1
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Aguilar MI, Yarovsky I. Quest for New Generation Biocompatible Materials: Tailoring β-Peptide Structure and Interactions via Synergy of Experiments and Modelling. J Mol Biol 2024:168646. [PMID: 38848868 DOI: 10.1016/j.jmb.2024.168646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Peptide-based self-assembly has been used to produce a wide range of nanostructures. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been shown to undergo supramolecular self-assembly, and have been used to produce materials for applications in tissue engineering, cell culture and drug delivery. In order to engineer new materials with specific structure and function, theoretical molecular modelling can provide significant insights into the collective balance of non-covalent interactions that drive the self-assembly and determine the structure of the resultant supramolecular materials under different conditions. However, this approach has only recently become feasible for peptide-based self-assembled nanomaterials, particularly those that incorporate non α-amino acids. This perspective provides an overview of the challenges associated with computational modelling of the self-assembly of β-peptides and the recent success using a combination of experimental and computational techniques to provide insights into the self-assembly mechanisms and fully atomistic models of these new biocompatible materials.
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Affiliation(s)
- Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia.
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2
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Day K, Schneible JD, Young AT, Pozdin VA, Van Den Driessche G, Gaffney LA, Prodromou R, Freytes DO, Fourches D, Daniele M, Menegatti S. Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. J Mater Chem B 2021; 8:7413-7427. [PMID: 32661544 DOI: 10.1039/d0tb01189d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The impact of next-generation biorecognition elements (ligands) will be determined by the ability to remotely control their binding activity for a target biomolecule in complex environments. Compared to conventional mechanisms for regulating binding affinity (pH, ionic strength, or chaotropic agents), light provides higher accuracy and rapidity, and is particularly suited for labile targets. In this study, we demonstrate a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins. Light triggers a cis/trans isomerization of the azobenzene, which results in a major structural rearrangement of the cyclic peptide from a non-binding to a binding configuration. Critical to this goal are the ability to achieve efficient photo-isomerization under low light dosage and the temporal stability of both cis and trans isomers. We demonstrated our method by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function. Starting from a known VCAM1-binding linear peptide, an ensemble of azobenzene-cyclized variants with selective light-controlled binding were identified by combining in silico design with experimental characterization via spectroscopy and surface plasmon resonance. Variant cycloAZOB[G-VHAKQHRN-K] featured rapid, light-controlled binding of VCAM1 (KD,trans/KD,cis ∼ 130). Biotin-cycloAZOB[G-VHAKQHRN-K] was utilized to label brain microvascular endothelial cells (BMECs), showing co-localization with anti-VCAM1 antibodies in cis configuration and negligible binding in trans configuration.
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Affiliation(s)
- Kevin Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina, USA.
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3
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Ishikawa M, Hamada K, Yamada Y, Kumai J, Katagiri F, Kikkawa Y, Nomizu M. Conformational dependence of integrin‐binding peptides derived from homologous loop regions in the laminin α chains. J Pept Sci 2020; 26:e3284. [DOI: 10.1002/psc.3284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/28/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Masaya Ishikawa
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
| | - Keisuke Hamada
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
| | - Yuji Yamada
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
| | - Jun Kumai
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
| | - Fumihiko Katagiri
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
| | - Yamato Kikkawa
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
| | - Motoyoshi Nomizu
- Department of Clinical Biochemistry School of Pharmacy, Tokyo University of Pharmacy and Life Sciences Tokyo Japan
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4
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Rinaldi S. The Diverse World of Foldamers: Endless Possibilities of Self-Assembly. Molecules 2020; 25:E3276. [PMID: 32708440 PMCID: PMC7397133 DOI: 10.3390/molecules25143276] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.
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Affiliation(s)
- Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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5
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Milbeo P, Simon M, Didierjean C, Wenger E, Aubert E, Martinez J, Amblard M, Calmès M, Legrand B. A bicyclic unit reversal to stabilize the 12/14-helix in mixed homochiral oligoureas. Chem Commun (Camb) 2020; 56:7921-7924. [DOI: 10.1039/d0cc02902e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Incorporation of highly constrained building blocks into oligoureas: a simple bicycle reversal leads to tunable 12/14-helices formation.
