1
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Yang J, Quan Y, Ouyang Y, Tan KO, Weber RT, Griffin RG, Raines RT. Peptidic "Molecular Beacon" for Collagen. Biomacromolecules 2024. [PMID: 39225003 DOI: 10.1021/acs.biomac.4c01000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Collagen-mimetic peptides (CMP) have been invaluable tools for understanding the structure and function of collagen, which is the most abundant protein in animals. CMPs have also been developed as probes that detect damaged collagen because of the specificity required to form a collagen triple helix. These probes are not, however, ratiometric. Here, we used EPR spectroscopy to determine the end-to-end distances of CMPs that do not form stable homotrimeric helices. We found that those distances are shorter than the distances in the context of a collagen triple helix, suggesting their potential utility as a "molecular beacon" and guiding the choice and location of a pendant fluorophore-quencher pair. We then showed that a molecular beacon based on a glycine-(2S,4S)-4-fluoroproline-(2S,4R)-4-hydroxyproline tripeptide repeat and EDANS-DABCYL pair enabled the ratiometric detection of its binding to both other CMPs and natural mammalian collagen. These results provide guidance for the development of a new modality for detecting damaged collagen in physiological settings.
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Affiliation(s)
- Jinyi Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yifan Quan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yifu Ouyang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kong Ooi Tan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ralph T Weber
- Bruker Biospin Corporation, Billerica, Massachusetts 01821, United States
| | - Robert G Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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3
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Yao L, Ling B, Zhao S, Yu F, Liu H, Wang S, Xiao J. Versatile Self-Assembly of Triblock Peptides into Stable Collagen Mimetic Heterotrimers. Int J Mol Sci 2024; 25:6550. [PMID: 38928256 PMCID: PMC11203499 DOI: 10.3390/ijms25126550] [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: 04/13/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
The construction of peptides to mimic heterogeneous proteins such as type I collagen plays a pivotal role in deciphering their function and pathogenesis. However, progress in the field has been severely hampered by the lack of capability to create stable heterotrimers with desired functional sequences and without the effect of homotrimers. We have herein developed a set of triblock peptides that can assemble into collagen mimetic heterotrimers with desired amino acids and are free from the interference of homotrimers. The triblock peptides comprise a central collagen-like block and two oppositely charged N-/C-terminal blocks, which display inherent incompetency of homotrimer formation. The favorable electrostatic attraction between two paired triblock peptides with complementary terminal charged sequences promptly leads to stable heterotrimers with controlled chain composition. The independence of the collagen-like block from the two terminal blocks endows this system with the adaptability to incorporate desired amino acid sequences while maintaining the heterotrimer structure. The triblock peptides provide a versatile and robust tool to mimic the composition and function of heterotrimer collagen and may have great potential in the design of innovative peptides mimicking heterogeneous proteins.
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Affiliation(s)
- Linyan Yao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
- School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Biyang Ling
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Sha Zhao
- College of Chemistry and Molecular Engineering, Beijing NMR Center, Peking University, Beijing 100871, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering, Beijing NMR Center, Peking University, Beijing 100871, China
| | - Jianxi Xiao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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4
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Falanga A, Bellavita R, Braccia S, Galdiero S. Hydrophobicity: The door to drug delivery. J Pept Sci 2024; 30:e3558. [PMID: 38115215 DOI: 10.1002/psc.3558] [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] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
The engineering of intracellular delivery systems with the goal of achieving personalized medicine has been encouraged by advances in nanomaterial science as well as a greater understanding of diseases and of the biochemical pathways implicated in many disorders. The development of vectors able to transport the drug to a target location and release it only on demand is undoubtedly the primary issue. From a molecular perspective, the topography of drug carrier surfaces is directly related to the design of an effective drug carrier because it provides a physical hint to modifying its interactions with biological systems. For instance, the initial ratio of hydrophilic to hydrophobic surfaces and the changes brought about by external factors enable the release or encapsulation of a therapeutic molecule and the ability of the nanosystem to cross biological barriers and reach its target without causing systemic toxicity. The first step in creating new materials with enhanced functionality is to comprehend and characterize the interplay between hydrophilic and hydrophobic molecules at the molecular level. Therefore, the focus of this review is on the function of hydrophobicity, which is essential for matching the complexity of biological environments with the intended functionality.
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Affiliation(s)
- Annarita Falanga
- Department of Agricultural Sciences, University of Naples "Federico II", Naples, Italy
- CiRPEB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
| | - Rosa Bellavita
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Simone Braccia
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
| | - Stefania Galdiero
- CiRPEB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy
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5
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Patel K, Karmakar S, Tothadi S, Reddy JP, Prabhakaran P. "Fluorine Effects" in Conformational Orchestration of α/β Hybrid Peptide with a 9-membered Pseudo β-Turn Motif. Chemistry 2024; 30:e202303757. [PMID: 38165894 DOI: 10.1002/chem.202303757] [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: 11/11/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/04/2024]
Abstract
Fluorine, the tiny robust atom, with its unique features has captured the attention of scientists in recent times, especially in drug discovery with its integration in small molecules, peptides, and proteins. However, studies to understand the 'fluorine effects' on the conformation of molecules that follow 'beyond the rule of 5' are in the infancy yet significant in molecular design and function. For the first time, using short hybrid peptide sequence as an appropriate model, we examined the substitution effect (size, stereoelectronic effect, and hydrogen bonding) using X-ray diffraction, 2D-NMR, and CD studies. The comparative study on their folding patterns with hydrogen-substituted analogs can provide valuable insights into fluorinated substrates' design.
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Affiliation(s)
- Karma Patel
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
| | - Sintu Karmakar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
| | - Srinu Tothadi
- Analytical and Environmental Sciences Division and Centralized Instrument Facility (AESD&CIF), CSIR-Central Salt & Marine Chemicals Research Institute (CSMCRI), Bhavnagar, India-, 364002
| | - J Prakasha Reddy
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
| | - Panchami Prabhakaran
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
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6
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Iio C, Sato K, Mase N, Narumi T. Substitution Effects of Alkene Dipeptide Isosteres on Adjacent Peptide Bond Rotation. Chem Pharm Bull (Tokyo) 2024; 72:596-599. [PMID: 38945948 DOI: 10.1248/cpb.c24-00254] [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: 07/02/2024]
Abstract
Alkene dipeptide isosteres (ADIs) are promising surrogates of peptide bonds that enhance the bioactive peptide resistance to enzymatic hydrolysis in medicinal chemistry. In this study, we investigated the substitution effects of an ADI on the energy barrier of cis-trans isomerization in the acetyl proline methyl ester (Ac-Pro-OMe) model. The (E)-alkene-type proline analog, which favors a cis-amide conformation, exhibits a lower rotational barrier than native Ac-Pro-OMe. A van't Hoff analysis suggests that the energy barrier is primarily reduced by enthalpic repulsion. It was concluded that although carbon-carbon double bonds and pyrrolidine rings individually increase the rigidity of the incorporation site, their combination can provide structural flexibility and disrupt bioactive conformations. This work provides new insights into ADI-based drug design.
