1
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Saunders GJ, Spring SA, Jayawant E, Wilkening I, Roesner S, Clarkson GJ, Dixon AM, Notman R, Shipman M. Synthesis and Functionalization of Azetidine-Containing Small Macrocyclic Peptides. Chemistry 2024; 30:e202400308. [PMID: 38488326 DOI: 10.1002/chem.202400308] [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: 02/25/2024] [Indexed: 04/11/2024]
Abstract
Cyclic peptides are increasingly important structures in drugs but their development can be impeded by difficulties associated with their synthesis. Here, we introduce the 3-aminoazetidine (3-AAz) subunit as a new turn-inducing element for the efficient synthesis of small head-to-tail cyclic peptides. Greatly improved cyclizations of tetra-, penta- and hexapeptides (28 examples) under standard reaction conditions are achieved by introduction of this element within the linear peptide precursor. Post-cyclization deprotection of the amino acid side chains with strong acid is realized without degradation of the strained four-membered azetidine. A special feature of this chemistry is that further late-stage modification of the resultant macrocyclic peptides can be achieved via the 3-AAz unit. This is done by: (i) chemoselective deprotection and substitution at the azetidine nitrogen, or by (ii) a click-based approach employing a 2-propynyl carbamate on the azetidine nitrogen. In this way, a range of dye and biotin tagged macrocycles are readily produced. Structural insights gained by XRD analysis of a cyclic tetrapeptide indicate that the azetidine ring encourages access to the less stable, all-trans conformation. Moreover, introduction of a 3-AAz into a representative cyclohexapeptide improves stability towards proteases compared to the homodetic macrocycle.
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Affiliation(s)
- George J Saunders
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Sam A Spring
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Eleanor Jayawant
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Stefan Roesner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Guy J Clarkson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Michael Shipman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
- The Palatine Centre, Stockton Road, Durham, DH1 3LE, U.K
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2
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Chen H, Zhang Q. Native Peptide Cyclization, Sequential Chemoselective Amidation in Water. J Am Chem Soc 2023; 145:27218-27224. [PMID: 38079358 PMCID: PMC11131159 DOI: 10.1021/jacs.3c10341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Chemical synthesis offers robust tactics for structural alterations of peptides and proteins. It remains a labor-intensive and complex process due to the challenges in selectively modifying diverse amino acid side chains and termini. Direct α-peptide ligation without premodification is a significant hurdle, especially when aiming to include all proteinogenic amino acids at the ligation site. We introduce Native Peptide Cyclization (NPC), a chemoselective method enabling intramolecular peptidyl ligation without the need for premodification. NPC cyclizes unprotected linear peptides through controlled, sequential C- and N-terminal activation via pH modulation. Water-based NPC simplifies peptide ligation, easing the labor-intensive nature of peptide synthesis, aiding efficient cyclic peptide preparation and enabling cost-effective macrocycle-based therapeutics.
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Affiliation(s)
- Huan Chen
- Department of Chemistry, State University of New York, University at Albany, Albany, New York 12222, United States
| | - Qiang Zhang
- Department of Chemistry, State University of New York, University at Albany, Albany, New York 12222, United States
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3
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Ghosh U, Kumar V, Singh G, Kanti Chakraborty T. Conformation Based in silico Studies of Cyclic Tetrapeptides with βγ Fused Turns as Thrombin Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Uttam Ghosh
- Department of Organic Chemistry Indian Institute of Science Bengaluru 560012 India
| | - Vikash Kumar
- CSIR-Central Drug Research Institute Lucknow 226031 India
| | - Gajendra Singh
- CSIR-Central Drug Research Institute Lucknow 226031 India
- School of Life Sciences Central University of Rajasthan Bandar Sindri Ajmer 305817 Rajasthan India
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4
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Debnath S, Vignesh SR, Satpati P, Chatterjee S. Position of Geminal Substitution of γ Amino Acid Residues Modulates Their Ability to Form Isolated Non‐Helical C
12
β‐turn Mimics. ChemistrySelect 2023. [DOI: 10.1002/slct.202204255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Swapna Debnath
- Department of Chemistry Indian Institute of Technology, Guwahati Guwahati Assam India
| | - S. R. Vignesh
- Biosciences and Bioengineering Indian Institute of Technology Guwahati, Guwahati Assam India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering Indian Institute of Technology Guwahati, Guwahati Assam India
| | - Sunanda Chatterjee
- Department of Chemistry Indian Institute of Technology, Guwahati Guwahati Assam India
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5
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Chernykh AV, Aloshyn D, Kuchkovska YO, Daniliuc CG, Tolmachova NA, Kondratov IS, Zozulya S, Grygorenko OO, Haufe G. Impact of β-perfluoroalkyl substitution of proline on the proteolytic stability of its peptide derivatives. Org Biomol Chem 2022; 20:9337-9350. [PMID: 36107003 DOI: 10.1039/d2ob01430k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A series of all stereoisomers of β-CF3 or β-C2F5 substituted prolines and their dipeptide derivatives were synthesized. Mouse plasma stability assay was carried out to study the impact of fluoroalkyl substituents on the proteolytic stability of proline-derived peptides. The effect of the (R)-/(S)-configuration at the C-2 atom in combination with electronic and steric effects imposed by fluoroalkyl groups was addressed to rationalize the difference in the half-life stability of diastereomeric β-CF3-Pro-Gly and β-C2F5-Pro-Gly derivatives and compared to those of parent (S)-Pro-Gly and (R)-Pro-Gly dipeptides. The steric effect was predominant when the β-CF3 or β-C2F5 group was placed properly to create a spatial interference within the pockets of proteases, thereby protecting the substances from degradation (e.g., for cis-isomeric derivatives). Otherwise, a smaller electronic effect accelerating proteolysis was in charge (i.e., for the (2S,3S) isomers).