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Affiliation(s)
- Pierre Milbeo
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | | | | | | | - Jean Martinez
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Monique Calmès
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron
- IBMM
- University of Montpellier
- ENSCM
- CNRS
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6
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Christofferson AJ, Al-Garawi ZS, Todorova N, Turner J, Del Borgo MP, Serpell LC, Aguilar MI, Yarovsky I. Identifying the Coiled-Coil Triple Helix Structure of β-Peptide Nanofibers at Atomic Resolution. ACS NANO 2018; 12:9101-9109. [PMID: 30157375 DOI: 10.1021/acsnano.8b03131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peptide self-assembly represents a powerful bottom-up approach to the fabrication of nanomaterials. β3-Peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone, and we reported fibers derived from the self-assembly of β3-peptides that adopt 14-helical structures. β3-Peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. To develop structure-based criteria for the design of β3-peptide-based biomaterials with tailored function, we investigated the structure of a tri-β3-peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β3[LIA] in water and used to inform and validate the model structure. Models with 3-fold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macroscale fibers derived from β3-peptide-based materials provide valuable insight into the effects of the geometric placement of the side chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology.
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Affiliation(s)
| | - Zahraa S Al-Garawi
- School of Life Sciences , University of Sussex , Falmer , East Sussex BN1 9QG , U.K
- Chemistry Department , Mustansiriyah University , Baghdad Iraq
| | - Nevena Todorova
- School of Engineering , RMIT University , Melbourne , Victoria 3001 , Australia
| | - Jack Turner
- School of Life Sciences , University of Sussex , Falmer , East Sussex BN1 9QG , U.K
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Melbourne , Victoria 3800 , Australia
| | - Louise C Serpell
- School of Life Sciences , University of Sussex , Falmer , East Sussex BN1 9QG , U.K
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Melbourne , Victoria 3800 , Australia
| | - Irene Yarovsky
- School of Engineering , RMIT University , Melbourne , Victoria 3001 , Australia
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7
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Sun X, Li Y, Liu T, Li Z, Zhang X, Chen X. Peptide-based imaging agents for cancer detection. Adv Drug Deliv Rev 2017; 110-111:38-51. [PMID: 27327937 PMCID: PMC5235994 DOI: 10.1016/j.addr.2016.06.007] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 12/31/2022]
Abstract
Selective receptor-targeting peptide based agents have attracted considerable attention in molecular imaging of tumor cells that overexpress corresponding peptide receptors due to their unique properties such as rapid clearance from circulation as well as high affinities and specificities for their targets. The rapid growth of chemistry modification techniques has enabled the design and development of various peptide-based imaging agents with enhanced metabolic stability, favorable pharmacokinetics, improved binding affinity and selectivity, better imaging ability as well as biosafety. Among them, many radiolabeled peptides have already been translated into the clinic with impressive diagnostic accuracy and sensitivity. This review summarizes the current status in the development of peptide-based imaging agents with an emphasis on the consideration of probe design including the identification of suitable peptides, the chemical modification of probes and the criteria for clinical translation. Specific examples in clinical trials have been provided as well with respect to their diagnostic capability compared with other FDA approved imaging agents.
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Affiliation(s)
- Xiaolian Sun
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Yesen Li
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Ting Liu
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Zijing Li
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xianzhong Zhang
- Center for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, MD 20892, United States.