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Affiliation(s)
- Chihiro Iio
- Graduate School of Medical Photonics, Shizuoka University
| | - Kohei Sato
- Graduate School of Integrated Science and Technology, Shizuoka University
| | - Nobuyuki Mase
- Graduate School of Integrated Science and Technology, Shizuoka University
| | - Tetsuo Narumi
- Graduate School of Medical Photonics, Shizuoka University
- Graduate School of Integrated Science and Technology, Shizuoka University
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7
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Aguilar CJ, Sarwar M, Prabakar S, Zhang W, Harris PWR, Brimble MA, Kavianinia I. Harnessing the power of a photoinitiated thiol-ene "click" reaction for the efficient synthesis of S-lipidated collagen model peptide amphiphiles. Org Biomol Chem 2023; 21:9150-9158. [PMID: 37822146 DOI: 10.1039/d3ob01469j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
A photoinitiated thiol-ene "click" reaction was used to synthesize S-lipidated collagen model peptide amphiphiles. Use of 2-iminothiolane provided an epimerization-free thiol handle required for thiol-ene based incorporation of lipid moieties onto collagen-based peptide sequences. This approach not only led to improvements in the triple helical characteristics of the resulting collagen model peptides but also increased the aqueous solubility of the peptide amphiphiles. As a result, this methodology holds significant potential for the design and advancement of functional peptide amphiphiles, offering enhanced capabilities across a wide range of applications.
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Affiliation(s)
- Clouie Justin Aguilar
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand.
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Makhdoom Sarwar
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
- Department of Obstetrics and Gynaecology, University of Otago, Christchurch, 2 Riccarton Avenue, Christchurch 8011, New Zealand
| | - Sujay Prabakar
- Leather and Shoe Research Association of New Zealand, PO Box 8094, Hokowhitu, Palmerston North 4446, New Zealand
| | - Wenkai Zhang
- Leather and Shoe Research Association of New Zealand, PO Box 8094, Hokowhitu, Palmerston North 4446, New Zealand
| | - Paul W R Harris
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand.
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Margaret A Brimble
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand.
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Iman Kavianinia
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand.
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
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8
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Borgula IM, Shuvaev S, Abston E, Rotile NJ, Weigand-Whittier J, Zhou IY, Caravan P, Raines RT. Detection of Pulmonary Fibrosis with a Collagen-Mimetic Peptide. ACS Sens 2023; 8:4008-4013. [PMID: 37930825 PMCID: PMC10842190 DOI: 10.1021/acssensors.3c00717] [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] [Indexed: 11/08/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a disease of unknown etiology that is characterized by excessive deposition and abnormal remodeling of collagen. IPF has a mean survival time of only 2-5 years from diagnosis, creating a need to detect IPF at an earlier stage when treatments might be more effective. We sought to develop a minimally invasive probe that could detect molecular changes in IPF-associated collagen. Here, we describe the design, synthesis, and performance of [68Ga]Ga·DOTA-CMP, which comprises a positron-emitting radioisotope linked to a collagen-mimetic peptide (CMP). This peptide mimics the natural structure of collagen and detects irregular collagen matrices by annealing to damaged collagen triple helices. We assessed the ability of the peptide to detect aberrant lung collagen selectively in a bleomycin-induced mouse model of pulmonary fibrosis using positron emission tomography (PET). [68Ga]Ga·DOTA-CMP PET demonstrated higher and selective uptake in a fibrotic mouse lung compared to controls, minimal background signal in adjacent organs, and rapid clearance via the renal system. These studies suggest that [68Ga]Ga·DOTA-CMP identifies fibrotic lungs and could be useful in the early diagnosis of IPF.
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Affiliation(s)
- Isabella M. Borgula
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sergey Shuvaev
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02124, United States
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Eric Abston
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
- Department of Thoracic Surgery, Massachusetts General Hospital, Boston, Massachusetts 02124, United States
| | - Nicholas J. Rotile
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Jonah Weigand-Whittier
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Iris Y. Zhou
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Peter Caravan
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02124, United States
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Qiu R, Li X, Huang K, Bai W, Zhou D, Li G, Qin Z, Li Y. Cis-trans isomerization of peptoid residues in the collagen triple-helix. Nat Commun 2023; 14:7571. [PMID: 37989738 PMCID: PMC10663571 DOI: 10.1038/s41467-023-43469-8] [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: 06/10/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
Cis-peptide bonds are rare in proteins, and building blocks less favorable to the trans-conformer have been considered destabilizing. Although proline tolerates the cis-conformer modestly among all amino acids, for collagen, the most prevalent proline-abundant protein, all peptide bonds must be trans to form its hallmark triple-helix structure. Here, using host-guest collagen mimetic peptides (CMPs), we discover that surprisingly, even the cis-enforcing peptoid residues (N-substituted glycines) form stable triple-helices. Our interrogations establish that these peptoid residues entropically stabilize the triple-helix by pre-organizing individual peptides into a polyproline-II helix. Moreover, noting that the cis-demanding peptoid residues drastically reduce the folding rate, we design a CMP whose triple-helix formation can be controlled by peptoid cis-trans isomerization, enabling direct targeting of fibrotic remodeling in myocardial infarction in vivo. These findings elucidate the principles of peptoid cis-trans isomerization in protein folding and showcase the exploitation of cis-amide-favoring residues in building programmable and functional peptidomimetics.
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Affiliation(s)
- Rongmao Qiu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Xiaojing Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Kui Huang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Weizhe Bai
- Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Daoning Zhou
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China
| | - Gang Li
- Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
| | - Zhao Qin
- Department of Civil & Environmental Engineering, College of Engineering & Computer Science, Syracuse University, Syracuse, New York, 13244, USA.
| | - Yang Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
- Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, 519000, China.
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10
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Abstract
Collagen provides mechanical and biological support for virtually all human tissues in the extracellular matrix (ECM). Its defining molecular structure, the triple-helix, could be damaged and denatured in disease and injuries. To probe collagen damage, the concept of collagen hybridization has been proposed, revised, and validated through a series of investigations reported as early as 1973: a collagen-mimicking peptide strand may form a hybrid triple-helix with the denatured chains of natural collagen but not the intact triple-helical collagen proteins, enabling assessment of proteolytic degradation or mechanical disruption to collagen within a tissue-of-interest. Here we describe the concept and development of collagen hybridization, summarize the decades of chemical investigations on rules underlying the collagen triple-helix folding, and discuss the growing biomedical evidence on collagen denaturation as a previously overlooked ECM signature for an array of conditions involving pathological tissue remodeling and mechanical injuries. Finally, we propose a series of emerging questions regarding the chemical and biological nature of collagen denaturation and highlight the diagnostic and therapeutic opportunities from its targeting.