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Affiliation(s)
- Anton V Chernykh
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine.
| | - Danylo Aloshyn
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine
| | | | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | | | - Ivan S Kondratov
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry, National Academy of Sciences of, Ukraine, Murmanska Street 1, Kyïv 02660, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine.
| | - Günter Haufe
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, Universität Münster, Waldeyerstraße 15, 48149 Münster, Germany
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6
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Oroz P, Navo CD, Avenoza A, Busto JH, Corzana F, Jiménez-Osés G, Peregrina JM. Towards Enantiomerically Pure Unnatural α-Amino Acids via Photoredox Catalytic 1,4-Additions to a Chiral Dehydroalanine. J Org Chem 2022; 87:14308-14318. [PMID: 36179039 PMCID: PMC9639051 DOI: 10.1021/acs.joc.2c01774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chemo- and diastereoselective 1,4-conjugate additions of anionic and radical C-nucleophiles to a chiral bicyclic dehydroalanine (Dha) are described. Of particular importance, radical carbon photolysis by a catalytic photoredox process using a simple method with a metal-free photocatalyst provides exceptional yields and selectivities at room temperature. Moreover, these 1,4-conjugate additions offer an excellent starting point for synthesizing enantiomerically pure carbon-β-substituted unnatural α-amino acids (UAAs), which could have a high potential for applications in chemical biology.
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Affiliation(s)
- Paula Oroz
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Claudio D. Navo
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Alberto Avenoza
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Jesús H. Busto
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Gonzalo Jiménez-Osés
- Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain,Ikerbasque, Basque
Foundation for Science, 48013 Bilbao, Spain
| | - Jesús M. Peregrina
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain,
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7
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Jwad R, Weissberger D, Hunter L. Strategies for Fine-Tuning the Conformations of Cyclic Peptides. Chem Rev 2020; 120:9743-9789. [PMID: 32786420 DOI: 10.1021/acs.chemrev.0c00013] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.
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Affiliation(s)
- Rasha Jwad
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
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8
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Proulx C, Zhang J, Sabatino D, Chemtob S, Ong H, Lubell WD. Synthesis and Biomedical Potential of Azapeptide Modulators of the Cluster of Differentiation 36 Receptor (CD36). Biomedicines 2020; 8:biomedicines8080241. [PMID: 32717955 PMCID: PMC7459725 DOI: 10.3390/biomedicines8080241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
The innovative development of azapeptide analogues of growth hormone releasing peptide-6 (GHRP-6) has produced selective modulators of the cluster of differentiation 36 receptor (CD36). The azapeptide CD36 modulators curb macrophage-driven inflammation and mitigate atherosclerotic and angiogenic pathology. In macrophages activated with Toll-like receptor-2 heterodimer agonist, they reduced nitric oxide production and proinflammatory cytokine release. In a mouse choroidal explant microvascular sprouting model, they inhibited neovascularization. In murine models of cardiovascular injury, CD36-selective azapeptide modulators exhibited cardioprotective and anti-atherosclerotic effects. In subretinal inflammation models, they altered activated mononuclear phagocyte metabolism and decreased immune responses to alleviate subsequent inflammation-dependent neuronal injury associated with retinitis pigmentosa, diabetic retinopathy and age-related macular degeneration. The translation of GHRP-6 to potent and selective linear and cyclic azapeptide modulators of CD36 is outlined in this review which highlights the relevance of turn geometry for activity and the biomedical potential of prototypes for the beneficial treatment of a wide range of cardiovascular, metabolic and immunological disorders.
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Affiliation(s)
- Caroline Proulx
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jinqiang Zhang
- Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China;
| | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, 400 South Orange Ave, South Orange, NJ 07079, USA;
| | - Sylvain Chemtob
- Département d’Ophtalmologie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C3J7, Canada;
| | - Huy Ong
- Faculté de Pharmacie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C3J7, Canada;
| | - William D. Lubell
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C3J7, Canada
- Correspondence:
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9
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Sarojini V, Cameron AJ, Varnava KG, Denny WA, Sanjayan G. Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function. Chem Rev 2019; 119:10318-10359. [PMID: 31418274 DOI: 10.1021/acs.chemrev.8b00737] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.