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8
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Uribe L, Gauss J, Diezemann G. Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides. J Phys Chem B 2015; 119:8313-20. [DOI: 10.1021/acs.jpcb.5b04044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lalita Uribe
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
- Graduate
School Materials Science in Mainz, Universität Mainz, Staudinger Weg
9, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut
für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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9
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Sharma GV, Venkateshwarlu G, Katukuri S, Ramakrishna KV, Sarma AV. Design and synthesis of novel oxetane β3-amino acids and α, β-peptides. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.02.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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10
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Gorham R, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive C, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. J Med Chem 2015; 58:814-26. [PMID: 25494040 PMCID: PMC4306506 DOI: 10.1021/jm501345y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 01/21/2023]
Abstract
Compstatin peptides are complement inhibitors that bind and inhibit cleavage of complement C3. Peptide binding is enhanced by hydrophobic interactions; however, poor solubility promotes aggregation in aqueous environments. We have designed new compstatin peptides derived from the W4A9 sequence (Ac-ICVWQDWGAHRCT-NH2, cyclized between C2 and C12), based on structural, computational, and experimental studies. Furthermore, we developed and utilized a computational framework for the design of peptides containing non-natural amino acids. These new compstatin peptides contain polar N-terminal extensions and non-natural amino acid substitutions at positions 4 and 9. Peptides with α-modified non-natural alanine analogs at position 9, as well as peptides containing only N-terminal polar extensions, exhibited similar activity compared to W4A9, as quantified via ELISA, hemolytic, and cell-based assays, and showed improved solubility, as measured by UV absorbance and reverse-phase HPLC experiments. Because of their potency and solubility, these peptides are promising candidates for therapeutic development in numerous complement-mediated diseases.
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Affiliation(s)
- Ronald
D. Gorham
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
| | - David L. Forest
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - George A. Khoury
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Consuelo N. Beecher
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Evangeline D. Healy
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Phanourios Tamamis
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Cynthia
K. Larive
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Christodoulos A. Floudas
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monte J. Radeke
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Lincoln V. Johnson
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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11
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Sharma GVM, Sridhar T, Veena B, Purushotham Reddy P, Reddy SV, Bruneau C, Kunwar AC. Synthesis and conformational studies of α/β2,3-peptides derived from alternating β2,3-amino acids and l-Ala repeats. NEW J CHEM 2015. [DOI: 10.1039/c4nj02031f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new class of α/β2,3-peptides were synthesized from C-linked carbo-β2,3-amino acids (β2,3-Caas) and investigated to understand the impact of the side chains (allyl/propargyl) at the Cα-position on their conformations.
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Affiliation(s)
- Gangavaram V. M. Sharma
- Organic and Biomolecular Chemistry Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500 007
- India
| | - Tailor Sridhar
- Organic and Biomolecular Chemistry Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500 007
- India
| | - Bacchu Veena
- Organic and Biomolecular Chemistry Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500 007
- India
| | - Pothula Purushotham Reddy
- Centre for Nuclear Magnetic Resonance and Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500 007
- India
| | - Sheri Venkata Reddy
- Organic and Biomolecular Chemistry Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500 007
- India
| | | | - Ajit C. Kunwar
- Centre for Nuclear Magnetic Resonance and Structural Chemistry
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500 007
- India
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12
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Németh LJ, Hegedüs Z, Martinek TA. Predicting Order and Disorder for β-Peptide Foldamers in Water. J Chem Inf Model 2014; 54:2776-83. [DOI: 10.1021/ci5003476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lukács J. Németh
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6, H-6720 Szeged, Hungary
| | - Zsófia Hegedüs
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6, H-6720 Szeged, Hungary
| | - Tamás A. Martinek
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6, H-6720 Szeged, Hungary
- Institute
of Pharmaceutical Chemistry, University of Szeged, Eötvös
u. 6, H-6720 Szeged, Hungary
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13
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Sharma GVM, Thodupunuri P, Sirisha K, Basha SJ, Gurava Reddy P, Sarma AVS. Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study. J Org Chem 2014; 79:8614-28. [PMID: 25180942 DOI: 10.1021/jo501267k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
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14
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Sharma GVM, Yadav TA, Marumudi K, Thodupunuri P, Reddy PP, Kunwar AC. Three-Residue Turn in β-Peptides Nucleated by a 12/10 Helix. Chem Asian J 2014; 9:3153-62. [DOI: 10.1002/asia.201402465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 01/07/2023]
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15
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Kiss L, Fülöp F. Synthesis of carbocyclic and heterocyclic β-aminocarboxylic acids. Chem Rev 2013; 114:1116-69. [PMID: 24299148 DOI: 10.1021/cr300454h] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Loránd Kiss
- Institute of Pharmaceutical Chemistry, University of Szeged , H-6720 Szeged, Eötvös utca 6, Hungary
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16
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Kiss L, Nonn M, Sillanpää R, Fustero S, Fülöp F. Efficient regio- and stereoselective access to novel fluorinated β-aminocyclohexanecarboxylates. Beilstein J Org Chem 2013; 9:1164-9. [PMID: 23843909 PMCID: PMC3701410 DOI: 10.3762/bjoc.9.130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/21/2013] [Indexed: 11/26/2022] Open
Abstract
A regio- and stereoselective method has been developed for the synthesis of novel fluorinated 2-aminocyclohexanecarboxylic acid derivatives with the fluorine attached to position 4 of the ring. The synthesis starts from either cis- or trans-β-aminocyclohex-4-enecarboxylic acids and involves regio- and stereoselective transformation of the ring C–C double bond through iodooxazine formation and hydroxylation, followed by hydroxy–fluorine or oxo–fluorine exchange.