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Affiliation(s)
- Xiaojing Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Department of Radiology, Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qi Zhang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Department of Radiology, Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - S. Michael Yu
- Department of Biomedical Engineering, Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Yang Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Department of Radiology, Cardiac Surgery and Structural Heart Disease Unit of Cardiovascular Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
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11
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Zhang Q, Li X, Huang K, Huang Y, Zhao S, Liu S, Li Y. Controlling the Trimerization of the Collagen Triple-Helix by Solvent Switching. Biomacromolecules 2023; 24:1689-1699. [PMID: 36967667 DOI: 10.1021/acs.biomac.2c01475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Collagen hybridizing peptides (CHPs) are a powerful tool for targeting collagen damage in pathological tissues due to their ability to specifically form a hybrid collagen triple-helix with the denatured collagen chains. However, CHPs have a strong tendency to self-trimerize, requiring preheating or complicated chemical modifications to dissociate their homotrimers into monomers, which hinders their applications. To control the self-assembly of CHP monomers, we evaluated the effects of 22 cosolvents on the triple-helix structure: unlike typical globular proteins, the CHP homotrimers (as well as the hybrid CHP-collagen triple helix) cannot be destabilized by the hydrophobic alcohols and detergents (e.g., SDS) but can be effectively dissociated by the cosolvents that dominate hydrogen bonds (e.g., urea, guanidinium salts, and hexafluoroisopropanol). Our study provided a reference for the solvent effects on natural collagen and a simple effective solvent-switch method, enabling CHP utilization in automated histopathology staining and in vivo imaging and targeting of collagen damage.
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12
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Terrien A, Rahgoshay K, Renaglia E, Lensen N, Jacquot Y, Marquant R, Brigaud T, Loison C, Chaume G, Miclet E. Inviting C5-Trifluoromethylated Pseudoprolines into Collagen Mimetic Peptides. Biomacromolecules 2023; 24:1555-1562. [PMID: 36786736 DOI: 10.1021/acs.biomac.2c01242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Numerous collagen mimetic peptides (CMPs) have been engineered using proline derivatives substituted at their C(3) and/or C(4) position in order to stabilize or functionalize collagen triple-helix mimics. However, no example has been reported so far with C(5) substitutions. Here, we introduce a fluorinated CMP incorporating trifluoromethyl groups at the C(5) position of pseudoproline residues. In tripeptide models, our CD, NMR, and molecular dynamics (MD) studies have shown that, when properly arranged, these residues meet the structural requirements for a triple-helix assembly. Two host-guest CMPs were synthesized and analyzed by CD spectroscopy. The NMR analysis in solution of the most stable confirmed the presence of structured homotrimers that we interpret as triple helices. MD calculations showed that the triple-helix model remained stable throughout the simulation with all six trifluoromethyl groups pointing outward from the triple helix. Pseudoprolines substituted at the C(5) positions appeared as valuable tools for the design of new fluorinated collagen mimetic peptides.
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Affiliation(s)
- Anaïs Terrien
- Laboratoire des Biomolécules, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Keyvan Rahgoshay
- CY Cergy Paris Université, CNRS, BioCIS, 95000 Cergy-Pontoise, France
| | - Emelyne Renaglia
- CY Cergy Paris Université, CNRS, BioCIS, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- CY Cergy Paris Université, CNRS, BioCIS, 95000 Cergy-Pontoise, France
| | - Yves Jacquot
- CiTCoM, CNRS UMR 8038, INSERM U1268, Faculty of Pharmacy of Paris, University Paris Cité, 75270 Paris Cedex 06, France
| | - Rodrigue Marquant
- Laboratoire des Biomolécules, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Thierry Brigaud
- CY Cergy Paris Université, CNRS, BioCIS, 95000 Cergy-Pontoise, France
| | - Claire Loison
- Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Grégory Chaume
- Laboratoire des Biomolécules, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 4 place Jussieu, 75252 Paris Cedex 05, France.,CY Cergy Paris Université, CNRS, BioCIS, 95000 Cergy-Pontoise, France
| | - Emeric Miclet
- Laboratoire des Biomolécules, Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 4 place Jussieu, 75252 Paris Cedex 05, France
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13
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Goncalves AG, Hartzell EJ, Sullivan MO, Chen W. Recombinant protein polymer-antibody conjugates for applications in nanotechnology and biomedicine. Adv Drug Deliv Rev 2022; 191:114570. [PMID: 36228897 DOI: 10.1016/j.addr.2022.114570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/03/2022] [Accepted: 10/04/2022] [Indexed: 01/24/2023]
Abstract
Currently, there are over 100 antibody-based therapeutics on the market for the treatment of various diseases. The increasing importance of antibody treatment is further highlighted by the recent FDA emergency use authorization of certain antibody therapies for COVID-19 treatment. Protein-based materials have gained momentum for antibody delivery due to their biocompatibility, tunable chemistry, monodispersity, and straightforward synthesis and purification. In this review, we discuss progress in engineering the molecular features of protein-based biomaterials, in particular recombinant protein polymers, for introducing novel functionalities and enhancing the delivery properties of antibodies and related binding protein domains.
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Affiliation(s)
- Antonio G Goncalves
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States.
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States.
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14
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Li X, Wei F, Le X, Wang L, Wang D, Chen C, Xu S, Liao X, Zhao Y. Solvent modulated structural transition of self-assemblies formed by bola-form hexapeptide amphiphiles. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Nanda R, Hazan S, Sauer K, Aladin V, Keinan-Adamsky K, Corzilius B, Shahar R, Zaslansky P, Goobes G. Molecular differences in collagen organization and in organic-inorganic interfacial structure of bones with and without osteocytes. Acta Biomater 2022; 144:195-209. [PMID: 35331939 DOI: 10.1016/j.actbio.2022.03.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 12/22/2022]
Abstract
Bone is a fascinating biomaterial composed mostly of type-I collagen fibers as an organic phase, apatite as an inorganic phase, and water molecules residing at the interfaces between these phases. They are hierarchically organized with minor constituents such as non-collagenous proteins, citrate ions and glycosaminoglycans into a composite structure that is mechanically durable yet contains enough porosity to accommodate cells and blood vessels. The nanometer scale organization of the collagen fibrous structure and the mineral constituents in bone were recently extensively scrutinized. However, molecular details at the lowest hierarchical level still need to be unraveled to better understand the exact atomic-level arrangement of all these important components in the context of the integral structure of the bone. In this report, we unfold some of the molecular characteristics differentiating between two load-bearing (cleithrum) bones, one from sturgeon fish, where the matrix contains osteocytes and one from pike fish where the bone tissue is devoid of these bone cells. Using enhanced solid-state NMR measurements, we underpin disparities in the collagen fibril structure and dynamics, the mineral phases, the citrate content at the organic-inorganic interface and water penetrability in the two bones. These findings suggest that different strategies are undertaken in the erection of the mineral-organic interfaces in various bones characterized by dissimilar osteogenesis or remodeling pathways and may have implications for the mechanical properties of the particular bone. STATEMENT OF SIGNIFICANCE: Bone boasts unique interactions between collagen fibers and mineral phases through interfaces holding together this bio-composite structure. Over evolution, fish have gone from mineralizing their bones aided by certain bone cells called osteocytes, like tetrapod, to mineralization without these cells. Here, we report atomic level differences in collagen fiber cross linking and organization, porosity of the mineral phases and content of citrate molecules at the bio-mineral interface in bones from modern versus ancient fish. The dissimilar structural features may suggest disparate mechanical properties for the two bones. Fundamental level understanding of the organic and inorganic components in bone and the interfacial interactions holding them together is essential for successful bone repair and for treating better tissue pathologies.