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Affiliation(s)
- Vijayalekshmi Sarojini
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology , Wellington 6140 , New Zealand
| | - Alan J Cameron
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | - Kyriakos G Varnava
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | | | - Gangadhar Sanjayan
- Division of Organic Chemistry , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411 008 , India
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10
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D'Amato A, Pierri G, Tedesco C, Della Sala G, Izzo I, Costabile C, De Riccardis F. Reverse Turn and Loop Secondary Structures in Stereodefined Cyclic Peptoid Scaffolds. J Org Chem 2019; 84:10911-10928. [PMID: 31339718 DOI: 10.1021/acs.joc.9b01509] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Controlling the network of intramolecular interactions encoded by Nα-chiral side chains and the equilibria between cis- and trans-amide junctions in cyclic peptoid architectures constitutes a significant challenge for the construction of stable reverse turn and loop structures. In this contribution, we reveal, with the support of NMR spectroscopy, single-crystal X-ray crystallography and density functional theory calculations, the relevant noncovalent interactions stabilizing tri-, tetra-, hexa-, and octameric cyclic peptoids (as free hosts and host-guest complexes) with strategically positioned N-(S)-(1-phenylethyl)/N-benzyl side chains, and how these interactions influence the backbone topological order. With the help of theoretical models and spectroscopic/diffractometric studies, we disclose new γ-/β-turn and loop structures present in α-peptoid-based macrocycles and classify them according ϕ, ψ, and ω torsion angles. In our endeavor to characterize emergent secondary structures, we solved the solid-state structure of the largest metallated cyclic peptoid ever reported, characterized by an unprecedented alternated cis/trans amide bond linkage. Overall, our results indicate that molecules endowed with different elements of asymmetry (central and conformational) provide new architectural elements of facile atroposelective construction and broad conformational stability as the minimalist scaffold for novel stereodefined peptidomimetic foldamers and topologically biased libraries necessary for future application of peptoids in all fields of science.
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Affiliation(s)
- Assunta D'Amato
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Giovanni Pierri
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Consiglia Tedesco
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Giorgio Della Sala
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Chiara Costabile
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
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11
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Chingle R, Mulumba M, Chung NN, Nguyen TMD, Ong H, Ballet S, Schiller PW, Lubell WD. Solid-Phase Azopeptide Diels–Alder Chemistry for Aza-pipecolyl Residue Synthesis To Study Peptide Conformation. J Org Chem 2019; 84:6006-6016. [DOI: 10.1021/acs.joc.8b03283] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Nga N. Chung
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montréal, Québec H2W 1R7, Canada
| | - Thi M.-D. Nguyen
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montréal, Québec H2W 1R7, Canada
| | | | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Peter W. Schiller
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montréal, Québec H2W 1R7, Canada
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12
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Davison EK, Cameron AJ, Harris PWR, Brimble MA. Synthesis of endolides A and B: naturally occurring N-methylated cyclic tetrapeptides. MEDCHEMCOMM 2019; 10:693-698. [PMID: 31191859 DOI: 10.1039/c9md00050j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/01/2019] [Indexed: 01/16/2023]
Abstract
Endolides A and B are naturally occurring, N-methylated, cyclic tetrapeptides possessing an unusual 3-(3-furyl)alanine amino acid and outstanding biological profiles. 1-Propanephosphonic anhydride (T3P) was used to mediate a solution-phase cyclisation reaction of the linear tetrapeptides, thus achieving the first syntheses of both endolides A and B. The stereoselectivity of the tetrapeptide cyclisation reactions was found to be reagent-controlled, and was independent of the C-terminal configuration of the linear peptide starting materials.
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Affiliation(s)
- Emma K Davison
- School of Chemical Sciences , University of Auckland , 23 Symonds St. , Auckland , 1010 , New Zealand . .,School of Biological Sciences , University of Auckland , 3 Symonds St. , Auckland , 1010 , New Zealand
| | - Alan J Cameron
- School of Chemical Sciences , University of Auckland , 23 Symonds St. , Auckland , 1010 , New Zealand . .,School of Biological Sciences , University of Auckland , 3 Symonds St. , Auckland , 1010 , New Zealand.,The Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland , 1010 , New Zealand
| | - Paul W R Harris
- School of Chemical Sciences , University of Auckland , 23 Symonds St. , Auckland , 1010 , New Zealand . .,School of Biological Sciences , University of Auckland , 3 Symonds St. , Auckland , 1010 , New Zealand.,The Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland , 1010 , New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences , University of Auckland , 23 Symonds St. , Auckland , 1010 , New Zealand . .,School of Biological Sciences , University of Auckland , 3 Symonds St. , Auckland , 1010 , New Zealand.,The Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland , 1010 , New Zealand
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13
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Huang KJ, Huang YC, Lin YA. Synthesis of Histidine-Containing Oligopeptides via Histidine-Promoted Peptide Ligation. Chem Asian J 2018; 13:400-403. [PMID: 29345421 DOI: 10.1002/asia.201701802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/18/2018] [Indexed: 12/12/2022]
Abstract
Histidine-containing peptides are valuable therapeutic agents for a treatment of neurodegenerative diseases. However, the synthesis of histidine-containing peptides is not trivial due to the potential of imidazole sidechain of histidine to act as a nucleophile if unprotected. A peptide ligation method utilizing the imidazole sidechain of histidine has been developed. The key imidazolate intermediate that acts as an internal acyl transfer catalyst during ligation is generated by deprotonation. Transesterification with amino acids or peptides tethered with C-terminal thioester followed by N→N acyl shifts led to the final ligated products. A range of histidine-containing dipeptides could be synthesized in moderate to good yields via this method without protecting the imidazole sidechain. The protocol was further extended to tripeptide synthesis via a long-range N→N acyl transfer, and tetrapeptide synthesis.
