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Komarov IV, Bugrov VA, Cherednychenko A, Grygorenko OO. Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules. CHEM REC 2024; 24:e202300276. [PMID: 37847887 DOI: 10.1002/tcr.202300276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/29/2023] [Indexed: 10/19/2023]
Abstract
In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein-ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein-ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein-ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some "rules of thumb" have started to emerge on how to minimize entropy-enthalpy compensation and design efficient rigidified or flexible ligands.
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Affiliation(s)
- Igor V Komarov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Volodymyr A Bugrov
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Anton Cherednychenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
| | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Enamine Ltd., Winston Churchill Street 78, Kyiv, 02094, Ukraine
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2
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Li J, Li Q, Xia S, Tu J, Zheng L, Wang Q, Jiang S, Wang C. Design of MERS-CoV entry inhibitory short peptides based on helix-stabilizing strategies. Bioorg Med Chem Lett 2024; 97:129569. [PMID: 38008340 DOI: 10.1016/j.bmcl.2023.129569] [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: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
Interaction between Middle East respiratory syndrome coronavirus (MERS-CoV) spike (S) protein heptad repeat-1 domain (HR1) and heptad repeat-2 domain (HR2) is critical for the MERS-CoV fusion process. This interaction is mediated by the α-helical region from HR2 and the hydrophobic groove in a central HR1 trimeric coiled coil. We sought to develop a short peptidomimetic to act as a MERS-CoV fusion inhibitor by reproducing the key recognition features of HR2 helix. This was achieved by the use of helix-stabilizing strategies, including substitution with unnatural helix-favoring amino acids, introduction of ion pair interactions, and conjugation of palmitic acid. The resulting 23-mer lipopeptide, termed AEEA-C16, inhibits MERS-CoV S protein-mediated cell-cell fusion at a low micromolar level comparable to that of the 36-mer HR2 peptide HR2P-M2. Collectively, our studies provide new insights into developing short peptide-based antiviral agents to treat MERS-CoV infection.
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Affiliation(s)
- Jichun Li
- College of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, 26 Yuxiang Street, Shijiazhuang 050018, China; State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Qing Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Shanghai 200032, China
| | - Jiahuang Tu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing 100850, China
| | - Longbo Zheng
- Key Laboratory of Structure-based Drug Design & Discovery of the Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH/CAMS, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Shanghai 200032, China.
| | - Chao Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, 27 Tai-Ping Road, Beijing 100850, China.
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3
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Bathgate RAD, Praveen P, Sethi A, Furuya WI, Dhingra RR, Kocan M, Ou Q, Valkovic AL, Gil-Miravet I, Navarro-Sánchez M, Olucha-Bordonau FE, Gundlach AL, Rosengren KJ, Gooley PR, Dutschmann M, Hossain MA. Noncovalent Peptide Stapling Using Alpha-Methyl-l-Phenylalanine for α-Helical Peptidomimetics. J Am Chem Soc 2023; 145:20242-20247. [PMID: 37439676 DOI: 10.1021/jacs.3c02743] [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: 07/14/2023]
Abstract
Peptides and peptidomimetics are attractive drug candidates because of their high target specificity and low-toxicity profiles. Developing peptidomimetics using hydrocarbon (HC)-stapling or other stapling strategies has gained momentum because of their high stability and resistance to proteases; however, they have limitations. Here, we take advantage of the α-methyl group and an aromatic phenyl ring in a unique unnatural amino acid, α-methyl-l-phenylalanine (αF), and propose a novel, noncovalent stapling strategy to stabilize peptides. We utilized this strategy to create an α-helical B-chain mimetic of a complex insulin-like peptide, human relaxin-3 (H3 relaxin). Our comprehensive data set (in vitro, ex vivo, and in vivo) confirmed that the new high-yielding B-chain mimetic, H3B10-27(13/17αF), is remarkably stable in serum and fully mimics the biological function of H3 relaxin. H3B10-27(13/17αF) is an excellent scaffold for further development as a drug lead and an important tool to decipher the physiological functions of the neuropeptide G protein-coupled receptor, RXFP3.