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16
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Pons A, Decaens J, Najjar R, Otog N, Arribat M, Jolly S, Couve-Bonnaire S, Sebban M, Coadou G, Oulyadi H, Speybrouck D, Iwasa S, Charette AB, Poisson T, Jubault P. Fluorocyclopropane-Containing Proline Analogue: Synthesis and Conformation of an Item in the Peptide Chemist's Toolbox. ACS OMEGA 2022; 7:4868-4878. [PMID: 35187307 PMCID: PMC8851640 DOI: 10.1021/acsomega.1c05337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/10/2021] [Indexed: 05/27/2023]
Abstract
Over the years, numerous modifications to the structure of proline have been made in order to tune its effects on bioactive compounds. Notably, the introduction of a cyclopropane ring or a fluorine atom has produced interesting results. Herein, we describe the synthesis of a proline containing fluorocyclopropane. This modified amino acid was inserted into a tripeptide, whose conformation was studied by nuclear magnetic resonance and density functional theory calculations.
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Affiliation(s)
- Amandine Pons
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Jonathan Decaens
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Riham Najjar
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Nansalmaa Otog
- Department
of Applied Chemistry and Life Science, Toyohashi
University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Mathieu Arribat
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Sandrine Jolly
- Analytical
Sciences—Discovery Sciences, Janssen
Research & Development, a Division of Janssen-Cilag, Campus de Maigremont, CS10615, F-27106 Val de Reuil Cedex, France
| | - Samuel Couve-Bonnaire
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Muriel Sebban
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Gael Coadou
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Hassan Oulyadi
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - David Speybrouck
- Analytical
Sciences—Discovery Sciences, Janssen
Research & Development, a Division of Janssen-Cilag, Campus de Maigremont, CS10615, F-27106 Val de Reuil Cedex, France
| | - Seiji Iwasa
- Department
of Applied Chemistry and Life Science, Toyohashi
University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - André B. Charette
- Centre
in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department
of Chemistry, Université de Montréal, P.O. Box 6128, Station Downtown, Montréal, Québec H3C3J7, Canada
| | - Thomas Poisson
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
- Institut
Universitaire de France, 1 rue Descartes, 75231 Paris, France
| | - Philippe Jubault
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
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17
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Sahariah B, Sarma BK. Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts. J Phys Chem B 2021; 125:13394-13405. [PMID: 34851647 DOI: 10.1021/acs.jpcb.1c07875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol-1) nO → σ*Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their Cα-Cβ bonds. As the nO → σ*Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual nN(amide) → σ*C-N interaction (∼0.3 kcal·mol-1) was observed between the peptidic nitrogen lone pair (nN) and the antibonding orbital (σ*C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.
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Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
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18
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Mondal R, Agbaria M, Nairoukh Z. Fluorinated Rings: Conformation and Application. Chemistry 2021; 27:7193-7213. [PMID: 33512034 DOI: 10.1002/chem.202005425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/16/2022]
Abstract
The introduction of fluorine atoms into molecules and materials across many fields of academic and industrial research is now commonplace, owing to their unique properties. A particularly interesting feature is the impact of fluorine substitution on the relative orientation of a C-F bond when incorporated into organic molecules. In this Review, we will be discussing the conformational behavior of fluorinated aliphatic carbo- and heterocyclic systems. The conformational preference of each system is associated with various interactions introduced by fluorine substitution such as charge-dipole, dipole-dipole, and hyperconjugative interactions. The contribution of each interaction on the stabilization of the fluorinated alicyclic system, which manifests itself in low conformations, will be discussed in detail. The novelty of this feature will be demonstrated by presenting the most recent applications.
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Affiliation(s)
- Rajarshi Mondal
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Mohamed Agbaria
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Zackaria Nairoukh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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19
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Xu Y, Kirchner M. Collagen Mimetic Peptides. Bioengineering (Basel) 2021; 8:5. [PMID: 33466358 PMCID: PMC7824840 DOI: 10.3390/bioengineering8010005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022] Open
Abstract
Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in many physiological and pathogenic processes. Applications of CMPs have advanced our understanding of the structure and molecular properties of a collagen triple helix-the building block of collagen-and the interactions of collagen with important molecular ligands. The accumulating knowledge is also paving the way for developing novel CMPs for biomedical applications. Indeed, for the past 50 years, CMP research has been a fast-growing, far-reaching interdisciplinary field. The major development and achievement of CMPs were documented in a few detailed reviews around 2010. Here, we provided a brief overview of what we have learned about CMPs-their potential and their limitations. We focused on more recent developments in producing heterotrimeric CMPs, and CMPs that can form collagen-like higher order molecular assemblies. We also expanded the traditional view of CMPs to include larger designed peptides produced using recombinant systems. Studies using recombinant peptides have provided new insights on collagens and promoted progress in the development of collagen mimetic fibrillar self-assemblies.
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Affiliation(s)
- Yujia Xu
- Department of Chemistry, Hunter College of the City University of New York, 695 Park Ave., New York, NY 10065, USA;
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20
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Jourdain de Muizon C, Ramanoudjame SM, Esteoulle L, Ling C, Brou G, Anton N, Vandamme T, Delsuc MA, Bonnet D, Kieffer B. Self-organization Properties of a GPCR-Binding Peptide with a Fluorinated Tail Studied by Fluorine NMR Spectroscopy. Chembiochem 2020; 22:657-661. [PMID: 32986915 DOI: 10.1002/cbic.202000601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/25/2020] [Indexed: 12/31/2022]
Abstract
Conjugation of the bioactive apelin-17 peptide with a fluorocarbon chain results in self-organization of the peptide into micelles. Fluorine NMR spectroscopy studies show that the fluoropeptide's micelles are monodisperse, while proton NMR indicates that the peptide moiety remains largely disordered despite micellization. A very fast exchange rate is measured between the free and micellar states of the peptide which enables the number of molecules present in the micelle to be estimated as 200, in agreement with values found by dynamic light scattering measurements.
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Affiliation(s)
| | - Sridévi M Ramanoudjame
- Laboratoire d'Innovation Thérapeutique, LabEx MEDALIS, Université de Strasbourg, CNRS UMR, 7200 Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch-Graffenstaden, France
| | - Lucie Esteoulle
- Laboratoire d'Innovation Thérapeutique, LabEx MEDALIS, Université de Strasbourg, CNRS UMR, 7200 Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch-Graffenstaden, France
| | - Claude Ling
- Departement of Integrative Structural Biology, IGBMC, Université de Strasbourg, INSERM U596, CNRS UMR, 7104 1, rue Laurent Fries, 67404, Illkirch, France
| | - Germain Brou
- Conception et Applications de Molécules Bioactives, Université de Strasbourg, CNRS UMR 7199, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch-Graffenstaden, France
| | - Nicolas Anton
- Conception et Applications de Molécules Bioactives, Université de Strasbourg, CNRS UMR 7199, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch-Graffenstaden, France
| | - Thierry Vandamme
- Conception et Applications de Molécules Bioactives, Université de Strasbourg, CNRS UMR 7199, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch-Graffenstaden, France
| | - Marc-André Delsuc
- Departement of Integrative Structural Biology, IGBMC, Université de Strasbourg, INSERM U596, CNRS UMR, 7104 1, rue Laurent Fries, 67404, Illkirch, France.,CASC4DE Le Lodge 20, Avenue du Neuhof, 67100, Strasbourg, France
| | - Dominique Bonnet
- Laboratoire d'Innovation Thérapeutique, LabEx MEDALIS, Université de Strasbourg, CNRS UMR, 7200 Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch-Graffenstaden, France
| | - Bruno Kieffer
- Departement of Integrative Structural Biology, IGBMC, Université de Strasbourg, INSERM U596, CNRS UMR, 7104 1, rue Laurent Fries, 67404, Illkirch, France
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21
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Chen S, Ruan Y, Lu JL, Hunter L, Hu XG. Diastereoselective synthesis and conformational analysis of 4,5-difluoropipecolic acids. Org Biomol Chem 2020; 18:8192-8198. [PMID: 33030197 DOI: 10.1039/d0ob01811b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Stereoselectively-fluorinated analogs of pipecolic acid have been investigated through a combined theoretical and experimental approach. Three of the four possible diastereoisomers of 4,5-difluoropipecolic acid were successfully synthesized via deoxyfluorination chemistry, navigating a complex reaction network that included neighboring group participation, rearrangement, and elimination pathways. A DFT-based conformational study, supported by NMR J-based analysis, revealed that the different diastereoisomers of 4,5-difluoropipecolic acid preferentially adopt different puckers of the six-membered ring. These findings could have future relevance for the conformational control of biologically active peptides.
