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Iglesias V, Bárcenas O, Pintado-Grima C, Burdukiewicz M, Ventura S. Structural information in therapeutic peptides: Emerging applications in biomedicine. FEBS Open Bio 2024. [PMID: 38877295 DOI: 10.1002/2211-5463.13847] [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: 02/29/2024] [Revised: 05/08/2024] [Accepted: 05/27/2024] [Indexed: 06/16/2024] Open
Abstract
Peptides are attracting a growing interest as therapeutic agents. This trend stems from their cost-effectiveness and reduced immunogenicity, compared to antibodies or recombinant proteins, but also from their ability to dock and interfere with large protein-protein interaction surfaces, and their higher specificity and better biocompatibility relative to organic molecules. Many tools have been developed to understand, predict, and engineer peptide function. However, most state-of-the-art approaches treat peptides only as linear entities and disregard their structural arrangement. Yet, structural details are critical for peptide properties such as solubility, stability, or binding affinities. Recent advances in peptide structure prediction have successfully addressed the scarcity of confidently determined peptide structures. This review will explore different therapeutic and biotechnological applications of peptides and their assemblies, emphasizing the importance of integrating structural information to advance these endeavors effectively.
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Affiliation(s)
- Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Barcelona, Spain
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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Mi T, Nguyen D, Gao Z, Burgess K. Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs). Nat Commun 2024; 15:4217. [PMID: 38760359 PMCID: PMC11101637 DOI: 10.1038/s41467-024-48323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
Helix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA
| | - Duyen Nguyen
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA
| | - Zhe Gao
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, College Station, TX, 77842, USA.
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3
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Chen CY, Elmore S, Lalami I, Neal H, Vadlamudi RK, Raj GV, Ahn JM. Oligo-benzamide-based peptide mimicking tools for modulating biology. Methods Enzymol 2024; 698:221-245. [PMID: 38886033 DOI: 10.1016/bs.mie.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The oligo-benzamide scaffold is a rigid organic framework that can hold 2-3 functional groups as O-alkyl substituents on its benzamide units, mirroring their natural arrangement in an α-helix. Oligo-benzamides demonstrated outstanding α-helix mimicry and can be readily synthesized by following high yielding and iterative reaction steps in both solution-phase and solid-phase. A number of oligo-benzamides have been designed to emulate α-helical peptide segments in biologically active proteins and showed strong protein binding, in turn effectively disrupting protein-protein interactions in vitro and in vivo. In this chapter, the design of oligo-benzamides for mimicking α-helices, efficient synthetic routes for producing them, and their biomedical studies showing remarkable potency in inhibiting protein functions are discussed.
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Affiliation(s)
- Chia-Yuan Chen
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Scott Elmore
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Ismail Lalami
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Henry Neal
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States.
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Chandramohan A, Josien H, Yuen TY, Duggal R, Spiegelberg D, Yan L, Juang YCA, Ge L, Aronica PG, Kaan HYK, Lim YH, Peier A, Sherborne B, Hochman J, Lin S, Biswas K, Nestor M, Verma CS, Lane DP, Sawyer TK, Garbaccio R, Henry B, Kannan S, Brown CJ, Johannes CW, Partridge AW. Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists. Nat Commun 2024; 15:489. [PMID: 38216578 PMCID: PMC10786919 DOI: 10.1038/s41467-023-43346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 11/06/2023] [Indexed: 01/14/2024] Open
Abstract
Although stapled α-helical peptides can address challenging targets, their advancement is impeded by poor understandings for making them cell permeable while avoiding off-target toxicities. By synthesizing >350 molecules, we present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects. Key insights include a clear correlation between lipophilicity and permeability, removal of positive charge to avoid off-target toxicities, judicious anionic residue placement to enhance solubility/behavior, optimization of C-terminal length/helicity to enhance potency, and optimization of staple type/number to avoid polypharmacology. Workflow application gives peptides with >292x improved cell proliferation potencies and no off-target cell proliferation effects ( > 3800x on-target index). Application of these 'design rules' to a distinct Mdm2(X) peptide series improves ( > 150x) cellular potencies and removes off-target toxicities. The outlined workflow should facilitate therapeutic impacts, especially for those targets such as Mdm2(X) that have hydrophobic interfaces and are targetable with a helical motif.
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Affiliation(s)
| | | | - Tsz Ying Yuen
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore
| | | | - Diana Spiegelberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Lin Yan
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | - Lan Ge
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Pietro G Aronica
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore
| | | | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore
| | | | | | | | | | | | - Marika Nestor
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore
| | - David P Lane
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | | | | | - Brian Henry
- MSD International, Singapore, 138665, Singapore.
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore.
| | | | - Charles W Johannes
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore.
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.
- EPOC Scientific LLC, Stoneham, MA, 02180, USA.
| | - Anthony W Partridge
- MSD International, Singapore, 138665, Singapore.
- Genentech, South San Francisco, CA, 94080, USA.
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Abdulkadir S, Li C, Jiang W, Zhao X, Sang P, Wei L, Hu Y, Li Q, Cai J. Modulating Angiogenesis by Proteomimetics of Vascular Endothelial Growth Factor. J Am Chem Soc 2021; 144:270-281. [PMID: 34968032 DOI: 10.1021/jacs.1c09571] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Angiogenesis, formation of new blood vessels from the existing vascular network, is a hallmark of cancer cells that leads to tumor vascular proliferation and metastasis. This process is mediated through the binding interaction of VEGF-A with VEGF receptors. However, the balance between pro-angiogenic and anti-angiogenic effect after ligand binding yet remains elusive and is therefore challenging to manipulate. To interrogate this interaction, herein we designed a few sulfono-γ-AA peptide based helical peptidomimetics that could effectively mimic a key binding interface on VEGF (helix-α1) for VEGFR recognition. Intriguingly, although both sulfono-γ-AA peptide sequences V2 and V3 bound to VEGF receptors tightly, in vitro angiogenesis assays demonstrated that V3 potently inhibited angiogenesis, whereas V2 activated angiogenesis effectively instead. Our findings suggested that this distinct modulation of angiogenesis might be due to the result of selective binding of V2 to VEGFR-1 and V3 to VEGFR-2, respectively. These molecules thus provide us a key to switch the angiogenic signaling, a biological process that balances the effects of pro-angiogenic and anti-angiogenic factors, where imbalances lead to several diseases including cancer. In addition, both V2 and V3 exhibited remarkable stability toward proteolytic hydrolysis, suggesting that V2 and V3 are promising therapeutic agents for the intervention of disease conditions arising due to angiogenic imbalances and could also be used as novel molecular switching probes to interrogate the mechanism of VEGFR signaling. The findings also further demonstrated the potential of sulfono-γ-AA peptides to mimic the α-helical domain for protein recognition and modulation of protein-protein interactions.
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Affiliation(s)
- Sami Abdulkadir
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Chunpu Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.,Department of Medical Oncology, Cancer Institute of Medicine, Shuguang Hospital; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wei Jiang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.,Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Xue Zhao
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Lulu Wei
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yong Hu
- Institute of Materials Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Qi Li
- Department of Medical Oncology, Cancer Institute of Medicine, Shuguang Hospital; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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