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Affiliation(s)
- Ross A D Bathgate
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Praveen Praveen
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ashish Sethi
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3052, Australia
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Werner I Furuya
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Rishi R Dhingra
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Martina Kocan
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Qinghao Ou
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Adam L Valkovic
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Isis Gil-Miravet
- Predepartmental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, Avenida de Vicent Sos Baynat, s/n, 12071 Castelló de La Plana, Spain
| | - Mónica Navarro-Sánchez
- Predepartmental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, Avenida de Vicent Sos Baynat, s/n, 12071 Castelló de La Plana, Spain
| | - Francisco E Olucha-Bordonau
- Predepartmental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, Avenida de Vicent Sos Baynat, s/n, 12071 Castelló de La Plana, Spain
| | - Andrew L Gundlach
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mathias Dutschmann
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mohammed Akhter Hossain
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
- School of Chemistry, The University of Melbourne, Parkville, VIC 3052, Australia
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Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 DOI: 10.3390/biom13060981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
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Affiliation(s)
- Tarsila G Castro
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristina E A Sousa
- BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Artur Cavaco-Paulo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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5
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Torrez RM, Nagaraja S, Menon A, Chang L, Ohi MD, Garner AL. Comparative Biochemical Studies of Disease-Associated Human Dicer Mutations on Processing of a Pre-microRNA and snoRNA. Biochemistry 2023. [PMID: 37130292 DOI: 10.1021/acs.biochem.2c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dicer is an RNase III enzyme that is responsible for the maturation of small RNAs such as microRNAs. As Dicer's cleavage products play key roles in promoting cellular homeostasis through the fine-tuning of gene expression, dysregulation of Dicer activity can lead to several human diseases, including cancers. Mutations in Dicer have been found to induce tumorigenesis and lead to the development of a rare pleiotropic tumor predisposition syndrome found in children and young adults called DICER1 syndrome. These patients harbor germline and somatic mutations in Dicer that lead to defective microRNA processing and activity. While most mutations occur within Dicer's catalytic RNase III domains, alterations within the Platform-PAZ (Piwi-Argonaute-Zwille) domain also cause loss of microRNA production. Using a combination of in vitro biochemical and cellular studies, we characterized the effect of disease-relevant Platform-PAZ-associated mutations on the processing of a well-studied oncogenic microRNA, pre-microRNA-21. We then compared these results to those of a representative from another Dicer substrate class, the small nucleolar RNA, snord37. From this analysis, we provide evidence that mutations within the Platform-PAZ domain result in differential impacts on RNA binding and processing, adding new insights into the complexities of Dicer processing of small RNA substrates.
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Affiliation(s)
- Rachel M Torrez
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Shruti Nagaraja
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
| | - Louise Chang
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, United States
| | - Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United States
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6
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Design and Synthesis of Novel Helix Mimetics Based on the Covalent H-Bond Replacement and Amide Surrogate. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020780. [PMID: 36677838 PMCID: PMC9863496 DOI: 10.3390/molecules28020780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/27/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
A novel hydrogen bond surrogate-based (HBS) α-helix mimetic was designed by the combination of covalent H-bond replacement and the use of an ether linkage to substitute an amide bond within a short peptide sequence. The new helix template could be placed in position other than the N-terminus of a short peptide, and the CD studies demonstrate that the template adopts stable conformations in aqueous buffer at exceptionally high temperatures.
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Mallart S, Ingenito R, Bianchi E, Bresciani A, Esposito S, Gallo M, Magotti P, Monteagudo E, Orsatti L, Roversi D, Santoprete A, Tucci F, Veneziano M, Bartsch R, Boehm C, Brasseur D, Bruneau P, Corbier A, Froissant J, Gauzy-Lazo L, Gervat V, Marguet F, Menguy I, Minoletti C, Nicolas MF, Pasquier O, Poirier B, Raux A, Riva L, Janiak P, Strobel H, Duclos O, Illiano S. Identification of Potent and Long-Acting Single-Chain Peptide Mimetics of Human Relaxin-2 for Cardiovascular Diseases. J Med Chem 2021; 64:2139-2150. [PMID: 33555858 DOI: 10.1021/acs.jmedchem.0c01533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The insulin-like peptide human relaxin-2 was identified as a hormone that, among other biological functions, mediates the hemodynamic changes occurring during pregnancy. Recombinant relaxin-2 (serelaxin) has shown beneficial effects in acute heart failure, but its full therapeutic potential has been hampered by its short half-life and the need for intravenous administration limiting its use to intensive care units. In this study, we report the development of long-acting potent single-chain relaxin peptide mimetics. Modifications in the B-chain of relaxin, such as the introduction of specific mutations and the trimming of the sequence to an optimal size, resulted in potent, structurally simplified peptide agonists of the relaxin receptor Relaxin Family Peptide Receptor 1 (RXFP1) (e.g., 54). Introduction of suitable spacers and fatty acids led to the identification of single-chain lipidated peptide agonists of RXFP1, with sub-nanomolar activity, high subcutaneous bioavailability, extended half-lives, and in vivo efficacy (e.g., 64).