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Affiliation(s)
- Suo Chen
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Yao Ruan
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Ji-Liang Lu
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China.
| | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia.
| | - Xiang-Guo Hu
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P. R. China. and Key Laboratory of Small Functional Organic Molecules, Jiangxi Normal University, Nanchang, 330022, P. R. China
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22
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Kanai S, Machida K, Masuda R, Koide T. Peptide precursors that acquire denatured collagen-hybridizing ability by O-to-N acyl migration at physiological pH. Org Biomol Chem 2020; 18:2823-2827. [PMID: 32232252 DOI: 10.1039/c9ob02136a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Here, we report peptide probes with either single or cyclic double stranded collagen-like sequences that spontaneously acquire collagen-hybridizing ability at physiological pH. These peptides have ester bonds derived from O-acyl isopeptide units that are converted to amide bonds via intramolecular O-to-N acyl migration by a pH shift. The peptides that do not require pre-treatment for disassembly will be useful as prodrugs in theranostic treatments targeting unfolded collagen.
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Affiliation(s)
- Sayaka Kanai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Japan
| | - Koshi Machida
- Waseda Research Institute for Science and Engineering, Waseda University, Japan.
| | - Ryo Masuda
- Waseda Research Institute for Science and Engineering, Waseda University, Japan.
| | - Takaki Koide
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Japan and Waseda Research Institute for Science and Engineering, Waseda University, Japan.
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23
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Hulgan SAH, Jalan AA, Li IC, Walker DR, Miller MD, Kosgei AJ, Xu W, Phillips GN, Hartgerink JD. Covalent Capture of Collagen Triple Helices Using Lysine–Aspartate and Lysine–Glutamate Pairs. Biomacromolecules 2020; 21:3772-3781. [DOI: 10.1021/acs.biomac.0c00878] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sarah A. H. Hulgan
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Abhishek A. Jalan
- Department of Biochemistry, University of Bayreuth, Bayreuth 95447, Germany
| | - I-Che Li
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Douglas R. Walker
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Mitchell D. Miller
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Abigael J. Kosgei
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Weijun Xu
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - George N. Phillips
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D. Hartgerink
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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24
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Abstract
Collagen is the most abundant protein in humans and the major component of human skin. Collagen mimetic peptides (CMPs) can anneal to damaged collagen in vitro and in vivo. A duplex of CMPs was envisioned as a macromolecular mimic for damaged collagen. The duplex was synthesized on a solid support from the amino groups of a lysine residue and by using olefin metathesis to link the N termini. The resulting cyclic peptide, which is a monomer in solution, binds to CMPs to form a triple helix. Among these, CMPs that are engineered to avoid the formation of homotrimers but preorganized to adopt the conformation of a collagen strand exhibit enhanced association. Thus, this cyclic peptide enables the assessment of CMPs for utility in annealing to damaged collagen. Such CMPs have potential use in the diagnosis and treatment of fibrotic diseases and wounds.
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Affiliation(s)
| | - I Caglar Tanrikulu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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25
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Wang S, Zhang H, He W, Zhou H, Tao Y. Sequence-controlled proline-based polyacrylamides via RAFT polymerization: Influence of sequence structure on polymers performances. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2019.109357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Dones JM, Tanrikulu IC, Chacko JV, Schroeder AB, Hoang TT, Gibson ALF, Eliceiri KW, Raines RT. Optimization of interstrand interactions enables burn detection with a collagen-mimetic peptide. Org Biomol Chem 2019; 17:9906-9912. [PMID: 31720665 DOI: 10.1039/c9ob01839e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Collagen is an abundant component of the extracellular matrix and connective tissues. Some collagen-mimetic peptides (CMPs) that do not form homotrimers can anneal to damaged tissue. Here, through a computational screen, we identify (flpHypGly)7 as an optimal monomeric CMP for heterotrimer formation. We find that (flpHypGly)7 forms stable triple helices with (ProProGly)7 but not with itself. The nonnatural amino acid HflpOH, which is (2S,4S)-4-fluoroproline, is not toxic to human fibroblasts or keratinocytes. Conjugation of (flpHypGly)7 to a fluorescent dye enables the facile detection of burned collagenous tissue with high specificity. The ubiquity of collagen and the prevalence of injuries and diseases that disrupt endogenous collagen suggests widespread utility for this approach.