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Affiliation(s)
- Kai-Jin Huang
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung, 80424, Taiwan
| | - Yi-Chen Huang
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung, 80424, Taiwan
| | - Yuya A Lin
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung, 80424, Taiwan
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14
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Cameron AJ, Squire CJ, Edwards PJB, Harjes E, Sarojini V. Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides. Chem Asian J 2017; 12:3195-3202. [PMID: 29098772 DOI: 10.1002/asia.201701422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/30/2017] [Indexed: 12/31/2022]
Abstract
Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.
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Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
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15
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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16
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Solid-phase synthesis, cyclization, and site-specific functionalization of aziridine-containing tetrapeptides. Nat Protoc 2017; 12:1277-1287. [PMID: 28538738 DOI: 10.1038/nprot.2017.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyclic tetrapeptides comprise a potent and selective class of molecules with a wide range of biological activities, including the phytotoxic activity of tentoxin and the histone deacetylase (HDAC) inhibitory effects of chlamydocin. The incorporation of a functional aziridine group within cyclic peptides enables their conformational control and allows for late-stage and site-selective functionalization of these molecules, thereby creating the potential for covalent protein labeling. This protocol describes the solid-phase synthesis, cyclization, and site-specific structural modification of aziridine-containing tetrapeptides. The linear precursors are assembled by solid-phase peptide synthesis using Fmoc-protected amino acid building blocks, followed by head-to-tail peptide cyclization. Cyclization is performed using a slow reverse-addition method that prevents the formation of undesired higher-order cyclo-oligomeric side products. Site-specific structural modification of the resulting macrocycles is described using sodium azide or thiophenol as representative examples. It requires ∼4 d to prepare peptide macrocycles from their respective Fmoc-protected amino acid starting materials, an improvement upon the 3 weeks required for conventional solution-phase methods. This protocol also addresses important considerations regarding the handling of these compounds, whose electrophilic aziridine functionalities can otherwise be prone to undesired side reactions. With recent developments in aziridine-containing macrocyclic peptide synthesis and the potential for covalent protein labeling, these scaffolds represent a valuable addition to many screening libraries, and we expect that access to these macrocycles will facilitate efforts in drug discovery and molecular probe development.
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17
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Chen CC, Wang SF, Su YY, Lin YA, Lin PC. Copper(I)-Mediated Denitrogenative Macrocyclization for the Synthesis of Cyclic α3
β-Tetrapeptide Analogues. Chem Asian J 2017; 12:1326-1337. [DOI: 10.1002/asia.201700339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 03/23/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Chun-Chi Chen
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Sheng-Fu Wang
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Yung-Yu Su
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Yuya A. Lin
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Po-Chiao Lin
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
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18
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Zhang S, De Leon Rodriguez LM, Lacey E, Piggott AM, Leung IKH, Brimble MA. Cyclization of Linear Tetrapeptides Containing N
-Methylated Amino Acids by using 1-Propanephosphonic Acid Anhydride. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences; The University of Auckland; 23 Symonds St 1142 Auckland New Zealand
| | - Luis M. De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; 1142 Auckland New Zealand
| | - Ernest Lacey
- Microbial Screening Technologies; Building C; 28-54 Percival Rd. 2164 Smithfield NSW Australia
| | - Andrew M. Piggott
- Department of Chemistry and Biomolecular Sciences; Macquarie University; 2109 NSW Australia
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland; 23 Symonds St 1142 Auckland New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St 1142 Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; 1142 Auckland New Zealand
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19
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Chung BKW, White CJ, Scully CCG, Yudin AK. The reactivity and conformational control of cyclic tetrapeptides derived from aziridine-containing amino acids. Chem Sci 2016; 7:6662-6668. [PMID: 28567256 PMCID: PMC5450523 DOI: 10.1039/c6sc01687a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/29/2016] [Indexed: 12/25/2022] Open
Abstract
Among the smallest of the macrocyclic peptides, 12- and 13-membered cyclic tetrapeptides are particularly noteworthy because they exhibit a broad spectrum of biological activities due to their innate capacity to mimic β-turns in proteins. In this report, we demonstrate that aziridine-containing cyclic tetrapeptides offer a platform to interrogate the conformational properties of tetrapeptides. We show that aziridine ring-opening of 12-membered cyclic tetrapeptides yields exclusively 13-membered α3β macrocycles, regardless of peptide sequence, nucleophile, aziridine β-carbon substitution, or stereochemistry. NMR and computational studies on two related aziridine-containing cyclic tetrapeptides revealed that the amide conformations of their N-acyl aziridines are similar, and are likely the determinant of the observed ring-opening regioselectivity. Interestingly, some of the resulting 13-membered α3β macrocycles were found to be conformationally heterogeneous. This study on the reactivity and conformational control of aziridine-containing cyclic tetrapeptides provides useful insight on the design and development of macrocyclic therapeutics.