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Affiliation(s)
- Sergio Mallart
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Raffaele Ingenito
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Elisabetta Bianchi
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Alberto Bresciani
- Department of Translational Biology, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Simone Esposito
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Mariana Gallo
- Structural Biology, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Paola Magotti
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Edith Monteagudo
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Laura Orsatti
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Daniela Roversi
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Alessia Santoprete
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Federica Tucci
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Maria Veneziano
- DMPK, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Régine Bartsch
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Claudius Boehm
- Industrial Affairs, iCMC, Sanofi-Aventis R&D, Industriepark Höchst, Frankfurt 65926, Germany
| | - Denis Brasseur
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Patricia Bruneau
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Alain Corbier
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Jacques Froissant
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Laurence Gauzy-Lazo
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Vincent Gervat
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Frank Marguet
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Isabelle Menguy
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Claire Minoletti
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Marie-Françoise Nicolas
- Preclinical Development Sciences, Sanofi R&D, 13 quai Jules Guesde, Vitry sur Seine 94400, France
| | - Olivier Pasquier
- DMPK France, Sanofi R&D, 3 digue d'Alfortville, Alfortville 94140, France
| | - Bruno Poirier
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Alexandre Raux
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Laurence Riva
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Philip Janiak
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Hartmut Strobel
- Peptides and Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, Pomezia, Rome 00 071, Italy
| | - Olivier Duclos
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
| | - Stephane Illiano
- Cardio-Vascular and metabolism, Sanofi R&D, 1 rue Pierre Brossolette, Chilly Mazarin 91385, France
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Beyer CD, Reback ML, Heinen N, Thavalingam S, Rosenhahn A, Metzler-Nolte N. Low Fouling Peptides with an All (d) Amino Acid Sequence Provide Enhanced Stability against Proteolytic Degradation While Maintaining Low Antifouling Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10996-11004. [PMID: 32830498 DOI: 10.1021/acs.langmuir.0c01790] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Peptide-functionalized surfaces, composed of optimized l-peptides, show a high resistance toward nonspecific adsorption of proteins. As l-peptides are known to be prone to proteolytic degradation, the aim of this work is to enhance the stability against enzymatic degradation by using the all d-peptide mirror image of the optimized l-peptides and to determine if the all d-enantiomer retains the protein-resistant and antifouling properties. Two l-peptides and their d-peptide mirror images, some of them containing the nonproteinogenic amino acid α-aminoisobutyric acid (Aib), were synthesized and tested against non-specific adsorption of the proteins lysozyme and fibrinogen and the settlement of marine diatom Navicula perminuta and marine bacteria Cobetia marina. Both the d-enantiomer and the insertion of Aib protected the peptides from proteolytic degradation. Protein resistance was enhanced with the d-enantiomers while maintaining the resistance toward diatoms.
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Affiliation(s)
- Cindy D Beyer
- Analytical Chemistry I-Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
| | - Matthew L Reback
- Inorganic Chemistry I-Bioinorganic Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Natalie Heinen
- Analytical Chemistry I-Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
| | - Sugina Thavalingam
- Inorganic Chemistry I-Bioinorganic Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Axel Rosenhahn
- Analytical Chemistry I-Biointerfaces, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I-Bioinorganic Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
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9
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Pal S, Banerjee S, Kumar A, Prabhakaran EN. H-Bond Surrogate-Stabilized Shortest Single-Turn α-Helices: sp 2 Constraints and Residue Preferences for the Highest α-Helicities. ACS OMEGA 2020; 5:13902-13912. [PMID: 32566857 PMCID: PMC7301546 DOI: 10.1021/acsomega.0c01277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 05/08/2023]
Abstract
Short α-helical sequences of proteins fail to maintain their native conformation when taken out of their protein context. Several covalent constraints have been designed, including the covalent H-bond surrogate (HBS)-where a peptide backbone i + 4 → i H-bond is replaced by a covalent surrogate-to nucleate α-helix in short sequences (>7 < 15 amino acids). But constraining the shortest sequences (four amino acids) into a single α-helical turn is still a significant challenge. Here, we introduce an HBS model that can be placed in unstructured tetrapeptides without excising any of its residues, and that biases them predominantly into remarkably stable single α-helical turns in varying solvents, pH values, and temperatures. Circular dichroism (CD), Fourier transform infrared (FT-IR) absorption, one-dimensional (1D)-NMR, two-dimensional (2D)-NMR spectral and computational analyses of the HBS-constrained tetrapeptide analogues reveal that (a) the number of sp2 atoms in the HBS-constrained backbone influences their predominance and rigidity in the α-helical conformation; and (b) residue preferences at the unnatural HBS-constrained positions influence their α-helicities, with Moc[GFA]G-OMe (1a) showing the highest known α-helicity (θn→π*MRE ∼-25.3 × 103 deg cm2 dmol-1 at 228 nm) for a single α-helical turn. Current findings benefit chemical biological applications desiring predictable access to single α-helical turns in tetrapeptides.
