; 14:100-106. [PMID: 30380184 DOI: 10.1002/cmdc.201800647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Indexed: 12/20/2022]
Abstract
Progress in drug delivery is hampered by a lack of efficient strategies to target drugs with high specificity and precise spatiotemporal regulation. The remote control of nanoparticles and drugs with light allows regulation of their action site and dosage. Peptide-based drugs are highly specific, non-immunogenic, and can be designed to cross the plasma membrane. In order to combine target specificity and remote control of drug action, here we describe a versatile strategy based on a generalized template to design nanoswitchable peptides that modulate protein-protein interactions upon light activation. This approach is demonstrated to promote photomodulation of two important targets involved in apoptosis (the interactions Bcl-xL-Bak and MDM2-p53), but can be also applied to a large pool of therapeutically relevant protein-protein interactions mediated by α-helical motifs. The template can be adjusted using readily available information about hot spots (residues contributing most to the binding energy) at the protein-protein interface of interest.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain
| | | | - Giacomo Mari
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.,University of Bologna, Bologna, 40126, Italy
| | - Kay Eckelt
- Institute for Bioengineering of Catalonia (IBEC), Barcelona, 08028, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Pau Gorostiza
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.,Institute for Bioengineering of Catalonia (IBEC), Barcelona, 08028, Spain.,Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028, Barcelona, Spain.,University of Barcelona (UB), Barcelona, 080280, Spain
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5
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Robertson NS, Spring DR. Using Peptidomimetics and Constrained Peptides as Valuable Tools for Inhibiting Protein⁻Protein Interactions. Molecules 2018; 23:molecules23040959. [PMID: 29671834 PMCID: PMC6017787 DOI: 10.3390/molecules23040959] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 02/07/2023] Open
Abstract
Protein–protein interactions (PPIs) are tremendously important for the function of many biological processes. However, because of the structure of many protein–protein interfaces (flat, featureless and relatively large), they have largely been overlooked as potential drug targets. In this review, we highlight the current tools used to study the molecular recognition of PPIs through the use of different peptidomimetics, from small molecules and scaffolds to peptides. Then, we focus on constrained peptides, and in particular, ways to constrain α-helices through stapling using both one- and two-component techniques.
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Affiliation(s)
- Naomi S Robertson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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6
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Azzarito V, Rowell P, Barnard A, Edwards TA, Macdonald A, Warriner SL, Wilson AJ. Probing Protein Surfaces: QSAR Analysis with Helix Mimetics. Chembiochem 2016; 17:768-73. [PMID: 26690307 PMCID: PMC6591138 DOI: 10.1002/cbic.201500504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 12/17/2022]
Abstract
α-Helix-mediated protein-protein interactions (PPIs) are important targets for small-molecule inhibition; however, generic approaches to inhibitor design are in their infancy and would benefit from QSAR analyses to rationalise the noncovalent basis of molecular recognition by designed ligands. Using a helix mimetic based on an oligoamide scaffold, we have exploited the power of a modular synthesis to access compounds that can readily be used to understand the noncovalent determinants of hDM2 recognition by this series of cell-active p53/hDM2 inhibitors.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Philip Rowell
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Anna Barnard
- Department of Chemistry, Imperial College London, London, London, SW7 2AZ, UK
- Institue of Chemical Biology, Imperial College London, London, SW7 2AZ, UK
| | - Thomas A Edwards
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew Macdonald
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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7
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Lim Z, Duggan PJ, Wan SS, Lessene G, Meyer AG, Tuck KL. Exploiting the Biginelli reaction: nitrogen-rich pyrimidine-based tercyclic α-helix mimetics. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Hu X, Dawson SJ, Nagaoka Y, Tanatani A, Huc I. Solid-Phase Synthesis of Water-Soluble Helically Folded Hybrid α-Amino Acid/Quinoline Oligoamides. J Org Chem 2016; 81:1137-50. [PMID: 26703882 DOI: 10.1021/acs.joc.5b02671] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here a solid phase synthesis methodology that allows the incorporation of α-amino acids (X) into quinoline (Q) oligoamide foldamer sequences. Water-soluble hybrid oligoamides based on the XQ2 trimer repeat motif were shown to adopt helical conformations presenting α-amino acid side chains in a predictable linear array on one face of the helix. In contrast, sequences based on the XQ dimer motif expressed less well-defined behavior, most likely due to local conformational variability precluding long-range order. Also presented is a full structural investigation by NMR of a dodecameric XQ2-type foldamer containing four different amino acid residues (Lys, Ala, Asp, and Ser).