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Affiliation(s)
- Benjamin K W Chung
- Davenport Research Laboratories , Department of Chemistry , The University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Christopher J White
- Davenport Research Laboratories , Department of Chemistry , The University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Conor C G Scully
- Davenport Research Laboratories , Department of Chemistry , The University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
| | - Andrei K Yudin
- Davenport Research Laboratories , Department of Chemistry , The University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada .
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20
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Neelamraju S, Johnston RL, Schön JC. A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide. J Chem Theory Comput 2016; 12:2471-9. [PMID: 27049524 DOI: 10.1021/acs.jctc.6b00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.
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Affiliation(s)
- Sridhar Neelamraju
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Roy L Johnston
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - J Christian Schön
- Max Planck Institute for Solid State Research , Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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21
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Babinska A, Clement CC, Swiatkowska M, Szymanski J, Shon A, Ehrlich YH, Kornecki E, Salifu MO. Development of new antiatherosclerotic and antithrombotic drugs utilizing F11 receptor (F11R/JAM-A) peptides. Biopolymers 2016; 102:322-34. [PMID: 24801754 DOI: 10.1002/bip.22503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/01/2014] [Accepted: 05/02/2014] [Indexed: 12/29/2022]
Abstract
Peptides with enhanced resistance to proteolysis, based on the amino acid sequence of the F11 receptor molecule (F11R, aka JAM-A/Junctional adhesion molecule-A), were designed, prepared, and examined as potential candidates for the development of anti-atherosclerotic and anti-thrombotic therapeutic drugs. A sequence at the N-terminal of F11R together with another sequence located in the first Ig-loop of this protein, were identified to form a steric active-site operating in the F11R-dependent adhesion between cells that express F11R molecules on their external surface. In silico modeling of the complex between two polypeptide chains with the sequences positioned in the active-site was used to generate peptide-candidates designed to inhibit homophilic interactions between surface-located F11R molecules. The two lead F11R peptides were modified with D-Arg and D-Lys at selective sites, for attaining higher stability to proteolysis in vivo. Using molecular docking experiments we tested different conformational states and the putative binding affinity between two selected D-Arg and D-Lys-modified F11R peptides and the proposed binding pocket. The inhibitory effects of the F11R peptide 2HN-(dK)-SVT-(dR)-EDTGTYTC-CONH2 on antibody-induced platelet aggregation and on the adhesion of platelets to cytokine-inflammed endothelial cells are reported in detail, and the results point out the significant potential utilization of F11R peptides for the prevention and treatment of atherosclerotic plaques and associated thrombotic events.
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Affiliation(s)
- A Babinska
- Division of Nephrology, Department of Medicine, State University of New York, Downstate Medical Center, Brooklyn, NY, 11203; Department of Cell Biology and Medicine, State University of New York, Downstate Medical Center, Brooklyn, NY, 11203
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22
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Reddy DN, Ballante F, Chuang T, Pirolli A, Marrocco B, Marshall GR. Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors. J Med Chem 2016; 59:1613-33. [PMID: 26681404 DOI: 10.1021/acs.jmedchem.5b01632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Selective inhibition of KDAC isoforms while maintaining potency remains a challenge. Using the largazole macrocyclic depsipeptide structure as a starting point for developing new KDACIs with increased selectivity, a combination of four different simplified largazole analogue (SLA) scaffolds with diverse zinc-binding groups (for a total of 60 compounds) were designed, synthesized, and evaluated against class I KDACs 1, 3, and 8, and class II KDAC6. Experimental evidence as well as molecular docking poses converged to establish the cyclic tetrapeptides (CTPs) as the primary determinant of both potency and selectivity by influencing the correct alignment of the zinc-binding group in the KDAC active site, providing a further basis for developing new KDACIs of higher isoform selectivity and potency.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Timothy Chuang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Adele Pirolli
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
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23
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Nair RV, Baravkar SB, Ingole TS, Sanjayan GJ. Synthetic turn mimetics and hairpin nucleators: Quo Vadimus? Chem Commun (Camb) 2014; 50:13874-84. [PMID: 25051222 DOI: 10.1039/c4cc03114h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.
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Affiliation(s)
- Roshna V Nair
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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24
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Culf AS, Čuperlović-Culf M, Léger DA, Decken A. Small head-to-tail macrocyclic α-peptoids. Org Lett 2014; 16:2780-3. [PMID: 24797336 DOI: 10.1021/ol501102b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute , 35 Providence Street, Moncton, NB E1C 8X3, Canada
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25
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Rabong C, Schuster C, Liptaj T, Prónayová N, Delchev VB, Jordis U, Phopase J. NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water. RSC Adv 2014. [DOI: 10.1039/c4ra01210k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.