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Affiliation(s)
- Loránd Kiss
- University of Szeged, Institute of Pharmaceutical Chemistry, Szeged, Hungary
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17
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Sharma GVM, Sridhar T, Reddy PP, Kunwar AC. Synthesis and Structural Studies of α/β-Peptides Derived from Fused Furano-pyran β-Amino Acid and L-Ala. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Cherepanova M, Kiss L, Sillanpää R, Fülöp F. Synthesis of novel functionalized cispentacins through C–C oxidative cleavage of diendo-norbornene β-amino acid. RSC Adv 2013. [DOI: 10.1039/c3ra41963k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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19
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Kiss L, Cherepanova M, Forró E, Fülöp F. A New Access Route to Functionalized Cispentacins from Norbornene β-Amino Acids. Chemistry 2012; 19:2102-7. [DOI: 10.1002/chem.201203183] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/13/2012] [Indexed: 01/30/2023]
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20
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Sharma GVM, Yadav TA, Choudhary M, Kunwar AC. Design of β-Amino Acid with Backbone–Side Chain Interactions: Stabilization of 14/15-Helix in α/β-Peptides. J Org Chem 2012; 77:6834-48. [DOI: 10.1021/jo300865d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Gangavaram V. M. Sharma
- Organic and
Biomolecuar Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Thota Anupama Yadav
- Organic and
Biomolecuar Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Madavi Choudhary
- Centre for Nuclear Magnetic Resonance, CSIR-Indian Institute of Chemical Technology, Hyderabad
500 007, India
| | - Ajit C. Kunwar
- Centre for Nuclear Magnetic Resonance, CSIR-Indian Institute of Chemical Technology, Hyderabad
500 007, India
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21
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McGovern M, Abbott N, de Pablo JJ. Dimerization of helical β-peptides in solution. Biophys J 2012; 102:1435-42. [PMID: 22455927 PMCID: PMC3309405 DOI: 10.1016/j.bpj.2011.12.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 12/02/2011] [Accepted: 12/27/2011] [Indexed: 11/22/2022] Open
Abstract
Molecular simulations are used to examine the aggregation behavior of several β-peptides in explicit water. The particular peptides considered here adopt a helical, rodlike conformation in aqueous solution. Four distinct molecular sequences are considered. Earlier experimental studies have revealed the formation of ordered and disordered aggregates for such molecules, depending on sequence. The simulations reported here, which are conducted by resorting to metadynamics techniques, lead to free energy surfaces for dimerization of the peptides in water as a function of separation and relative orientation. Such surfaces are used to identify the molecular origins for the behaviors observed in the experiments.