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Affiliation(s)
- Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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27
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Harris T, Chenoweth DM. Sterics and Stereoelectronics in Aza-Glycine: Impact of Aza-Glycine Preorganization in Triple Helical Collagen. J Am Chem Soc 2019; 141:18021-18029. [DOI: 10.1021/jacs.9b05524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trevor Harris
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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28
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René A, Quilan M, Deng Y, Cheng Y, Teleha CA, Raboisson P, Bonfanti JF, Fortin J, Charette AB, Pannecoucke X, Poisson T, Jubault P. Practical Synthesis of Ethyl 3-Fluoro-1-pyrrole-2-carboxylate: A Key Fragment of a Potent Drug Candidate against Hepatitis B Virus. Org Process Res Dev 2019. [DOI: 10.1021/acs.oprd.9b00382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adeline René
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Maxime Quilan
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Yicheng Deng
- AcceleDev R&D Co., Ltd., Building J4, No. 15 Wanshou Road, Pukou Economy Development Zone, Nanjing City, China 211800
| | - Yang Cheng
- AcceleDev R&D Co., Ltd., Building J4, No. 15 Wanshou Road, Pukou Economy Development Zone, Nanjing City, China 211800
| | - Christopher A. Teleha
- Janssen Research & Development, Small Molecule Pharmaceutical Development, Janssen Pharmaceutical Companies of Johnson & Johnson, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Pierre Raboisson
- Janssen Research & Development, Medicinal Chemistry Infectious Diseases, Beerse, Belgium
| | - Jean-François Bonfanti
- Janssen Research & Development, Medicinal Chemistry Infectious Diseases, Centre de Recherche Janssen Cilag, Campus de Maigremont, BP 615, 27106 Val de Reuil Cedex, France
| | - Jérôme Fortin
- Janssen Research & Development, Medicinal Chemistry Infectious Diseases, Centre de Recherche Janssen Cilag, Campus de Maigremont, BP 615, 27106 Val de Reuil Cedex, France
| | - André. B. Charette
- Centre in Green Chemistry and Catalysis, Faculty of Arts and Sciences Department of Chemistry, Université de Montréal, P.O. Box 6128, Station Downtown Montréal, Québec, H3C3J7, Canada
| | - Xavier Pannecoucke
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Thomas Poisson
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris, France
| | - Philippe Jubault
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
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29
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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30
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Lu X, Duchimaza-Heredia J, Cui Q. Analysis of Density Functional Tight Binding with Natural Bonding Orbitals. J Phys Chem A 2019; 123:7439-7453. [PMID: 31373822 DOI: 10.1021/acs.jpca.9b05072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The description of chemical bonding by the density functional tight binding (DFTB) model is analyzed using natural bonding orbitals (NBOs) and compared to results from density functional theory (B3LYP/aug-cc-pVTZ) calculations. Several molecular systems have been chosen to represent fairly diverse bonding scenarios that include standard covalent bonds, hypervalent interactions, multicenter bonds, metal-ligand interactions (with and without the pseudo-Jahn-Teller effect), and through-space donor-acceptor interactions. Overall, the results suggest that DFTB3/3OB provides physically sound descriptions for the different bonding scenarios analyzed here, as reflected by the general agreement between DFTB3 and B3LYP NBO properties, such as the nature of the NBOs, the magnitudes of natural charges and bond orders, and the dominant donor-acceptor interactions. The degree of ligand-to-metal charge transfer and the ionic nature of pentavalent phosphate are overestimated, likely reflecting the minimal-basis nature of DFTB3/3OB. Moreover, certain orbital interactions, such as geminal interactions, are observed to be grossly overestimated by DFTB3 for hypervalent phosphate and several transition metal compounds that involve copper and nickel. The study indicates that results from NBO analysis can be instructive for identifying electronic structure descriptions at the approximate quantum-mechanical level that require improvement and thus for guiding the systematic improvement of these methods.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
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31
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Cutini M, Bocus M, Ugliengo P. Decoding Collagen Triple Helix Stability by Means of Hybrid DFT Simulations. J Phys Chem B 2019; 123:7354-7364. [DOI: 10.1021/acs.jpcb.9b05222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Cutini
- University of Torino, Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, Via P. Giuria 7, 10125 Turin, Italy
| | - Massimo Bocus
- University of Torino, Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, Via P. Giuria 7, 10125 Turin, Italy
| | - Piero Ugliengo
- University of Torino, Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, Via P. Giuria 7, 10125 Turin, Italy
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32
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Li IC, Hulgan SAH, Walker DR, Farndale RW, Hartgerink JD, Jalan AA. Covalent Capture of a Heterotrimeric Collagen Helix. Org Lett 2019; 21:5480-5484. [DOI: 10.1021/acs.orglett.9b01771] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- I-Che Li
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Sarah A. H. Hulgan
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Douglas R. Walker
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Richard W. Farndale
- University of Cambridge Department of Biochemistry, Downing Site, Cambridge CB2 1QW, U.K
| | - Jeffrey D. Hartgerink
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Abhishek A. Jalan
- University of Bayreuth Department of Biochemistry, Universitätsstraße 30, Bayreuth 95447, Germany
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33
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Hofman GJ, Ottoy E, Light ME, Kieffer B, Martins JC, Kuprov I, Sinnaeve D, Linclau B. Synthesis and Conformational Properties of 3,4-Difluoro-l-prolines. J Org Chem 2019; 84:3100-3120. [PMID: 30777755 DOI: 10.1021/acs.joc.8b02920] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fluorinated proline derivatives have found diverse applications in areas ranging from medicinal chemistry over structural biochemistry to organocatalysis. Depending on the stereochemistry of monofluorination at the proline 3- or 4-position, different effects on the conformational properties of proline (ring pucker, cis/ trans isomerization) are introduced. With fluorination at both 3- and 4-positions, matching or mismatching effects can occur depending on the relative stereochemistry. Here we report, in full, the syntheses and conformational properties of three out of the four possible 3,4-difluoro-l-proline diastereoisomers. The yet unreported conformational properties are described for (3 S,4 S)- and (3 R,4 R)-difluoro-l-proline, which are shown to bias ring pucker and cis/ trans ratios on the same order of magnitude as their respective monofluorinated progenitors, although with significantly faster amide cis/ trans isomerization rates. The reported analogues thus expand the scope of available fluorinated proline analogues as tools to tailor proline's distinct conformational and dynamical properties, allowing for the interrogation of its role in, for instance, protein stability or folding.
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Affiliation(s)
- Gert-Jan Hofman
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.,Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Mark E Light
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Bruno Kieffer
- Biomolecular NMR , University of Strasbourg , IGBMC, CNRS UMR 7104, INSERM U1258, 1 rue Laurent Fries/BP 10142 , Illkirch Cedex 67404 , France
| | - Jose C Martins
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Ilya Kuprov
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Bruno Linclau
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
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34
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Verhoork SJM, Killoran PM, Coxon CR. Fluorinated Prolines as Conformational Tools and Reporters for Peptide and Protein Chemistry. Biochemistry 2018; 57:6132-6143. [DOI: 10.1021/acs.biochem.8b00787] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sanne J. M. Verhoork
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
| | - Patrick M. Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
| | - Christopher R. Coxon
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
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35
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Chow WY, Forman CJ, Bihan D, Puszkarska AM, Rajan R, Reid DG, Slatter DA, Colwell LJ, Wales DJ, Farndale RW, Duer MJ. Proline provides site-specific flexibility for in vivo collagen. Sci Rep 2018; 8:13809. [PMID: 30218106 PMCID: PMC6138679 DOI: 10.1038/s41598-018-31937-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/28/2018] [Indexed: 02/02/2023] Open
Abstract
Fibrillar collagens have mechanical and biological roles, providing tissues with both tensile strength and cell binding sites which allow molecular interactions with cell-surface receptors such as integrins. A key question is: how do collagens allow tissue flexibility whilst maintaining well-defined ligand binding sites? Here we show that proline residues in collagen glycine-proline-hydroxyproline (Gly-Pro-Hyp) triplets provide local conformational flexibility, which in turn confers well-defined, low energy molecular compression-extension and bending, by employing two-dimensional 13C-13C correlation NMR spectroscopy on 13C-labelled intact ex vivo bone and in vitro osteoblast extracellular matrix. We also find that the positions of Gly-Pro-Hyp triplets are highly conserved between animal species, and are spatially clustered in the currently-accepted model of molecular ordering in collagen type I fibrils. We propose that the Gly-Pro-Hyp triplets in fibrillar collagens provide fibril "expansion joints" to maintain molecular ordering within the fibril, thereby preserving the structural integrity of ligand binding sites.