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Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Christoph Schuster
- Department of Environmental Geosciences
- University of Vienna
- A-1090 Vienna, Austria
| | - Tibor Liptaj
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Nadežda Prónayová
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Vassil B. Delchev
- Department of Physical Chemistry
- University of Plovdiv
- 4000 Plovdiv, Bulgaria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Jaywant Phopase
- Integrative Regenerative Medicine Centre (IGEN) & Department of Physics
- Chemistry and Biology (IFM)
- 58183 Linköping, Sweden
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26
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Davis LO. Recent Developments in the Synthesis and Applications of Pyrazolidines. A Review. ORG PREP PROCED INT 2013. [DOI: 10.1080/00304948.2013.834769] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Oakley MT, Oheix E, Peacock AFA, Johnston RL. Computational and Experimental Investigations into the Conformations of Cyclic Tetra-α/β-peptides. J Phys Chem B 2013; 117:8122-34. [DOI: 10.1021/jp4043039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark T. Oakley
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Emmanuel Oheix
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Anna F. A. Peacock
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Roy L. Johnston
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
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28
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Caumes C, Fernandes C, Roy O, Hjelmgaard T, Wenger E, Didierjean C, Taillefumier C, Faure S. Cyclic α,β-tetrapeptoids: sequence-dependent cyclization and conformational preference. Org Lett 2013; 15:3626-9. [PMID: 23806006 DOI: 10.1021/ol401478j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The presence of at least one N-Cα branched side chain is crucial for successful cyclization of α,β-tetrapeptoids. The ctct amide sequence revealed in the crystal structure of the 14-membered cyclotetrapeptoid 8 is also the most populated conformation in solution and is reminiscent of the predominant amide arrangement of the 12-membered cyclic tetrapeptides (CTPs).
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Affiliation(s)
- Cécile Caumes
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP10448, F-63000 Clermont-Ferrand, France
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29
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Oakley MT, Johnston RL. Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling. J Chem Theory Comput 2013; 9:650-657. [PMID: 23596359 PMCID: PMC3624815 DOI: 10.1021/ct3005084] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Indexed: 12/18/2022]
Abstract
Cyclic tetrapeptides are an important class of biologically active molecules that exhibit interesting conformational dynamics, with slow interconversion of several different structures. We present calculations on their energy landscapes using discrete path sampling. In acyclic peptides and large cyclic peptides, isomers containing cis-peptide groups are much less stable than the all-trans isomers and separated from them by large barriers. Strain in small cyclic peptides causes the cis and trans isomers to be closer in energy and separated by much lower barriers. If d-amino acids or proline residues are introduced, isomers containing cis-peptides become more stable than the all-trans structures. We also show that changing the polarity of the solvent has a significant effect on the energy landscapes of cyclic tetrapeptides, causing changes in the orientations of the peptide groups and in the degree of intramolecular hydrogen bonding.
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Affiliation(s)
- Mark T. Oakley
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15
2TT, U.K
| | - Roy L. Johnston
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15
2TT, U.K
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30
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Vangala M, Dhokale SA, Gawade RL, Pattuparambil RR, Puranik VG, Dhavale DD. Sugar furanoid trans-vicinal diacid as a γ-turn inducer: synthesis and conformational study. Org Biomol Chem 2013; 11:6874-8. [DOI: 10.1039/c3ob41462k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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Shagun VA, Smirnov VI, Sinegovskaya LM, Nosyreva VV, Borisova AP, Shemyakina OA, Mal’kina AG. Reaction between β-phenyl-α-alanine and 4-hydroxy-4-methylpent-2-ynenitrile: a spectroscopic and quantum chemical study. Russ Chem Bull 2012. [DOI: 10.1007/s11172-011-0380-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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33
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Neveu C, Lefranc B, Tasseau O, Do-Rego JC, Bourmaud A, Chan P, Bauchat P, Le Marec O, Chuquet J, Guilhaudis L, Boutin JA, Ségalas-Milazzo I, Costentin J, Vaudry H, Baudy-Floc'h M, Vaudry D, Leprince J. Rational design of a low molecular weight, stable, potent, and long-lasting GPR103 aza-β3-pseudopeptide agonist. J Med Chem 2012; 55:7516-24. [PMID: 22800498 DOI: 10.1021/jm300507d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
26RFa, a novel RFamide neuropeptide, is the endogenous ligand of the former orphan receptor GPR103. Intracerebroventricular injection of 26RFa and its C-terminal heptapeptide, 26RFa((20-26)), stimulates food intake in rodents. To develop potent, stable ligands of GPR103 with low molecular weight, we have designed a series of aza-β(3)-containing 26RFa((20-26)) analogues for their propensity to establish intramolecular hydrogen bonds, and we have evaluated their ability to increase [Ca(2+)](i) in GPR103-transfected cells. We have identified a compound, [Cmpi(21),aza-β(3)-Hht(23)]26RFa((21-26)), which was 8-fold more potent than 26RFa((20-26)) in mobilizing [Ca(2+)](i). This pseudopeptide was more stable in serum than 26RFa((20-26)) and exerted a longer lasting orexigenic effect in mice. This study constitutes an important step toward the development of 26RFa analogues that could prove useful for the treatment of feeding disorders.
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Affiliation(s)
- Cindy Neveu
- Laboratory of Neuronal and Neuroendocrine Differentiation and Communication, Institute for Research and Innovation in Biomedicine (IRIB), INSERM U982, 76821 Mont-Saint-Aignan, France
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34
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White CJ, Yudin AK. A versatile scaffold for site-specific modification of cyclic tetrapeptides. Org Lett 2012; 14:2898-901. [PMID: 22612626 DOI: 10.1021/ol301178r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel scaffold that can be used to prepare conformationally homogeneous cyclic tetrapeptides equipped with a β-amino acid residue is disclosed. It is shown that regioselective structural modification can be accomplished using thiols and azide nucleophiles, commonly associated with rich downstream chemistry. The method should find application in efforts to constrain privileged tripeptide sequences in rigid molecular scaffolds.
