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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Gray VP, Amelung CD, Duti IJ, Laudermilch EG, Letteri RA, Lampe KJ. Biomaterials via peptide assembly: Design, characterization, and application in tissue engineering. Acta Biomater 2022; 140:43-75. [PMID: 34710626 PMCID: PMC8829437 DOI: 10.1016/j.actbio.2021.10.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 12/16/2022]
Abstract
A core challenge in biomaterials, with both fundamental significance and technological relevance, concerns the rational design of bioactive microenvironments. Designed properly, peptides can undergo supramolecular assembly into dynamic, physical hydrogels that mimic the mechanical, topological, and biochemical features of native tissue microenvironments. The relatively facile, inexpensive, and automatable preparation of peptides, coupled with low batch-to-batch variability, motivates the expanded use of assembling peptide hydrogels for biomedical applications. Integral to realizing dynamic peptide assemblies as functional biomaterials for tissue engineering is an understanding of the molecular and macroscopic features that govern assembly, morphology, and biological interactions. In this review, we first discuss the design of assembling peptides, including primary structure (sequence), secondary structure (e.g., α-helix and β-sheets), and molecular interactions that facilitate assembly into multiscale materials with desired properties. Next, we describe characterization tools for elucidating molecular structure and interactions, morphology, bulk properties, and biological functionality. Understanding of these characterization methods enables researchers to access a variety of approaches in this ever-expanding field. Finally, we discuss the biological properties and applications of peptide-based biomaterials for engineering several important tissues. By connecting molecular features and mechanisms of assembling peptides to the material and biological properties, we aim to guide the design and characterization of peptide-based biomaterials for tissue engineering and regenerative medicine. STATEMENT OF SIGNIFICANCE: Engineering peptide-based biomaterials that mimic the topological and mechanical properties of natural extracellular matrices provide excellent opportunities to direct cell behavior for regenerative medicine and tissue engineering. Here we review the molecular-scale features of assembling peptides that result in biomaterials that exhibit a variety of relevant extracellular matrix-mimetic properties and promote beneficial cell-biomaterial interactions. Aiming to inspire and guide researchers approaching this challenge from both the peptide biomaterial design and tissue engineering perspectives, we also present characterization tools for understanding the connection between peptide structure and properties and highlight the use of peptide-based biomaterials in neural, orthopedic, cardiac, muscular, and immune engineering applications.
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Affiliation(s)
- Vincent P Gray
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Connor D Amelung
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Israt Jahan Duti
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Emma G Laudermilch
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Rachel A Letteri
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States.
| | - Kyle J Lampe
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903, United States.
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3
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Madhanagopal B, More SH, Bansode ND, Ganesh KN. Conformation and Morphology of 4-(NH 2/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers. ACS OMEGA 2020; 5:21781-21795. [PMID: 32905392 PMCID: PMC7469381 DOI: 10.1021/acsomega.0c02826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
The relative stereochemistry of C2 and C4 in 4-substituted prolyl polypeptides plays an important role in defining the derived conformation in solution. cis-(2S,4S)-Amino/hydroxy-l-prolyl polypeptide (lC-Amp 9/lC-Hyp 9) shows a PPII conformation in phosphate buffer and a β-structure in a relatively hydrophobic solvent, trifluoroethanol (TFE). It is now demonstrated that the homochiral enantiomeric cis-substituted d-prolyl polypeptide (dC-Amp 9/dC-Hyp 9) exhibits mirror image β-structures in TFE. In the case of alternating heterochiral prolyl peptides, it is the trans-substituted [lT(2S,4R)-dT(2R,4S)] n prolyl polypeptide that shows β-structures in TFE, while the cis-substituted [lC(2S,4S)-dC(2R,4R)] n prolyl polypeptide is disordered in both phosphate buffer and TFE. The results highlight the important chirality-specific structural requirements for β-structure formation. The observed conformation in solution (circular dichroism (CD)) is also correlated with the morphology of the self-assemblies (field emission scanning electron microscopy (FESEM)), with the PPII form leading to spherical nanoparticles and β-structures leading to nanofiber formation. The results shed light on the role of relative stereochemistry at C2 and C4 in defining the polyproline peptide conformation in solution and how different conformations drive self-assemblies of peptides toward specific nanostructures.