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Affiliation(s)
- Wing Ying Chow
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK ,0000 0001 0610 524Xgrid.418832.4Present Address: Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) im Forschungsverbund Berlin e.V., Campus Berlin-Buch, Robert-Rössle-Str 10, 13125 Berlin, Germany
| | - Chris J. Forman
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK ,0000 0001 2299 3507grid.16753.36Present Address: Northwestern University, 633 Clark St, Evanston, IL 60208 USA
| | - Dominique Bihan
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Downing Site, Cambridge, CB2 1QW UK ,0000 0004 1936 7697grid.22072.35Present Address: University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4 Canada
| | - Anna M. Puszkarska
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Rakesh Rajan
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - David G. Reid
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - David A. Slatter
- 0000 0001 0807 5670grid.5600.3Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Lucy J. Colwell
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - David J. Wales
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Richard W. Farndale
- 0000000121885934grid.5335.0Department of Biochemistry, University of Cambridge, Downing Site, Cambridge, CB2 1QW UK
| | - Melinda J. Duer
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
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36
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Chow WY, Forman CJ, Bihan D, Puszkarska AM, Rajan R, Reid DG, Slatter DA, Colwell LJ, Wales DJ, Farndale RW, Duer MJ. Proline provides site-specific flexibility for in vivo collagen. Sci Rep 2018. [PMID: 30218106 DOI: 10.1038/s41598‐018‐31937‐x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fibrillar collagens have mechanical and biological roles, providing tissues with both tensile strength and cell binding sites which allow molecular interactions with cell-surface receptors such as integrins. A key question is: how do collagens allow tissue flexibility whilst maintaining well-defined ligand binding sites? Here we show that proline residues in collagen glycine-proline-hydroxyproline (Gly-Pro-Hyp) triplets provide local conformational flexibility, which in turn confers well-defined, low energy molecular compression-extension and bending, by employing two-dimensional 13C-13C correlation NMR spectroscopy on 13C-labelled intact ex vivo bone and in vitro osteoblast extracellular matrix. We also find that the positions of Gly-Pro-Hyp triplets are highly conserved between animal species, and are spatially clustered in the currently-accepted model of molecular ordering in collagen type I fibrils. We propose that the Gly-Pro-Hyp triplets in fibrillar collagens provide fibril "expansion joints" to maintain molecular ordering within the fibril, thereby preserving the structural integrity of ligand binding sites.
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Affiliation(s)
- Wing Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) im Forschungsverbund Berlin e.V., Campus Berlin-Buch, Robert-Rössle-Str 10, 13125, Berlin, Germany
| | - Chris J Forman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Northwestern University, 633 Clark St, Evanston, IL, 60208, USA
| | - Dominique Bihan
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge, CB2 1QW, UK.,University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Anna M Puszkarska
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Rakesh Rajan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David A Slatter
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Lucy J Colwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge, CB2 1QW, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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37
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Testa A, Lucas X, Castro GV, Chan KH, Wright JE, Runcie AC, Gadd MS, Harrison WTA, Ko EJ, Fletcher D, Ciulli A. 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation. J Am Chem Soc 2018; 140:9299-9313. [PMID: 29949369 PMCID: PMC6430500 DOI: 10.1021/jacs.8b05807] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Indexed: 12/13/2022]
Abstract
Hydroxylation and fluorination of proline alters the pyrrolidine ring pucker and the trans:cis amide bond ratio in a stereochemistry-dependent fashion, affecting molecular recognition of proline-containing molecules by biological systems. While hydroxyprolines and fluoroprolines are common motifs in medicinal and biological chemistry, the synthesis and molecular properties of prolines containing both modifications, i.e., fluoro-hydroxyprolines, have not been described. Here we present a practical and facile synthesis of all four diastereoisomers of 3-fluoro-4-hydroxyprolines (F-Hyps), starting from readily available 4-oxo-l-proline derivatives. Small-molecule X-ray crystallography, NMR spectroscopy, and quantum mechanical calculations are consistent with fluorination at C3 having negligible effects on the hydrogen bond donor capacity of the C4 hydroxyl, but inverting the natural preference of Hyp from C4-exo to C4-endo pucker. In spite of this, F-Hyps still bind to the von Hippel-Lindau (VHL) E3 ligase, which naturally recognizes C4-exo Hyp in a stereoselective fashion. Co-crystal structures and electrostatic potential calculations support and rationalize the observed preferential recognition for (3 R,4 S)-F-Hyp over the corresponding (3 S,4 S) epimer by VHL. We show that (3 R,4 S)-F-Hyp provides bioisosteric Hyp substitution in both hypoxia-inducible factor 1 alpha (HIF-1α) substrate peptides and peptidomimetic ligands that form part of PROTAC (proteolysis targeting chimera) conjugates for targeted protein degradation. Despite a weakened affinity, Hyp substitution with (3 S,4 S)-F-Hyp within the PROTAC MZ1 led to Brd4-selective cellular degradation at concentrations >100-fold lower than the binary Kd for VHL. We anticipate that the disclosed chemistry of 3-fluoro-4-hydroxyprolines and their application as VHL ligands for targeted protein degradation will be of wide interest to medicinal organic chemists, chemical biologists, and drug discoverers alike.
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Affiliation(s)
- Andrea Testa
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Xavier Lucas
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Guilherme V. Castro
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Kwok-Ho Chan
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Jane E. Wright
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Andrew C. Runcie
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Morgan S. Gadd
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - William T. A. Harrison
- Department
of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K.
| | - Eun-Jung Ko
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Daniel Fletcher
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
| | - Alessio Ciulli
- Division
of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, Scotland, U.K.
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38
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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39
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Tolmachova NA, Kondratov IS, Dolovanyuk VG, Pridma SO, Chernykh AV, Daniliuc CG, Haufe G. Synthesis of new fluorinated proline analogues from polyfluoroalkyl β-ketoacetals and ethyl isocyanoacetate. Chem Commun (Camb) 2018; 54:9683-9686. [DOI: 10.1039/c8cc05912h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
New straightforward synthetic approach to hitherto unknown cis-/trans-CF3-prolines and other 3-polyfluoroalkyl proline analogues.
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Affiliation(s)
| | - Ivan S. Kondratov
- Enamine Ltd
- Kyiv
- Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
| | - Violetta G. Dolovanyuk
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv
- Ukraine
| | | | | | | | - Günter Haufe
- Organisch-Chemisches Institut
- Universität Münster
- Münster 48149
- Germany
- Cells-in-Motion Cluster of Excellence
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40
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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41
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Banerjee J, Azevedo HS. Crafting of functional biomaterials by directed molecular self-assembly of triple helical peptide building blocks. Interface Focus 2017; 7:20160138. [PMID: 29147553 PMCID: PMC5665793 DOI: 10.1098/rsfs.2016.0138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Collagen is the most abundant extracellular matrix protein in the body and has widespread use in biomedical research, as well as in clinics. In addition to difficulties in the production of recombinant collagen due to its high non-natural imino acid content, animal-derived collagen imposes several major drawbacks-variability in composition, immunogenicity, pathogenicity and difficulty in sequence modification-that may limit its use in the practical scenario. However, in recent years, scientists have shifted their attention towards developing synthetic collagen-like materials from simple collagen model triple helical peptides to eliminate the potential drawbacks. For this purpose, it is highly desirable to develop programmable self-assembling strategies that will initiate the hierarchical self-assembly of short peptides into large-scale macromolecular assemblies with recommendable bioactivity. Herein, we tried to elaborate our understanding related to the strategies that have been adopted by few research groups to trigger self-assembly in the triple helical peptide system producing fascinating supramolecular structures. We have also touched upon the major epitopes within collagen that can be incorporated into collagen mimetic peptides for promoting bioactivity.