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10
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Dharman P, Babu V, Basha KA. A facile synthesis of novel 5‐substituted pyridine 2 carboxamide derivatives and their biological evaluation and 3D QSAR studies. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Prabu Dharman
- Research & Development CentreBharathiar University Coimbatore India
| | | | - K. Anver Basha
- P.G. and Research Department of ChemistryC.Abdul Hakeem College Melvisharam India
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11
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Qin W, Xie M, Qin X, Fang Q, Yin F, Li Z. Recent advances in peptidomimetics antagonists targeting estrogen receptor α-coactivator interaction in cancer therapy. Bioorg Med Chem Lett 2018; 28:2827-2836. [DOI: 10.1016/j.bmcl.2018.05.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/25/2018] [Accepted: 05/30/2018] [Indexed: 02/07/2023]
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12
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De Bo G, Gall MAY, Kuschel S, De Winter J, Gerbaux P, Leigh DA. An artificial molecular machine that builds an asymmetric catalyst. NATURE NANOTECHNOLOGY 2018; 13:381-385. [PMID: 29610529 DOI: 10.1038/s41565-018-0105-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 05/29/2023]
Abstract
Biomolecular machines perform types of complex molecular-level tasks that artificial molecular machines can aspire to. The ribosome, for example, translates information from the polymer track it traverses (messenger RNA) to the new polymer it constructs (a polypeptide) 1 . The sequence and number of codons read determines the sequence and number of building blocks incorporated into the biomachine-synthesized polymer. However, neither control of sequence2,3 nor the transfer of length information from one polymer to another (which to date has only been accomplished in man-made systems through template synthesis) 4 is easily achieved in the synthesis of artificial macromolecules. Rotaxane-based molecular machines5-7 have been developed that successively add amino acids8-10 (including β-amino acids 10 ) to a growing peptide chain by the action of a macrocycle moving along a mono-dispersed oligomeric track derivatized with amino-acid phenol esters. The threaded macrocycle picks up groups that block its path and links them through successive native chemical ligation reactions 11 to form a peptide sequence corresponding to the order of the building blocks on the track. Here, we show that as an alternative to translating sequence information, a rotaxane molecular machine can transfer the narrow polydispersity of a leucine-ester-derivatized polystyrene chain synthesized by atom transfer radical polymerization 12 to a molecular-machine-made homo-leucine oligomer. The resulting narrow-molecular-weight oligomer folds to an α-helical secondary structure 13 that acts as an asymmetric catalyst for the Juliá-Colonna epoxidation14,15 of chalcones.
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Affiliation(s)
- Guillaume De Bo
- School of Chemistry, University of Manchester, Manchester, UK
| | | | - Sonja Kuschel
- School of Chemistry, University of Manchester, Manchester, UK
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, Mons, Belgium
| | - David A Leigh
- School of Chemistry, University of Manchester, Manchester, UK.
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13
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Nadimpally KC, Madica K, Kotmale AS, Gonnade RG, Sanjayan GJ. Helically Structured Peptide Architecture Engineered Using Dimedone as a Rigid Organic Scaffold. ChemistrySelect 2018. [DOI: 10.1002/slct.201702856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Krishna C. Nadimpally
- Division of Organic Chemistry; National Chemical Laboratory; Dr. Homi Bhabha Road Pune 411008 India
| | - Krishnaprasad Madica
- Division of Organic Chemistry; National Chemical Laboratory; Dr. Homi Bhabha Road Pune 411008 India
- Academy of Scientific and Innovative Research (AcSIR); CSIR; Pune 411008 India
| | - Amol S. Kotmale
- Central NMR facility; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road Pune 411008 India
| | - Rajesh G. Gonnade
- Center for Materials Characterization; National Chemical Laboratory; Dr. Homi Bhahba Road Pune 411008 India
| | - Gangadhar J. Sanjayan
- Division of Organic Chemistry; National Chemical Laboratory; Dr. Homi Bhabha Road Pune 411008 India
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14
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Burra G, Thakur AK. Inhibition of polyglutamine aggregation by SIMILAR huntingtin N-terminal sequences: Prospective molecules for preclinical evaluation in Huntington's disease. Biopolymers 2017; 108. [DOI: 10.1002/bip.23021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Gunasekhar Burra
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
| | - Ashwani Kumar Thakur
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
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15
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16
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17
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Diderich P, Bertoldo D, Dessen P, Khan MM, Pizzitola I, Held W, Huelsken J, Heinis C. Phage Selection of Chemically Stabilized α-Helical Peptide Ligands. ACS Chem Biol 2016; 11:1422-7. [PMID: 26929989 DOI: 10.1021/acschembio.5b00963] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Short α-helical peptides stabilized by linkages between constituent amino acids offer an attractive format for ligand development. In recent years, a range of excellent ligands based on stabilized α-helices were generated by rational design using α-helical peptides of natural proteins as templates. Herein, we developed a method to engineer chemically stabilized α-helical ligands in a combinatorial fashion. In brief, peptides containing cysteines in position i and i + 4 are genetically encoded by phage display, the cysteines are modified with chemical bridges to impose α-helical conformations, and binders are isolated by affinity selection. We applied the strategy to affinity mature an α-helical peptide binding β-catenin. We succeeded in developing ligands with Kd's as low as 5.2 nM, having >200-fold improved affinity. The strategy is generally applicable for affinity maturation of any α-helical peptide. Compared to hydrocarbon stapled peptides, the herein evolved thioether-bridged peptide ligands can be synthesized more easily, as no unnatural amino acids are required and the cyclization reaction is more efficient and yields no stereoisomers. A further advantage of the thioether-bridged peptide ligands is that they can be expressed recombinantly as fusion proteins.