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Affiliation(s)
- Michael McGovern
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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22
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André C, Legrand B, Deng C, Didierjean C, Pickaert G, Martinez J, Averlant-Petit MC, Amblard M, Calmes M. (S)-ABOC: A Rigid Bicyclic β-Amino Acid as Turn Inducer. Org Lett 2012; 14:960-3. [DOI: 10.1021/ol203406v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christophe André
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Cheng Deng
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Claude Didierjean
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Guillaume Pickaert
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Marie Christine Averlant-Petit
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
| | - Monique Calmes
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-UM1-UM2, Faculté de pharmacie, 15 Avenue Charles Flahault, 34093 Montpellier, France, Laboratoire de Chimie-Physique Macromoléculaire, UMR 7568 CNRS-Université de Lorraine, 1 rue Grandville, 54001 Nancy Cedex 1, France, and Laboratoire de Cristallographie, Résonance Magnétique et Modélisation, UMR 7036 CNRS-Université de Lorraine, Boulevard des Aiguillettes, 54506 Vandoeuvre-Lès-Nancy Cedex, France
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23
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Sharma GVM, Reddy NY, Ravi R, Sreenivas B, Sridhar G, Chatterjee D, Kunwar AC, Hofmann HJ. Synthesis of C-linked carbo-β2-amino acids and β2-peptides: design of new motifs for left-handed 12/10- and 10/12-mixed helices. Org Biomol Chem 2012; 10:9191-203. [DOI: 10.1039/c2ob26615f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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24
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Reddy BS, Reddy AB, Reddy GR, Reddy PR. Synthesis and Antibacterial Activity of Novel [3-(4-substitutedphenylamino)-8-azabicyclo [3.2.1] oct-8yl]-phenyl-methanone Derivatives. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2011. [DOI: 10.5012/jkcs.2011.55.6.969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Shandler SJ, Korendovych IV, Moore DT, Smith-Dupont KB, Streu CN, Litvinov RI, Billings PC, Gai F, Bennett JS, DeGrado WF. Computational design of a β-peptide that targets transmembrane helices. J Am Chem Soc 2011; 133:12378-81. [PMID: 21780757 PMCID: PMC3155016 DOI: 10.1021/ja204215f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design of β-peptide foldamers targeting the transmembrane (TM) domains of complex natural membrane proteins has been a formidable challenge. A series of β-peptides was designed to stably insert in TM orientations in phospholipid bilayers. Their secondary structures and orientation in the phospholipid bilayer was characterized using biophysical methods. Computational methods were then devised to design a β-peptide that targeted a TM helix of the integrin α(IIb)β(3). The designed peptide (β-CHAMP) interacts with the isolated target TM domain of the protein and activates the intact integrin in vitro.
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Affiliation(s)
- Scott J. Shandler
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ivan V. Korendovych
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - David T. Moore
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Department of Hematology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kathryn B. Smith-Dupont
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Craig N. Streu
- Department of Hematology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Rustem I. Litvinov
- Department of Hematology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Paul C. Billings
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joel S. Bennett
- Department of Hematology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - William F. DeGrado
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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26
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Nonn M, Kiss L, Forró E, Mucsi Z, Fülöp F. Synthesis of novel isoxazoline-fused cyclic β-amino esters by regio- and stereo-selective 1,3-dipolar cycloaddition. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Soengas RG, Estévez AM, Estévez JC, Estévez RJ. An overview on the synthesis of furanoid and pyranoid sugar α- and β-amino acids and related aminocycloalkanecarboxylic acids from carbohydrates. CR CHIM 2011. [DOI: 10.1016/j.crci.2010.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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28
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Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids. J Comput Chem 2010; 31:2063-77. [PMID: 20175215 DOI: 10.1002/jcc.21493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All-atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic beta-amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using beta(3)-homo-Alanine (beta(3)-hAla) diamide in water with SCC-DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the beta(3)-hAla diamide in water. The MM model is further applied to a beta-hepta-peptide in methanol solution. The calculated NOE values and (3)J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non-natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of beta amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that beta-amino-acid based random copolymers can develop a high degree of amphiphilicity without regular three-dimensional structure.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, Wisconsin 53706, USA
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29
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Synthesis of conformationally restricted 1,2,3-triazole-substituted ethyl β- and γ-aminocyclopentanecarboxylate stereoisomers. Multifunctionalized alicyclic amino esters. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Mondal J, Sung BJ, Yethiraj A. Sequence dependent self-assembly of β-peptides: Insights from a coarse-grained model. J Chem Phys 2010; 132:065103. [DOI: 10.1063/1.3314309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Kazi B, Kiss L, Forró E, Fülöp F. Synthesis of orthogonally protected azepane β-amino ester enantiomers. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2009.10.072] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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James WH, Baquero EE, Choi SH, Gellman SH, Zwier TS. Laser Spectroscopy of Conformationally Constrained α/β-Peptides: Ac-ACPC-Phe-NHMe and Ac-Phe-ACPC-NHMe. J Phys Chem A 2009; 114:1581-91. [PMID: 20039717 DOI: 10.1021/jp9090975] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William H. James