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Affiliation(s)
| | - Helena S. Azevedo
- School of Engineering and Material Science, Institute of Bioengineering, University of London, Queen Mary, Mile End Road, London E1 4NS, UK
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42
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Evaluating the role of puckering and fluorine atom in stability and folding of fluoroproline containing proteins. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0257-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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43
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San BH, Hwang J, Sampath S, Li Y, Bennink LL, Yu SM. Self-Assembled Water-Soluble Nanofibers Displaying Collagen Hybridizing Peptides. J Am Chem Soc 2017; 139:16640-16649. [PMID: 29091434 DOI: 10.1021/jacs.7b07900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Collagen hybridizing peptides (CHP) have been demonstrated as a powerful vehicle for targeting denatured collagen (dColl) produced by disease or injury. Conjugation of β-sheet peptide motif to the CHP results in self-assembly of nonaggregating β-sheet nanofibers with precise structure. Due to the molecular architecture of the nanofibers which puts high density of hydrophilic CHPs on the nanofiber surface at fixed distance, the nanofibers exhibit high water solubility, without any signs of intramolecular triple helix formation or fiber-fiber aggregation. Other molecules that are flanked with the triple helical forming GlyProHyp repeats can readily bind to the nanofibers by triple helical folding, allowing facile display of bioactive molecules at high density. In addition, the multivalency of CHPs allows the nanofibers to bind to dColl in vitro and in vivo with extraordinary affinity, particularly without preactivation that unravels the CHP homotrimers. The length of the nanofibers can be tuned from micrometers down to 100 nm by simple heat treatment, and when injected intravenously into mice, the small nanofibers can specifically target dColl in the skeletal tissues with little target-associated signals in the skin and other organs. The CHP nanofibers can be a useful tool for detecting and capturing dColl, understanding how ECM remodelling impacts disease progression, and development of new delivery systems that target such diseases.
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Affiliation(s)
- Boi Hoa San
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Jeongmin Hwang
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Sujatha Sampath
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Yang Li
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - Lucas L Bennink
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States
| | - S Michael Yu
- Department of Bioengineering, University of Utah , Salt Lake City, Utah 84112, United States.,Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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Affiliation(s)
- Christian Thiehoff
- Institute for Organic Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 40 48149 Münster Germany
| | - Yannick P. Rey
- Institute for Organic Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 40 48149 Münster Germany
| | - Ryan Gilmour
- Institute for Organic Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 40 48149 Münster Germany
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Domene C, Jorgensen C, Vanommeslaeghe K, Schofield CJ, MacKerell A. Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor. J Chem Theory Comput 2016; 11:3946-54. [PMID: 26574473 DOI: 10.1021/acs.jctc.5b00411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The hypoxia-inducible transcription factors (HIF) play a central role in the human oxygen sensing signaling pathway. The binding of the von Hippel-Lindau tumor suppressor protein (pVHL)-ElonginC-ElonginB complex (VCB) to HIF-1α is highly selective for the trans-4-hydroxylation form of when Pro564 in the C-terminal oxygen-dependent degradation domain (ODDD) of HIF-1α. The binding of HIFα for VCB is increased by ∼1000-fold upon addition of a single hydroxyl group to either of two conserved proline-residues. Here, we address how this addition governs selective recognition and characterizes the strength of the interaction of this "switch-like" signaling event. A new set of molecular mechanics parameters for 4-hydroxyproline has been developed following the CHARMM force field philosophy. Using the free energy perturbation (FEP) formalism, the difference in the binding free energies between HIF-1α in the nonhydroxylated and hydroxylated forms with the VCB complex was estimated using over 3 μs of MD trajectories. These results can favorably be compared to an experimental value of ∼4 kcal mol(-1). It is observed that the optimized hydrogen bonding network to the buried hydroxyprolyl group confers precise discrimination between hydroxylated and unmodified prolyl residues. These observations provide insight that will aid in developing therapeutic agents that block HIF-α recognition by pVHL.
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Affiliation(s)
- Carmen Domene
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 Penn St., Baltimore, Maryland 21201, United States.,Physical & Theoretical Chemistry Laboratory, South Parks Road, University of Oxford , Oxford OX1 3QZ, United Kingdom
| | - Christian Jorgensen
- Physical & Theoretical Chemistry Laboratory, South Parks Road, University of Oxford , Oxford OX1 3QZ, United Kingdom
| | - Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 Penn St., Baltimore, Maryland 21201, United States
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Alexander MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 Penn St., Baltimore, Maryland 21201, United States
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46
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Collagen structure: new tricks from a very old dog. Biochem J 2016; 473:1001-25. [PMID: 27060106 DOI: 10.1042/bj20151169] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
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48
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Kubyshkin V, Budisa N. cis-trans-Amide isomerism of the 3,4-dehydroproline residue, the 'unpuckered' proline. Beilstein J Org Chem 2016; 12:589-93. [PMID: 27340450 PMCID: PMC4901939 DOI: 10.3762/bjoc.12.57] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/08/2016] [Indexed: 11/23/2022] Open
Abstract
Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis-trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str., 10, 10623, Berlin, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str., 10, 10623, Berlin, Germany
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49
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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50
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Hu Y, Lin R, Zhang P, Fern J, Cheetham AG, Patel K, Schulman R, Kan C, Cui H. Electrostatic-Driven Lamination and Untwisting of β-Sheet Assemblies. ACS NANO 2016; 10:880-888. [PMID: 26646791 DOI: 10.1021/acsnano.5b06011] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptides or peptide conjugates capable of assembling into one-dimensional (1D) nanostructures have been extensively investigated over the past two decades due to their implications in human diseases and also their interesting applications as biomaterials. While many of these filamentous assemblies contain a β-sheet-forming sequence as the key design element, their eventual morphology could assume a variety of shapes, such as fibrils, ribbons, belts, or cylinders. Deciphering the key factors that govern the stacking fashion of individual β-sheets will help understand the polymorphism of peptide assemblies and greatly benefit the development of functional materials from customized molecular design. Herein, we report the decisive role of electrostatic interactions in the lamination and untwisting of 1D assemblies of short peptides. We designed and synthesized three short peptides containing only six amino acids (EFFFFE, KFFFFK, and EFFFFK) to elucidate the effective control of β-sheet stacking. Our results clearly suggest that electrostatic repulsions between terminal charges reduce the pitch of the twisting β-sheet tapes, thus leading to highly twisted, intertwined fibrils or twisted ribbons, whereas reducing this repulsion, either through molecular design of peptide with opposite terminal charges or through coassembly of two peptides carrying opposite charges, results in formation of infinite assemblies such as belt-like morphologies. We believe these observations provide important insight into the generic design of β-sheet assemblies.
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Affiliation(s)
- Yang Hu
- Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | | | | | | | | | - Kunal Patel
- Department of Biomedical Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | | | - Chengyou Kan
- Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
| | - Honggang Cui
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States
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