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Affiliation(s)
- Christopher J White
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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35
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Johannessen L, Remsberg J, Gaponenko V, Adams KM, Barchi JJ, Tarasov SG, Jiang S, Tarasova NI. Peptide structure stabilization by membrane anchoring and its general applicability to the development of potent cell-permeable inhibitors. Chembiochem 2011; 12:914-21. [PMID: 21365731 DOI: 10.1002/cbic.201000563] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Indexed: 11/08/2022]
Abstract
Isolated protein motifs that are involved in interactions with their binding partners can be used to inhibit these interactions. However, peptides corresponding to protein fragments tend to have no defined secondary or tertiary structure in the absence of scaffolding by the rest of protein molecule. This results in low inhibitor potency. NMR and CD spectroscopy studies of lipopeptide inhibitors of the Hedgehog pathway revealed that membrane anchoring allows the cell membrane to function as a scaffold and facilitate the folding of short peptides. In addition, lipidation enhances cell permeability and increases the concentration of the compounds near the membrane, thus facilitating potent inhibition. The general applicability of this rational approach was further confirmed by the generation of selective antagonists of the insulin-like growth factor 1 receptor with GI(50) values in the nanomolar range. Lipopeptides corresponding to protein fragments were found to serve as potent and selective inhibitors of a number of nondruggable molecular targets.
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Affiliation(s)
- Liv Johannessen
- Cancer and Inflammation Program, Center for Cancer Research NCI-Frederick, Frederick, MD, 21702, USA
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36
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Lim HA, Kang C, Chia CSB. Solid-Phase Synthesis and NMR Structural Studies of the Marine Antibacterial Cyclic Tetrapeptide: Cyclo[GSPE]. Int J Pept Res Ther 2010. [DOI: 10.1007/s10989-010-9216-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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37
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Chemo-, regio- and stereospecific addition of amino acids to acylacetylenes: a facile synthesis of new N-acylvinyl derivatives of amino acids. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.069] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Baeza JL, Gerona-Navarro G, Thompson K, Pérez de Vega MJ, Infantes L, García-López MT, González-Muñiz R, Martín-Martínez M. Further Evidence for 2-Alkyl-2-carboxyazetidines as γ-Turn Inducers. J Org Chem 2009; 74:8203-11. [DOI: 10.1021/jo901712x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José Luis Baeza
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Kevin Thompson
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Lourdes Infantes
- Instituto de Química Física Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
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Voss E, Arrault A, Bodiguel J, Jamart-Grégoire B. Efficient synthesis of enantiomerically pure (S)-δ-azaproline starting from (R)-α-hydroxy-γ-butyrolactone via the Mitsunobu reaction. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Horne W, Olsen C, Beierle J, Montero A, Ghadiri M. Probing the Bioactive Conformation of an Archetypal Natural Product HDAC Inhibitor with Conformationally Homogeneous Triazole‐Modified Cyclic Tetrapeptides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805900] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Balducci D, Bottoni A, Calvaresi M, Porzi G. Conformational analysis of hexapseudopeptides mimicking reverse turn structures induced by a modified (S)-proline. A combined spectroscopic and molecular dynamics investigation. Part 4. Mol Phys 2009. [DOI: 10.1080/00268970902845339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid side chains. The basic premise is that preorganization of the competing ligand enhances the binding affinity and potential selectivity of the inhibitor. In this chapter, current progress in these efforts is reviewed.
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Horne WS, Olsen CA, Beierle JM, Montero A, Reza Ghadiri M. Probing the bioactive conformation of an archetypal natural product HDAC inhibitor with conformationally homogeneous triazole-modified cyclic tetrapeptides. Angew Chem Int Ed Engl 2009; 48:4718-24. [PMID: 19267380 PMCID: PMC3041267 DOI: 10.1002/anie.200805900] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fooling enzymes with mock amides: Analogues of apicidin, a cyclic-tetrapeptide inhibitor of histone deacetylase (HDAC), were designed with a 1,4- or 1,5-disubstituted 1,2,3-triazole in place of a backbone amide bond to fix the bond in question in either a trans-like or a cis-like configuration. Thus, the binding affinity of distinct peptide conformations (see picture) could be probed. One analogue proved in some cases to be superior to apicidin as an HDAC inhibitor.
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Affiliation(s)
| | | | - John M. Beierle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Ana Montero
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - M. Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
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Salaün A, Mocquet C, Perochon R, Lecorgne A, Le Grel B, Potel M, Le Grel P. Aza-β3-cyclotetrapeptides. J Org Chem 2008; 73:8579-82. [DOI: 10.1021/jo8013963] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arnaud Salaün
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Clémence Mocquet
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Romain Perochon
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Aurélien Lecorgne
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Barbara Le Grel
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Michel Potel
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Philippe Le Grel
- ICMV and CSM, UMR CNRS 6226, Université de Rennes I, 263 avenue du Général Leclerc, 35042 Rennes, Cedex, France
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Tai DF, Lin YF. Molecularly imprinted cavities template the macrocyclization of tetrapeptides. Chem Commun (Camb) 2008:5598-600. [PMID: 18997964 DOI: 10.1039/b813439a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cavities formed using cyclic tetrapeptides (CTPs) or heat-induced conformers act as templates for cyclization; the cavities bind to linear tetrapeptides and enforce turn conformations to enhance cyclization to constrained CTPs.