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Affiliation(s)
- Xiaobo Hu
- Université de Bordeaux, CBMN (UMR5248) , Institut Européen de Chimie et Biologie, 2 Rue Escarpit, 33600 Pessac, France
| | - Simon J Dawson
- CNRS, CBMN (UMR 5248) , Institut Européen de Chimie et Biologie, 2 Rue Escarpit, 33600 Pessac, France
| | - Yui Nagaoka
- Department of Chemistry, Faculty of Science, Ochanomizu University , 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University , 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Ivan Huc
- Université de Bordeaux, CBMN (UMR5248) , Institut Européen de Chimie et Biologie, 2 Rue Escarpit, 33600 Pessac, France
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9
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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10
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Molecules 2015; 20:11569-603. [PMID: 26111183 PMCID: PMC6272567 DOI: 10.3390/molecules200611569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.
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12
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Burslem GM, Kyle HF, Breeze AL, Edwards TA, Nelson A, Warriner SL, Wilson AJ. Small-molecule proteomimetic inhibitors of the HIF-1α-p300 protein-protein interaction. Chembiochem 2014; 15:1083-7. [PMID: 24782431 PMCID: PMC4159589 DOI: 10.1002/cbic.201400009] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Indexed: 11/29/2022]
Abstract
The therapeutically relevant hypoxia inducible factor HIF-1α–p300 protein–protein interaction can be orthosterically inhibited with α-helix mimetics based on an oligoamide scaffold that recapitulates essential features of the C-terminal helix of the HIF-1α C-TAD (C-terminal transactivation domain). Preliminary SAR studies demonstrated the important role of side-chain size and hydrophobicity/hydrophilicity in determining potency. These small molecules represent the first biophysically characterised HIF-1α–p300 PPI inhibitors and the first examples of small-molecule aromatic oligoamide helix mimetics to be shown to have a selective binding profile. Although the compounds were less potent than HIF-1α, the result is still remarkable in that the mimetic reproduces only three residues from the 42-residue HIF-1α C-TAD from which it is derived.
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Affiliation(s)
- George M Burslem
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT (UK); Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT (UK)
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13
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Recapitulating the α-helix: nonpeptidic, low-molecular-weight ligands for the modulation of helix-mediated protein–protein interactions. Future Med Chem 2013; 5:2157-74. [DOI: 10.4155/fmc.13.176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein–protein interactions play critical roles in a wide variety of biological processes, and their dysregulations contribute to the pathogenesis of several diseases, including cancer. Chemical entities that can abrogate aberrant protein–protein interactions may provide novel therapeutic agents. A large number of protein–protein interactions are mediated by protein secondary structure, the most commonly encountered form of which is the α-helix. Accordingly, over the last decade, there has been a flood of nonpeptidic small molecules that recapitulate the projection and chemical nature of key side chains of the canonical α-helix as a strategy to disrupt helix-mediated protein–protein interactions. In this review, we discuss recent advances (post 2006) in the design of synthetic α-helix mimetics, which include single-faced and two-faced/amphipathic structures, for the modulation of protein–protein interactions.
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14
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Mignani S, El Kazzouli S, Bousmina MM, Majoral JP. Dendrimer Space Exploration: An Assessment of Dendrimers/Dendritic Scaffolding as Inhibitors of Protein–Protein Interactions, a Potential New Area of Pharmaceutical Development. Chem Rev 2013; 114:1327-42. [DOI: 10.1021/cr400362r] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Serge Mignani
- Laboratoire de Chimie et de
Biochimie Pharmacologiques
et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints Pères, 75006 Paris, France
| | - Saïd El Kazzouli
- Euro-Mediterranean University of Fez, Fès-Shore, Route de Sidi harazem, Fès, Morocco
| | - Mosto M. Bousmina
- Euro-Mediterranean University of Fez, Fès-Shore, Route de Sidi harazem, Fès, Morocco
- Hassan II Academy of Science and Technology, Avenue Mohammed
VI, 10222 Rabat, Morocco
| | - Jean-Pierre Majoral
- Laboratoire
de Chimie de Coordination, Centre National de la Recherche Scientifique, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
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15
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Nevola L, Rodriguez JM, Thompson S, Hamilton AD. Super-secondary structure peptidomimetics: design and synthesis of an α-α hairpin analogue. Supramol Chem 2013; 25:586-590. [PMID: 26052191 DOI: 10.1080/10610278.2013.817581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The α-α helix motif presents key recognition domains in protein-protein and protein-oligonucleotide binding, and is one of the most common super-secondary structures. Herein we describe the design, synthesis and structural characterization of an α-α hairpin analogue based on a tetra-coordinated Pd(II) bis-(iminoisoquinoline) complex as a template for the display of two α-helix mimics. This approach is exemplified by the attachment of two biphenyl peptidomimetics to reproduce the side-chains of the i and i+4 residues of two helices.