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Affiliation(s)
- Philippe Diderich
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Davide Bertoldo
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Pierre Dessen
- Swiss
Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Maola M. Khan
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Irene Pizzitola
- Ludwig
Center for Cancer Research, Department of Oncology, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Werner Held
- Ludwig
Center for Cancer Research, Department of Oncology, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Joerg Huelsken
- Swiss
Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute
of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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18
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Tian Y, Wang D, Li J, Shi C, Zhao H, Niu X, Li Z. A proline-derived transannular N-cap for nucleation of short α-helical peptides. Chem Commun (Camb) 2016; 52:9275-8. [DOI: 10.1039/c6cc04672j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a simple and practical proline-derived transannular N-cap as a helix nucleating template in diverse bio-related peptide sequences via macrolactamization on resin.
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Affiliation(s)
- Yuan Tian
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Dongyuan Wang
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Jingxu Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Chuan Shi
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Hui Zhao
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering
- Beijing Nuclear Magnetic Resonance Center
- Peking University
- Beijing
- China
| | - Zigang Li
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School of Peking University
- Shenzhen
- China
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19
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Mauran L, Kauffmann B, Odaert B, Guichard G. Stabilization of an α-helix by short adjacent accessory foldamers. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Puiu M, Idili A, Moscone D, Ricci F, Bala C. A modular electrochemical peptide-based sensor for antibody detection. Chem Commun (Camb) 2015; 50:8962-5. [PMID: 24975136 DOI: 10.1039/c4cc02858a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a modular electrochemical peptide-based sensor targeting the anti-deamidated gliadin peptide (DGP) antibody. A recognition peptide, here DGP, is grafted onto a supporting peptide bearing a redox label. The fabricated peptide-based sensor supports the detection of the target antibody (anti-DGP antibody) in the nanomolar range.
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Affiliation(s)
- Mihaela Puiu
- Laboratory for Quality Control and Process Monitoring, University of Bucharest, 030018-Bucharest, Romania
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22
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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23
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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de Araujo AD, Hoang HN, Kok WM, Diness F, Gupta P, Hill TA, Driver RW, Price DA, Liras S, Fairlie DP. Comparative α-Helicity of Cyclic Pentapeptides in Water. Angew Chem Int Ed Engl 2014; 53:6965-9. [DOI: 10.1002/anie.201310245] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/10/2014] [Indexed: 11/09/2022]
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25
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de Araujo AD, Hoang HN, Kok WM, Diness F, Gupta P, Hill TA, Driver RW, Price DA, Liras S, Fairlie DP. Comparative α-Helicity of Cyclic Pentapeptides in Water. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310245] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Bonache MÁ, Balsera B, López-Méndez B, Millet O, Brancaccio D, Gómez-Monterrey I, Carotenuto A, Pavone LM, Reille-Seroussi M, Gagey-Eilstein N, Vidal M, de la Torre-Martı́nez R, Fernández-Carvajal A, Ferrer-Montiel A, García-López MT, Martín-Martínez M, de Vega MJP, González-Muñiz R. De novo designed library of linear helical peptides: an exploratory tool in the discovery of protein-protein interaction modulators. ACS COMBINATORIAL SCIENCE 2014; 16:250-8. [PMID: 24725184 DOI: 10.1021/co500005x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important targets for pharmaceutical intervention because of their essential role in numerous physiological and pathological processes, but screening efforts using small-molecules have led to very low hit rates. Linear peptides could represent a quick and effective approach to discover initial PPI hits, particularly if they have inherent ability to adopt specific peptide secondary structures. Here, we address this hypothesis through a linear helical peptide library, composed of four sublibraries, which was designed by theoretical predictions of helicity (Agadir software). The 13-mer peptides of this collection fixes either a combination of three aromatic or two aromatic and one aliphatic residues on one face of the helix (Ac-SSEEX(5)ARNX(9)AAX(12)N-NH2), since these are structural features quite common at PPIs interfaces. The 81 designed peptides were conveniently synthesized by parallel solid-phase methodologies, and the tendency of some representative library components to adopt the intended secondary structure was corroborated through CD and NMR experiments. As proof of concept in the search for PPI modulators, the usefulness of this library was verified on the widely studied p53-MDM2 interaction and on the communication between VEGF and its receptor Flt-1, two PPIs for which a hydrophobic α-helix is essential for the interaction. We have demonstrated here that, in both cases, selected peptides from the library, containing the right hydrophobic sequence of the hot-spot in one of the protein partners, are able to interact with the complementary protein. Moreover, we have discover some new, quite potent inhibitors of the VEGF-Flt-1 interaction, just by replacing one of the aromatic residues of the initial F(5)Y(9)Y(12) peptide by W, in agreement with previous results on related antiangiogenic peptides. Finally, the HTS evaluation of the full collection on thermoTRPs has led to a few antagonists of TRPV1 and TRPA1 channels, which open new avenues on the way to innovative modulators of these channels.