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Esteban E. Baquero
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Soo Hyuk Choi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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33
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Srivastava R, Kumar Ray A, Diederichsen U. Higher Aggregation of β-Peptide Networks Controlled by Nucleobase Pairing. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900511] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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34
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Sussman F, Villaverde MC, Estévez JC, Estévez RJ. Searching the Conformational Space of Cyclic β-Amino Acid Peptides. J Phys Chem B 2009; 113:9669-80. [DOI: 10.1021/jp811321n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fredy Sussman
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Carmen Villaverde
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan Carlos Estévez
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ramón J. Estévez
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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35
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Mondal J, Sung BJ, Yethiraj A. Sequence-Directed Organization of β-Peptides in Self-Assembled Monolayers. J Phys Chem B 2009; 113:9379-85. [DOI: 10.1021/jp903341u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jagannath Mondal
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Bong June Sung
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
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36
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Miller CA, Gellman SH, Abbott NL, de Pablo JJ. Association of helical beta-peptides and their aggregation behavior from the potential of mean force in explicit solvent. Biophys J 2009; 96:4349-62. [PMID: 19486660 PMCID: PMC2711497 DOI: 10.1016/j.bpj.2008.11.076] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 11/20/2008] [Accepted: 11/24/2008] [Indexed: 11/19/2022] Open
Abstract
Helical beta-peptides have been shown to fold into well-defined structures. In aqueous solution, some beta-peptides self-assemble into nanoscale fibers, aggregates, and liquid crystalline phases. Molecular simulations, at an atomistic level, are used to examine, in a systematic manner, the interactions between distinct beta-peptide molecules. The relationship between side-chain chemistry (and position along the backbone) and, in particular, aggregation behaviors, is assessed by calculating the potential of mean force or dimerization free energy of two peptides in explicit water. The free energy profiles as a function of separation for helical, amphiphilic beta-peptides are consistent with experimental observations, and help explain the origins of aggregate or fiber formation in solution. Close examination of the energetic and entropic contributions to the free energy reveals that, depending on the position of certain side groups along the molecule, the tendency of two peptides to aggregate can be driven by entropy or by energy, respectively. In contrast to findings from previous works that employed a coarse representation of the solvent, it is shown that water-peptide interactions play key roles in the association behavior of beta-peptides.
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Affiliation(s)
- Clark A. Miller
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Juan J. de Pablo
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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37
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Kiss L, Nonn M, Forró E, Sillanpää R, Fülöp F. Synthesis of novel isoxazoline-fused cispentacin stereoisomers. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.119] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Miller CA, Abbott NL, de Pablo JJ. Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:2811-2823. [PMID: 19437698 DOI: 10.1021/la802973e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The surface activity of beta-peptides is investigated using molecular simulations. The type and display of hydrophobic and hydrophilic groups on helical beta-peptides is varied systematically. Peptides with 2/3 hydrophobic groups are found to be surface active, and to adopt an orientation parallel to the air-water interface. For select beta-peptides, we also determine the potential of mean force required to bring a peptide to the air-water interface. Facially amphiphilic helices with 2/3 hydrophobic groups are found to exhibit the lowest free energy of adsorption. The adsorption process is driven by a favorable energetic term and opposed by negative entropic changes. The temperature dependence of adsorption is also investigated; facially amphiphilic helices are found to adopt orientations that are largely independent of temperature, while nonfacially amphiphilic helices sample a broader range of interfacial orientations at elevated temperatures. The thermodynamics of adsorption of beta-peptides is compared to that of 1-octanol, a well-known surfactant, and ovispirin, a naturally occurring antimicrobial peptide. It is found that the essential difference lies in the sign of the entropy of adsorption, which is negative for beta- and alpha-peptides and positive for traditional surfactants such as octanol.
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Affiliation(s)
- Clark A Miller
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA
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39
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Novel functionalized cispentacin derivatives. Synthesis of 1,2,3-triazole-substituted 2-aminocyclopentanecarboxylate stereoisomers. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.11.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Miller CA, Gellman SH, Abbott NL, de Pablo JJ. Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models. Biophys J 2008; 95:3123-36. [PMID: 18621835 PMCID: PMC2547455 DOI: 10.1529/biophysj.108.134833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 05/14/2008] [Indexed: 11/18/2022] Open
Abstract
Synthetic beta-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of beta-peptides is greater than that of alpha-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical beta-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water.
