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Cummings AE, Miao J, Slough DP, McHugh SM, Kritzer JA, Lin YS. β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides. Biophys J 2019; 116:433-444. [PMID: 30661666 DOI: 10.1016/j.bpj.2018.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/19/2018] [Accepted: 12/13/2018] [Indexed: 01/11/2023] Open
Abstract
Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive molecules, but these are challenging to predict and difficult to verify experimentally. In our previous work, we used explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the global structural ensembles of cyclic hexapeptides containing different permutations of glycine, alanine, and valine. One peptide, cyclo-(VVGGVG) or P7, was predicted to be unusually well structured. In this work, we synthesized P7, along with a less well-structured control peptide, cyclo-(VVGVGG) or P6, and characterized their global structural ensembles in water using NMR spectroscopy. The NMR data revealed a structural ensemble similar to the prediction for P7 and showed that P6 was indeed much less well-structured than P7. We then simulated and experimentally characterized the global structural ensembles of several P7 analogs and discovered that β-branching at one critical position within P7 is important for overall structural stability. The simulations allowed deconvolution of thermodynamic factors that underlie this structural stabilization. Overall, the excellent correlation between simulation and experimental data indicates that our simulation platform will be a promising approach for designing well-structured CPs and also for understanding the complex interactions that control the conformations of constrained peptides and other macrocycles.
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Affiliation(s)
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts
| | - Diana P Slough
- Department of Chemistry, Tufts University, Medford, Massachusetts
| | - Sean M McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts.
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts.
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2
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Pilsl LKA, Reiser O. α/β-Peptide foldamers: state of the art. Amino Acids 2011; 41:709-18. [DOI: 10.1007/s00726-011-0894-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 03/18/2011] [Indexed: 11/24/2022]
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3
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Guthöhrlein EW, Malešević M, Majer Z, Sewald N. Secondary structure inducing potential of β-amino acids: Torsion angle clustering facilitates comparison and analysis of the conformation during MD trajectories. Biopolymers 2007; 88:829-39. [DOI: 10.1002/bip.20859] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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4
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Affiliation(s)
- R P Cheng
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA
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5
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Beumer R, Reiser O. β-Aminocyclopropanecarboxylic acids with α-amino acid side chain functionality. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00541-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Thakur AK, Kishore R. Influence of hydrophobic interactions on the conformational adaptability of the beta-Ala residue. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2001; 57:455-61. [PMID: 11437949 DOI: 10.1034/j.1399-3011.2001.00839.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The chemical synthesis and X-ray crystal structure analysis of a model peptide incorporating a conformationally flexible beta-Ala residue: Boc-beta-Ala-Pda, 1 (C23H46N2O3: molecular weight = 398.62) have been described. The peptide crystallized in the crystal system triclinic with space group P21: a = 5.116(3) A, b = 5.6770(10) A, c = 21.744(5) A; alpha = 87.45 degrees, beta = 86.87 degrees, gamma = 90.0 degrees; Z = 1. An attractive feature of the crystal molecular structure of 1 is the induction of a reasonably extended backbone conformation of the beta-Ala moiety, i.e. the torsion angles phi approximately -115 degrees, mu approximately 173 degrees and psi approximately 122 degrees, correspond to skew-, trans and skew+ conformation, respectively, by an unbranched hydrophobic alkyl chain, Pda, which prefers an all-anti orientation (theta1 approximately -153 degrees, theta2 approximately ellipsis theta14 approximately +/-178 degrees ). The observation is remarkable because, systematic conformational investigations of short linear beta-Ala peptides of the type Boc-beta-Ala-Xaa-OCH3 (Xaa = Aib or Acc6) have shown that the chemical and stereochemical characters of the neighboring moieties may be critical in dictating the overall folded and/or unfolded conformational features of the beta-Ala residue. The overall conformation of 1 is typical of a 'bar'. It appears convincing that, in addition to a number of hydrophobic contacts between the parallel arranged molecules, an array of conventional N-HellipsisO=C intermolecular H-bonding interactions stabilize the crystal molecular structure. Moreover, the resulting 14-membered pseudo-ring motif, generated by the amide-amide interactions between the adjacent molecules, is completely devoid of nonconventional C-HellipsisO interaction. The potentials of the conformational adaptation of the beta-Ala residue, to influence and stabilize different structural characteristics have been highlighted.