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Affiliation(s)
- M. Ángeles Bonache
- Instituto de Química-Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Beatriz Balsera
- Instituto de Química-Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Oscar Millet
- CICbioGUNE, Structural Biology Unit, 48160 Bilbao, Spain
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Isabel Gómez-Monterrey
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Luigi M. Pavone
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131, Naples, Italy
| | - Marie Reille-Seroussi
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
| | - Nathalie Gagey-Eilstein
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
| | - Michel Vidal
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
- UF
“Pharmacocinétique et pharmacochimie”, Hôpital Cochin, , AP-HP, 27 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Roberto de la Torre-Martı́nez
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | - Asia Fernández-Carvajal
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | - Antonio Ferrer-Montiel
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
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27
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Mazzier D, Peggion C, Toniolo C, Moretto A. Enhancement of the helical content and stability induced in a linear oligopeptide by ani, i+4 intramolecularly double stapled, overlapping, bicyclic [31, 22, 5]-(E)ene motif. Biopolymers 2014; 102:115-23. [DOI: 10.1002/bip.22438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/28/2013] [Accepted: 10/11/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Daniela Mazzier
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
| | - Alessandro Moretto
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
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28
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Hamed E, Xu T, Keten S. Poly(ethylene glycol) Conjugation Stabilizes the Secondary Structure of α-Helices by Reducing Peptide Solvent Accessible Surface Area. Biomacromolecules 2013; 14:4053-60. [DOI: 10.1021/bm401164t] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elham Hamed
- Department of Civil
and Environmental Engineering and Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Ting Xu
- Department of Materials
Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Sinan Keten
- Department of Civil
and Environmental Engineering and Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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29
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Inhibition of α-helix-mediated protein-protein interactions using designed molecules. Nat Chem 2013; 5:161-73. [PMID: 23422557 DOI: 10.1038/nchem.1568] [Citation(s) in RCA: 572] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a significant challenge because it is unclear how they can be effectively and selectively targeted using small molecules. Achieving this goal is critical given the defining role of these interactions in biological processes. A rational approach to inhibitor design based on the secondary structure at the interface is the focus of much research, and different classes of designed ligands have emerged, some of which effectively and selectively disrupt targeted PPIs. This Review discusses the relevance of PPIs and, in particular, the importance of α-helix-mediated PPIs to chemical biology and drug discovery with a focus on designing inhibitors, including constrained peptides, foldamers and proteomimetic-derived ligands. In doing so, key challenges and major advances in developing generic approaches for the elaboration of PPI inhibitors are highlighted. The challenges faced in developing such ligands as drug leads--and how criteria applied to these may differ from conventional small-molecule drugs--are summarized.
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Abstract
The human Mediator complex is a central integrator for transcription and represents a primary interface that allows DNA-binding transcription factors to communicate their regulatory signals to the RNA polymerase II enzyme. Because Mediator is dynamic both in terms of subunit composition and structure, it presents challenges as a target for small molecule probes. Moreover, little high-resolution structural information exists for Mediator. Its global requirement for transcription, as well as its distinct, transcription factor specific interaction surfaces, however, suggest that development of probes that bind specific Mediator subunits might enable gene- and pathway-specific modulation of transcription. Here we provide a brief overview of the Mediator complex, highlighting biological and structural features that make it an attractive target for molecular probes. We then outline several chemical strategies that might be effective for targeting the complex.