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Affiliation(s)
- Bharath
Raj Madhanagopal
- Indian
Institute of Science Education and Research (IISER), Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| | - Shahaji H. More
- Indian
Institute of Science Education and Research (IISER), Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| | - Nitin D. Bansode
- LCPO,
ENSCBP, UMR 5629, University of Bordeaux, Pessac 33600, France
| | - Krishna N. Ganesh
- Indian
Institute of Science Education and Research (IISER), Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
- Indian
Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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4
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Li X, Cao C, Wei P, Xu M, Liu Z, Liu L, Zhong Y, Li R, Zhou Y, Yi T. Self-Assembly of Amphiphilic Peptides for Recognizing High Furin-Expressing Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2019; 11:12327-12334. [PMID: 30864434 DOI: 10.1021/acsami.9b01281] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Self-assembled nanostructures of amphiphilic peptides have a wide range of applications in bioimaging and delivery systems. In this study, we design and synthesize a biocompatible amphiphilic peptide (C-3) consisting of an RVRRFFF sequence and a nitrobenzoxadiazole fluorophore that can self-assemble into stable micelles for specifically detecting furin, a kind of proprotein convertase with promoting tumor progression. The self-assembly of C-3 with a β-sheet nanostructure is capable of a rapid and specific response to furin in only 5 min in aqueous solution because of the existence of the RVRR motif in the C-3 molecule. The C-3 nanostructures thus can selectively distinguish high furin-expressing cancer cells, like MDA-MB-231 cells, a kind of human breast cancer cells, from normal cells. Furthermore, the C-3 self-assembly can stay in living cells for a long time and are capable of durable detection of intracellular furin, being good for tracer analysis. To our knowledge, this is the first example of self-assembly of a soluble amphiphilic peptide that can selectively detect furin in high furin-expressing live cells.
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Affiliation(s)
- Xiang Li
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Haiquan Road , Shanghai 201418 , P. R. China
| | - Chunyan Cao
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
| | - Peng Wei
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
| | - Mengyin Xu
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Haiquan Road , Shanghai 201418 , P. R. China
| | - Zhongkuan Liu
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
| | - Lingyan Liu
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
| | - Yaping Zhong
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
| | - Ruohan Li
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
| | - Yifeng Zhou
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Haiquan Road , Shanghai 201418 , P. R. China
| | - Tao Yi
- Department of Chemistry , Fudan University , 2005 Songhu Road , Shanghai 200438 , P. R. China
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5
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Kubyshkin V, Budisa N. Promotion of the collagen triple helix in a hydrophobic environment. Org Biomol Chem 2019; 17:2502-2507. [DOI: 10.1039/c9ob00070d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The collagen triple helix is better suited for octanol than for water.
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Affiliation(s)
| | - Nediljko Budisa
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
- University of Manitoba
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Zhou X, Su X, Tan Z, Zhou C. Synthesis of triblock amphiphilic copolypeptides with excellent antibacterial activity. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mantsyzov AB, Savelyev OY, Ivantcova PM, Bräse S, Kudryavtsev KV, Polshakov VI. Theoretical and NMR Conformational Studies of β-Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units. Front Chem 2018; 6:91. [PMID: 29644215 PMCID: PMC5883087 DOI: 10.3389/fchem.2018.00091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.
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Affiliation(s)
- Alexey B. Mantsyzov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Y. Savelyev
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Polina M. Ivantcova
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Konstantin V. Kudryavtsev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, Russia
| | - Vladimir I. Polshakov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
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Kubyshkin V, Budisa N. Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole-2-carboxylic acid. J Pept Sci 2018; 24:e3076. [PMID: 29582506 DOI: 10.1002/psc.3076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 12/12/2022]
Abstract
The polyproline-II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and "unstructured" denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline-II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan-1-ol/water partitioning and inclusion in detergent micelles of the oligo-Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo-Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline-II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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9
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Zhou X, Su X, Zhou C. Preparation of diblock amphiphilic polypeptide nanoparticles for medical applications. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Abstract
Amide rotation of peptidyl-prolyl fragments is an important factor in backbone structure organization of proteins. Computational studies have indicated that this rotation preferentially proceeds through a defined transition-state structure (syn/exo). Here, we complement the computational findings by determining the amide bond rotation barriers for derivatives of the two symmetric proline analogues, meso and racemic pyrrolidine-2,5-dicarboxylic acids. The rotations around these residues represent syn/exo-syn/exo and anti/endo-syn/exo hybrid transition states for the meso and racemic diastereomer, respectively. The rotation barriers are lower for the former rotation by about 9 kJ mol-1 (aqueous medium), suggesting a strong preference for the syn/exo (clockwise) rotation over the anti/endo (anticlockwise) rotation. The results show that both hybrid rotation processes are enthalpically driven but respond differently to solvent polarity changes due to the different transition state dipole-dipole interactions.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
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Bansode ND, Madhanagopal B, Sonar MV, Ganesh KN. Stereodependent and solvent-specific formation of unusual β-structure through side chain-backbone H-bonding in C4(S)-(NH2/OH/NHCHO)-L-prolyl polypeptides. Biopolymers 2017; 108. [DOI: 10.1002/bip.22981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/08/2016] [Accepted: 08/25/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Nitin D. Bansode
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - B. Madhanagopal
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - Mahesh V. Sonar
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - Krishna N. Ganesh
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
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12
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Lella M, Mahalakshmi R. Solvation driven conformational transitions in the second transmembrane domain of mycobacteriophage holin. Biopolymers 2017; 108. [DOI: 10.1002/bip.22894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/11/2016] [Accepted: 05/31/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal 462023 India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal 462023 India
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