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Affiliation(s)
- A K Thakur
- Institute of Microbial Technology, Chandigarh, India
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7
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Affiliation(s)
- Robert Günther
- Institut für Biochemie, Fakultät für Biowissenschaften, Pharmazie und Psychologie, Universität Leipzig, Talstr. 33, D-04103 Leipzig, Germany
| | - Hans-Jörg Hofmann
- Institut für Biochemie, Fakultät für Biowissenschaften, Pharmazie und Psychologie, Universität Leipzig, Talstr. 33, D-04103 Leipzig, Germany
| | - Krzysztof Kuczera
- Department of Chemistry and Department of Molecular Biosciences, University of Kansas, 2010 Mallot Hall, Lawrence, Kansas 66045, U.S.A
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8
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Beumer R, Bubert C, Cabrele C, Vielhauer O, Pietzsch M, Reiser O. The synthesis of diastereo- and enantiomerically pure beta-aminocyclopropanecarboxylic acids. J Org Chem 2000; 65:8960-9. [PMID: 11149838 DOI: 10.1021/jo005541l] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of diastereo- and enantiomerically pure beta-aminocyclopropanecarboxylic acids (beta-ACCs) is described. Starting from pyrrole, (rac)-4 is readily obtained, which was kinetically resolved by enzymatic hydrolysis. Subsequent oxidation of (-)-4 and deformylation gives rise to the cis-beta-ACC derivative (ent)-9, while (+)-10 was converted to the trans-beta-ACC derivative 8. Both 8 and (ent)-9 and their benzyl esters 13 and 16, being conformationally restricted beta-alanine or gamma-aminobutyric acid (GABA) derivatives, represent useful building blocks for peptides containing unnatural amino acids.
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Affiliation(s)
- R Beumer
- Department of Organic Chemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
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9
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Lombardi A, D'Auria G, Saviano M, Maglio O, Nastri F, Quartara L, Pedone C, Pavone V. Bicyclic peptides as type I/type II beta-turn scaffolds. Biopolymers 2000; 40:505-18. [PMID: 9062073 DOI: 10.1002/(sici)1097-0282(1996)40:5<505::aid-bip8>3.0.co;2-#] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We recently reported the rational design, synthetics, and structural characterization of the most potent and selective peptide-based neurokinin A antagonist thus far described: cyclo(Met1-Asp2-Trp3-Phe4-Dap5-Leu6)cyclo(2 beta-5 beta). Its bicyclic structure is characterized by a type I and a type II two beta-turn around Trp3-Phe4 and Leu6-Met1, respectively. In order to understand whether the two different beta-turned structures are determined by the bicyclic structure or by the amino acid type at the corner positions, we have synthesized the pseudo-symmetrical analogue cyclo(Phe1-Asp2-Trp3-Phe4-Dap5-Trp6)cyclo(2 beta-5 beta). The structural characterization in the crystal state and in solution, here reported, gives an experimental evidence that the backbone of the bicyclic structure is a rigid scaffold that can be used to build both a type I and type II beta-turn independently from the amino acid composition.
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Affiliation(s)
- A Lombardi
- Centro Interdipartimentale di Ricerca sui Peptidi Bioattivi CEINGE--Biotecnologie Avanzate, Napoli, Italy
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10
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Abstract
A large number of potent and selective therapeutic agents, useful for the treatment of several diseases, have been isolated from natural sources. For example, the most active thrombin inhibitors are those secreted by the salivary glands of leeches. One peculiar feature of these agents is the lack of any significant inhibitory cross-reaction with other serine proteinases. Hence, the knowledge of the exact mechanism of action of these molecules provides the basis for the development of new and efficient synthetic drugs. For this reason, many studies have been undertaken on the structure-activity relationships of natural thrombin inhibitors, and a large amount of detailed information has been obtained by the crystal structures of these inhibitors when complexed with thrombin. In this paper, we review natural and synthetic multisite thrombin inhibitors, whose structural aspects have been determined in detail. We also report here the approach used by us to develop a new class of synthetic, multisite directed thrombin inhibitors, named hirunorms, designed to mimic the distinctive binding mode of hirudin.