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Affiliation(s)
- Laura Nevola
- Yale University, Department of Chemistry, P.O. Box 208107, New Haven, CT 06511
| | - Johanna M Rodriguez
- Yale University, Department of Chemistry, P.O. Box 208107, New Haven, CT 06511
| | - Sam Thompson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, England
| | - Andrew D Hamilton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, England ; Yale University, Department of Chemistry, P.O. Box 208107, New Haven, CT 06511
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16
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Inhibition of α-helix-mediated protein-protein interactions using designed molecules. Nat Chem 2013; 5:161-73. [PMID: 23422557 DOI: 10.1038/nchem.1568] [Citation(s) in RCA: 572] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a significant challenge because it is unclear how they can be effectively and selectively targeted using small molecules. Achieving this goal is critical given the defining role of these interactions in biological processes. A rational approach to inhibitor design based on the secondary structure at the interface is the focus of much research, and different classes of designed ligands have emerged, some of which effectively and selectively disrupt targeted PPIs. This Review discusses the relevance of PPIs and, in particular, the importance of α-helix-mediated PPIs to chemical biology and drug discovery with a focus on designing inhibitors, including constrained peptides, foldamers and proteomimetic-derived ligands. In doing so, key challenges and major advances in developing generic approaches for the elaboration of PPI inhibitors are highlighted. The challenges faced in developing such ligands as drug leads--and how criteria applied to these may differ from conventional small-molecule drugs--are summarized.
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17
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Long K, Edwards TA, Wilson AJ. Microwave assisted solid phase synthesis of highly functionalized N-alkylated oligobenzamide α-helix mimetics. Bioorg Med Chem 2012; 21:4034-40. [PMID: 23117175 DOI: 10.1016/j.bmc.2012.09.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/26/2012] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions (PPIs) mediate cellular pathways and are implicated in numerous aberrant conditions. α-Helix mimetics-small molecules that reproduce the spatial projection of key residues from an α-helix involved in a PPI-are attractive generic templates for development of screening libraries, however library syntheses of α-helix mimetics with diverse functionality are less established. This manuscript describes the automated, microwave assisted solid phase synthesis based on one such scaffold; an N-alkylated oligobenzamide.
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Affiliation(s)
- Kérya Long
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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18
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Azzarito V, Prabhakaran P, Bartlett AI, Murphy NS, Hardie MJ, Kilner CA, Edwards TA, Warriner SL, Wilson AJ. 2-O-alkylated para-benzamide α-helix mimetics: the role of scaffold curvature. Org Biomol Chem 2012; 10:6469-72. [PMID: 22785578 DOI: 10.1039/c2ob26262b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The design and synthesis of a new 2-O-alklyated benzamide α-helix mimetic is described. Comparison with regioisomeric 3-O-alkylated benzamides permits a preliminary evaluation of the role that mimetic curvature has in determining molecular recognition properties.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
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19
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Pinto Gomes C, Metz A, Bats JW, Gohlke H, Göbel MW. Modular Solid-Phase Synthesis of Teroxazoles as a Class of α-Helix Mimetics. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200339] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Harris CJ, Hill RD, Sheppard DW, Slater MJ, Stouten PFW. The design and application of target-focused compound libraries. Comb Chem High Throughput Screen 2011; 14:521-31. [PMID: 21521154 PMCID: PMC3182092 DOI: 10.2174/138620711795767802] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 04/09/2011] [Indexed: 11/22/2022]
Abstract
Target-focused compound libraries are collections of compounds which are designed to interact with an individual protein target or, frequently, a family of related targets (such as kinases, voltage-gated ion channels, serine/cysteine proteases). They are used for screening against therapeutic targets in order to find hit compounds that might be further developed into drugs. The design of such libraries generally utilizes structural information about the target or family of interest. In the absence of such structural information, a chemogenomic model that incorporates sequence and mutagenesis data to predict the properties of the binding site can be employed. A third option, usually pursued when no structural data are available, utilizes knowledge of the ligands of the target from which focused libraries can be developed via scaffold hopping. Consequently, the methods used for the design of target-focused libraries vary according to the quantity and quality of structural or ligand data that is available for each target family. This article describes examples of each of these design approaches and illustrates them with case studies, which highlight some of the issues and successes observed when screening target-focused libraries.