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Affiliation(s)
- Dar-Fu Tai
- Department of Chemistry, National Dong-Hwa University, Hualien, Taiwan.
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A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank. J Comput Aided Mol Des 2008; 23:87-95. [PMID: 18797997 DOI: 10.1007/s10822-008-9241-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
Abstract
Reverse turns are often recognition sites for protein/protein interactions and, therefore, valuable potential targets for determining recognition motifs in development of potential therapeutics. A virtual combinatorial library of cyclic tetrapeptides (CTPs) was generated and the bonds in the low-energy structures were overlapped with canonical reverse-turn Calpha-Cbeta bonds (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005) to determine the utility of CTPs as reverse-turn peptidomimetics. All reverse turns in the Protein Data Bank (PDB) with a crystal structures resolution < or = 3.0 A were classified into the same known canonical reverse-turn Calpha-Cbeta bond clusters (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005). CTP reverse-turn mimics were compiled that mimicked both the relative orientations of three of the four as well as all four Calpha-Cbeta bonds in the reverse turns of the PDB. 54% of reverse turns represented in the PDB had eight or more CTPs structures that mimicked the orientation of all four of the Calpha-Cbeta bonds in the reverse turn.
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Comparative Study of Chemical Approaches to the Solid-Phase Synthesis of a Tumor-Seeking α-MSH Analogue. Int J Pept Res Ther 2008. [DOI: 10.1007/s10989-008-9143-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Che Y, Marshall GR. Privileged scaffolds targeting reverse-turn and helix recognition. Expert Opin Ther Targets 2008; 12:101-14. [PMID: 18076374 DOI: 10.1517/14728222.12.1.101] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein-protein interactions dominate molecular recognition in biologic systems. One major challenge for drug discovery arises from the very large surfaces that are characteristic of many protein-protein interactions. OBJECTIVES To identify 'drug-like' small molecule leads capable of modulating protein-protein interactions based on common protein-recognition motifs, such as alpha-helices, beta-strands, reverse-turns and polyproline motifs for example. OVERVIEW Many proteins/peptides are unstructured under physiologic conditions and only fold into ordered structures on binding to their cellular targets. Therefore, preorganization of an inhibitor into its protein-bound conformation reduces the entropy of binding and enhances the relative affinity of the inhibitor. Accordingly, this review describes a general strategy to address the challenge based on the 'privileged structure hypothesis' [Che, PhD thesis, Washington University, 2003] that chemical templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as small-molecule inhibitors of protein-protein interactions. The authors highlight recent advances in the design of privileged scaffolds targeting reverse-turn and helical recognition. CONCLUSIONS Privileged scaffolds targeting common protein-recognition motifs are useful to help elucidate the receptor-bound conformation and to provide non-peptidic, bioavailable substructures suitable for optimization to modulate protein-protein interactions.
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Affiliation(s)
- Ye Che
- Washington University, Center for Computational Biology and Department of Biochemistry and Molecular Biophysics, St. Louis, MO 63110, USA
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Gomes P, Vale N, Moreira R. Cyclization-activated prodrugs. Molecules 2007; 12:2484-506. [PMID: 18065953 PMCID: PMC6149143 DOI: 10.3390/12112484] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 11/08/2007] [Accepted: 11/09/2007] [Indexed: 11/16/2022] Open
Abstract
Many drugs suffer from an extensive first-pass metabolism leading to drug inactivation and/or production of toxic metabolites, which makes them attractive targets for prodrug design. The classical prodrug approach, which involves enzyme-sensitive covalent linkage between the parent drug and a carrier moiety, is a well established strategy to overcome bioavailability/toxicity issues. However, the development of prodrugs that can regenerate the parent drug through non-enzymatic pathways has emerged as an alternative approach in which prodrug activation is not influenced by inter- and intraindividual variability that affects enzymatic activity. Cyclization-activated prodrugs have been capturing the attention of medicinal chemists since the middle-1980s, and reached maturity in prodrug design in the late 1990 s. Many different strategies have been exploited in recent years concerning the development of intramoleculary-activated prodrugs spanning from analgesics to anti-HIV therapeutic agents. Intramolecular pathways have also a key role in two-step prodrug activation, where an initial enzymatic cleavage step is followed by a cyclization-elimination reaction that releases the active drug. This work is a brief overview of research on cyclization-activated prodrugs from the last two decades.
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Affiliation(s)
- Paula Gomes
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
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Arbor S, Kao J, Wu Y, Marshall GR. c[D-pro-Pro-D-pro-N-methyl-Ala] adopts a rigid conformation that serves as a scaffold to mimic reverse-turns. Biopolymers 2007; 90:384-93. [DOI: 10.1002/bip.20869] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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