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Affiliation(s)
- A Lombardi
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Napoli Federico II, Italy
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11
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Rossi F, Bucci E, Isernia C, Saviano M, Iacovino R, Romanelli A, Di Lello P, Grimaldi M, Montesarchio D, De Napoli L, Piccialli G, Benedetti E. Effect of lengthening of peptide backbone by insertion of chiral beta-homo amino acid residues: conformational behavior of linear peptides containing alternating L-leucine and beta-homo L-leucine residues. Biopolymers 2000; 53:140-9. [PMID: 10679618 DOI: 10.1002/(sici)1097-0282(200002)53:2<140::aid-bip4>3.0.co;2-g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The synthesis and the solution behavior of the linear peptides containing a beta-homo (beta-H) leucine residue-Boc-Leu-beta-HLeu-Leu-OMe, Boc-beta-HLeu-Leu-beta-HLeu-Leu-OMe, and Boc-Leu-beta-HLeu-Leu-beta-HLeu-Leu-OMe-as well as the solid structure of the tripeptide, are reported. The conformational behavior of the peptides was investigated in solution by two-dimensional nmr. Our data support the existence in solution with different families of conformers in rapid interchange. The crystals of the tripeptide are orthorhombic, space group P2(1)2(1)2, with a = 15.829(1) A, b = 29.659(1) A, c = 6.563(1) A, and Z = 4. The structure has been solved by direct methods and refined to final R1 and wR2 indexes of 0.0530 and 0.1436 for 2420 reflections with I > 2sigma(I). In the solid state, the tripeptide does not present intramolecular H bonds, and the peptide backbone of the two leucine residues adopts a quasi-extended conformation. For the beta-HLeu residue, the backbone conformation is specified by the torsion angles straight phi(2) = -120.9(4) degrees, mu(2) = 56.7(4) degrees, psi(3) = -133.2(4) degrees. The side chains of the three residues assume the same conformation (g(-), g(-), trans), and all peptide bonds, except the urethane group at the N-terminus, are in the trans conformation. Preliminary conformational energy calculations carried out on the Ac-NH-beta-HAla-NHMe underline that the conformations with mu angle equal to 180 degrees and 60 degrees assume lower energy with respect to the others. In addition, we found a larger conformational freedom for the psi angle with respect to the straight phi angle.
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Affiliation(s)
- F Rossi
- Centro di Studio di Biocristallografia, CNR, and Dipartimento di Chimica, Università degli Studi di Napoli "Federico II," Via Mezzocannone 4, I-80134 Napoli, Italy
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12
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Ashish, Banumathi S, Velmurugan D, Anushree, Kishore R. Induced Conformational Preferences in a Non-chiral β-Ala Residue: X-ray Diffraction, 1H NMR, FT-IR and CD Studies of Boc-β-Ala-D-Ala-NHCH3 and Boc-β-Ala-L-Ala-NHCH3. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00862-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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DeGrado WF, Schneider JP, Hamuro Y. The twists and turns of beta-peptides. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 54:206-17. [PMID: 10517158 DOI: 10.1034/j.1399-3011.1999.00131.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recently, it has been discovered that peptides composed of beta-amino acids are capable of adopting novel secondary structures demonstrating that peptides composed of alpha-amino acids are not unique in their ability to fold into well-defined structures. Cyclic as well as acyclic peptides composed of beta-amino acid residues adopt turn, helical, and sheet-like conformations. Here, we discuss the synthesis and conformational preferences of individual, substituted beta-amino acids as well as the structures that peptides composed of these residues, beta-peptides, may adopt.
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Affiliation(s)
- W F DeGrado
- Department of Biochemistry and Biophysics, Johnson Research Foundation, School of Medicine, The University of Pennsylvania, Philadelphia 19104-6059, USA
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14
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Appella DH, Christianson LA, Karle IL, Powell DR, Gellman SH. Synthesis and Characterization of trans-2-Aminocyclohexanecarboxylic Acid Oligomers: An Unnatural Helical Secondary Structure and Implications for β-Peptide Tertiary Structure. J Am Chem Soc 1999. [DOI: 10.1021/ja990748l] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel H. Appella
- Contribution from the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1396, and Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
| | - Laurie A. Christianson
- Contribution from the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1396, and Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
| | - Isabella L. Karle
- Contribution from the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1396, and Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
| | - Douglas R. Powell
- Contribution from the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1396, and Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
| | - Samuel H. Gellman
- Contribution from the Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1396, and Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
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