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Hydrogen-bonded synthetic mimics of protein secondary structure as disruptors of protein-protein interactions. Curr Top Microbiol Immunol 2011; 348:1-23. [PMID: 20827522 DOI: 10.1007/82_2010_91] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Small molecules which can mimic the key structural facets of protein secondary structure, in particular the α-helix, β-strand, and β-sheet, have been shown to be potent disruptors of protein-protein interactions. Researchers have recently taken the organizational imitation of protein secondary structure to a new level by using intramolecular hydrogen bonds as stabilizing forces in these small molecule mimetics. The inclusion of these interactions invokes a conformational bias of the system, allowing for greater control of the appearance, and thus often function, of these molecules by design.
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Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery. Top Curr Chem (Cham) 2011; 317:145-79. [DOI: 10.1007/128_2011_265] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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23
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Synthesis and biological activities of new di- and trimeric quinoline derivatives. Bioorg Med Chem 2010; 18:7132-43. [DOI: 10.1016/j.bmc.2010.07.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/12/2010] [Accepted: 07/13/2010] [Indexed: 11/17/2022]
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Wich P, Schmuck C. Reversible and Noncompetitive Inhibition of β-Tryptase by Protein Surface Binding of Tetravalent Peptide Ligands Identified from a Combinatorial Split-Mix Library. Angew Chem Int Ed Engl 2010; 49:4113-6. [DOI: 10.1002/anie.200907221] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wich P, Schmuck C. Reversible and Noncompetitive Inhibition of β-Tryptase by Protein Surface Binding of Tetravalent Peptide Ligands Identified from a Combinatorial Split-Mix Library. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907221] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Disrupting protein-protein interactions with non-peptidic, small molecule alpha-helix mimetics. Curr Opin Chem Biol 2010; 14:341-6. [PMID: 20430687 DOI: 10.1016/j.cbpa.2010.04.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 04/01/2010] [Accepted: 04/05/2010] [Indexed: 11/22/2022]
Abstract
Many biological processes are regulated by protein-protein interactions (PPIs) and as such their misregulation can cause a multitude of diseases. Often the interactions between large proteins are mediated by small protein secondary structural domains, which project a minimum number of specifically arranged residues into the complementary surface of an interacting protein. Nature has the advantage of time, and over time has optimized those secondary structures, such as alpha-helices, beta-sheets and beta-strands, found at the interfaces of PPIs. Inspired by Nature's extensive optimization, chemists have used these secondary structures as templates in the design of small molecules that may act as structural and functional mimics of large rhenylogically organized protein secondary structures. Herein recent applications of the indane, terphenyl, terphenyl-inspired templates, polycyclic ether and benzodiazepinedione scaffolds, as non-peptidic, small molecule alpha-helix mimetics, to disrupt PPIs are detailed.
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Campbell F, Plante JP, Edwards TA, Warriner SL, Wilson AJ. N-alkylated oligoamide α-helical proteomimetics. Org Biomol Chem 2010; 8:2344-51. [DOI: 10.1039/c001164a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Plante JP, Burnley T, Malkova B, Webb ME, Warriner SL, Edwards TA, Wilson AJ. Oligobenzamide proteomimetic inhibitors of the p53-hDM2 protein-protein interaction. Chem Commun (Camb) 2009:5091-3. [PMID: 20448956 PMCID: PMC2898631 DOI: 10.1039/b908207g] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 06/10/2009] [Indexed: 12/28/2022]
Abstract
Oligobenzamide inhibitors of the p53-hDM2 protein-protein interaction are described.
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Affiliation(s)
- Jeffrey P. Plante
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Thomas Burnley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Barbora Malkova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Michael E. Webb
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Stuart L. Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT. ; Fax: +44 (0)113 3431409; Tel: +44 (0)113 3436565
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, UK LS29JT.
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Wilson AJ. Inhibition of protein-protein interactions using designed molecules. Chem Soc Rev 2009; 38:3289-300. [PMID: 20449049 DOI: 10.1039/b807197g] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although many cellular processes depend upon enzymatic reactions, protein-protein interactions (PPIs) mediate a large number of important regulatory pathways and thus play a central role in disease development. In order to understand and selectively inhibit cellular signalling pathways, there is a pressing need for small molecules that target PPIs, particularly in the context of pharmaceutical development. This tutorial review will introduce the relevance of PPIs to chemical biology and highlight the key challenges in designing inhibitors. Some of the successes using conventional approaches to the identification of small-molecule PPI inhibitors will be highlighted, and also the reasons why these approaches have not always proven successful. Several general approaches tailored to particular protein topologies are emerging for the design of scaffolds that inhibit PPIs-these will form the major content of this review. Finally a summary of the challenges to be faced in developing inhibitors of PPIs into drug leads and how these challenges may differ from those encountered with enzyme-like targets will be given.
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Affiliation(s)
- Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, LS2 9JT, Leeds, UK.
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