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Affiliation(s)
| | - Dylan J Taatjes
- Dept. of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303 USA
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32
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Datta S, Samanta SK, Bhattacharya S. Induction of Supramolecular Chirality in the Self-Assemblies of Lipophilic Pyrimidine Derivatives by Choice of the Amino Acid-Based Chiral Spacer. Chemistry 2013; 19:11364-73. [DOI: 10.1002/chem.201300605] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Indexed: 11/11/2022]
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33
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Fuchs S, Nguyen HD, Phan TTP, Burton MF, Nieto L, de Vries-van Leeuwen IJ, Schmidt A, Goodarzifard M, Agten SM, Rose R, Ottmann C, Milroy LG, Brunsveld L. Proline primed helix length as a modulator of the nuclear receptor-coactivator interaction. J Am Chem Soc 2013; 135:4364-71. [PMID: 23437920 DOI: 10.1021/ja311748r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nuclear receptor binding to coactivator proteins is an obligate first step in the regulation of gene transcription. Nuclear receptors preferentially bind to an LXXLL peptide motif which is highly conserved throughout the 300 or so natural coactivator proteins. This knowledge has shaped current understanding of this fundamental protein-protein interaction, and continues to inspire the search for new drug therapies. However, sequence specificity beyond the LXXLL motif and the molecular functioning of flanking residues still requires urgent addressing. Here, ribosome display has been used to reassess the estrogen receptor for new and enlarged peptide recognition motifs, leading to the discovery of a potent and highly evolved PXLXXLLXXP binding consensus. Molecular modeling and X-ray crystallography studies have provided the molecular insights on the role of the flanking prolines in priming the length of the α-helix and enabling optimal interactions of the α-helix dipole and its surrounding amino acids with the surface charge clamp and the receptor activation function 2. These findings represent new structural parameters for modulating the nuclear receptor-coactivator interaction based on linear sequences of proteinogenic amino acids and for the design of chemically modified inhibitors.
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Affiliation(s)
- Sascha Fuchs
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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34
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Giorgi G, Favi G, Attanasi OA. Insights into diastereoisomeric characterization of tetrahydropyridazine amino acid derivatives: crystal structures and gas phase ion chemistry. Org Biomol Chem 2013; 11:5006-11. [DOI: 10.1039/c3ob41034j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Zhou PX, Zhou ZZ, Chen ZS, Ye YY, Zhao LB, Yang YF, Xia XF, Luo JY, Liang YM. Palladium-catalyzed insertion of α-diazocarbonyl compounds for the synthesis of cyclic amino esters. Chem Commun (Camb) 2013. [DOI: 10.1039/c2cc37464a] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Jadhav SV, Bandyopadhyay A, Gopi HN. Protein secondary structure mimetics: crystal conformations of α/γ4-hybrid peptide12-helices with proteinogenic side chains and their analogy with α- and β-peptide helices. Org Biomol Chem 2013; 11:509-14. [DOI: 10.1039/c2ob26805a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Baldauf C, Hofmann HJ. Ab initioMO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers ofω-Amino Acids. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200436] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Lin YC, Chen CT. Alkaline Earth Metal Ion Induced Coil-Helix-Coil Transition of Lysine-Coumarin-Azacrown Hybrid Foldamers with OFF-OFF-ON Fluorescence Switching. Chemistry 2012. [DOI: 10.1002/chem.201202998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sánchez-Martín MJ, Cruz A, Busquets MA, Haro I, Alsina MA, Pujol M. Physicochemical characterization of GBV-C E1 peptides as potential inhibitors of HIV-1 fusion peptide: Interaction with model membranes. Int J Pharm 2012; 436:593-601. [DOI: 10.1016/j.ijpharm.2012.07.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 11/29/2022]
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Yin H. Constrained peptides as miniature protein structures. ISRN BIOCHEMISTRY 2012; 2012:692190. [PMID: 25969758 PMCID: PMC4392992 DOI: 10.5402/2012/692190] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 09/03/2012] [Indexed: 11/23/2022]
Abstract
This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, 596 University of Colorado at Boulder, Boulder, CO 80309-0596, USA
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Empirical and computational design of iron-sulfur cluster proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1256-62. [PMID: 22342202 DOI: 10.1016/j.bbabio.2012.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/13/2012] [Accepted: 02/01/2012] [Indexed: 11/21/2022]
Abstract
Here, we compare two approaches of protein design. A computational approach was used in the design of the coiled-coil iron-sulfur protein, CCIS, as a four helix bundle binding an iron-sulfur cluster within its hydrophobic core. An empirical approach was used for designing the redox-chain maquette, RCM as a four-helix bundle assembling iron-sulfur clusters within loops and one heme in the middle of its hydrophobic core. We demonstrate that both ways of design yielded the desired proteins in terms of secondary structure and cofactors assembly. Both approaches, however, still have much to improve in predicting conformational changes in the presence of bound cofactors, controlling oligomerization tendency and stabilizing the bound iron-sulfur clusters in the reduced state. Lessons from both ways of design and future directions of development are discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Khoo KK, Wilson MJ, Smith BJ, Zhang MM, Gulyas J, Yoshikami D, Rivier JE, Bulaj G, Norton RS. Lactam-stabilized helical analogues of the analgesic μ-conotoxin KIIIA. J Med Chem 2011; 54:7558-66. [PMID: 21962108 DOI: 10.1021/jm200839a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
μ-Conotoxin KIIIA (μ-KIIIA) blocks mammalian voltage-gated sodium channels (VGSCs) and is a potent analgesic following systemic administration in mice. Previous structure-activity studies of μ-KIIIA identified a helical pharmacophore for VGSC blockade. This suggested a route for designing truncated analogues of μ-KIIIA by incorporating the key residues into an α-helical scaffold. As (i, i+4) lactam bridges constitute a proven approach for stabilizing α-helices, we designed and synthesized six truncated analogues of μ-KIIIA containing single lactam bridges at various locations. The helicity of these lactam analogues was analyzed by NMR spectroscopy, and their activities were tested against mammalian VGSC subtypes Na(V)1.1 through 1.7. Two of the analogues, Ac-cyclo9/13[Asp9,Lys13]KIIIA7-14 and Ac-cyclo9/13[Lys9,Asp13]KIIIA7-14, displayed μM activity against VGSC subtypes Na(V)1.2 and Na(V)1.6; importantly, the subtype selectivity profile for these peptides matched that of μ-KIIIA. Our study highlights structure-activity relationships within these helical mimetics and provides a basis for the design of additional truncated peptides as potential analgesics.
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Affiliation(s)
- Keith K Khoo
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Australia
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Galeazzi R, Martelli G, Mazzanti A, Orena M, Rinaldi S. Quaternary Centres as a Tool for Modulating Foldamer Conformation. Chemistry 2011; 17:12564-8. [DOI: 10.1002/chem.201102103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Indexed: 11/11/2022]
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Hoang HN, Driver RW, Beyer RL, Malde AK, Le GT, Abbenante G, Mark AE, Fairlie DP. Protein α-Turns Recreated in Structurally Stable Small Molecules. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hoang HN, Driver RW, Beyer RL, Malde AK, Le GT, Abbenante G, Mark AE, Fairlie DP. Protein α-Turns Recreated in Structurally Stable Small Molecules. Angew Chem Int Ed Engl 2011; 50:11107-11. [DOI: 10.1002/anie.201105119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Indexed: 11/08/2022]
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Miyamoto K, Jintoku H, Sawada T, Takafuji M, Sagawa T, Ihara H. Informative secondary chiroptics in binary molecular organogel systems for donor–acceptor energy transfer. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.05.131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Estieu-Gionnet K, Guichard G. Stabilized helical peptides: overview of the technologies and therapeutic promises. Expert Opin Drug Discov 2011; 6:937-63. [PMID: 22646216 DOI: 10.1517/17460441.2011.603723] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Helical structures in proteins and naturally occurring peptides play a major role in a variety of biological processes by mediating interactions with proteins and other macromolecules such as nucleic acids and lipid membranes. The use of short synthetic peptides encompassing helical segments to modulate or disrupt such interactions, when associated with human diseases, represents great pharmacological interest. AREAS COVERED Multiple chemical approaches have been developed to increase the conformational and metabolic stabilities of helical peptides and to improve their biomedical potential. After a brief overview of these technologies and the most recent developments, this review will focus on the main therapeutic areas and targets and will discuss their promise. EXPERT OPINION Potential benefits associated with increased helix stability extend beyond simple affinity enhancement. Some peptidomimetic helices are being endowed with features desirable for cellular activity such as increased resistance to proteolysis and/or cell permeability. Recent advances in the field of peptide and related peptidomimetic helices are not just conceptual, but are likely to be of practical utility in the process of optimizing peptides as clinical candidates, and developing medium-size therapeutics.
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Affiliation(s)
- Karine Estieu-Gionnet
- Institut Européen de Chimie et Biologie , Université de Bordeaux, CNRS UMR 5248, CBMN, 2 rue R. Escarpit, 33607 Pessac , France
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Núñez-Villanueva D, Bonache MÁ, Infantes L, García-López MT, Martín-Martínez M, González-Muñiz R. Quaternary α,α-2-Oxoazepane α-Amino Acids: Synthesis from Ornithine-Derived β-Lactams and Incorporation into Model Dipeptides. J Org Chem 2011; 76:6592-603. [DOI: 10.1021/jo200894d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - M. Ángeles Bonache
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Lourdes Infantes
- Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
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Coursindel T, Martinez J, Parrot I. Concise Pathway to New Multifunctionalized Constrained Pentacin Derivatives by Means of Two Stereospecific Tandem Reactions. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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