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Affiliation(s)
- Clark A Miller
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA
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41
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Miller CA, Hernández-Ortiz JP, Abbott NL, Gellman SH, de Pablo JJ. Dipole-induced self-assembly of helical beta-peptides. J Chem Phys 2008; 129:015102. [PMID: 18624501 DOI: 10.1063/1.2928700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, the interactions between beta-peptides are investigated for helix-forming peptides using molecular simulation. The role of electrostatic interactions in the self-assembly of these peptides is studied by calculating the dipole moment of various 14-helical beta-peptides using molecular dynamics simulations. The stability of a beta-peptide that is known to form a liquid crystalline phase is determined by calculating the potential of mean force using the expanded ensemble density of states method. This peptide is found to form a mechanically stable 14-helix in an implicit solvent model. The interaction between two of these peptides is examined by calculating the potential of mean force between the two peptides in implicit solvent. The peptides are shown to favorably associate in an end-to-end manner, driven largely by dipolar interactions. In order to understand the possible structures that form when many peptides interact in solution, a coarse-grained model is developed. Brownian dynamics simulations of the coarse-grained model at intermediate concentrations (1-50 mM) are performed, and the aggregation behavior is understood by calculating the diffusivity and the radial distribution function. An analysis of the resultant structures reveals that the coarse-grained model of the peptide leads to the formation of spherical clusters.
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Affiliation(s)
- Clark A Miller
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706-1691, USA
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Jones C, Qureshi M, Truscott F, Hsu ST, Morrison A, Smith M. A Nonpeptidic Reverse Turn that Promotes Parallel Sheet Structure Stabilized by CH⋅⋅⋅O Hydrogen Bonds in a Cyclopropane γ-Peptide. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802648] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Jones C, Qureshi M, Truscott F, Hsu ST, Morrison A, Smith M. A Nonpeptidic Reverse Turn that Promotes Parallel Sheet Structure Stabilized by CH⋅⋅⋅O Hydrogen Bonds in a Cyclopropane γ-Peptide. Angew Chem Int Ed Engl 2008; 47:7099-102. [DOI: 10.1002/anie.200802648] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue. J Phys Chem B 2008; 112:5439-48. [PMID: 18402479 DOI: 10.1021/jp077601y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All-atom molecular mechanical (MM) force field parameters are developed for a cyclic beta-amino acid, amino-cyclo-pentane-carboxylic acid (ACPC), using a multi-objective evolutionary algorithm. The MM model is benchmarked using several short, ACPC-containing alpha/beta-peptides in water and methanol with SCC-DFTB (self consistent charge-density functional tight binding)/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the tetra-alpha/beta-peptide in water. For the octa-alpha/beta-peptide in methanol, the MM and SCC-DFTB/MM simulations predict the 11- and 14/15-helical form as the more stable conformation, respectively; however, the two helical forms are very close in energy (2-4 kcal/mol) at both theoretical levels, which is also the conclusion from recent NMR experiments. As the first application, the MM model is applied to an alpha/beta-pentadeca-peptide in water with both explicit and implicit solvent models. The stability of the peptide is sensitive to the starting configuration in the explicit solvent simulations due to their limited length ( approximately 10-40 ns). Multiple ( approximately 20 x 20 ns) implicit solvent simulations consistently show that the 14/15-helix is the predominant conformation of this peptide, although substantially different conformations are also accessible. The calculated nuclear Overhauser effect (NOE) values averaged over different trajectories are consistent with experimental data, which emphasizes the importance of considering conformational heterogeneity in such comparisons for highly dynamical peptides.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Theoretical Chemistry Institute, The BACTER Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wiconsin 53706, USA
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Kiss L, Forró E, Sillanpää R, Fülöp F. Diastereo- and Enantioselective Synthesis of Orthogonally Protected 2,4-Diaminocyclopentanecarboxylates: A Flip from β-Amino- to β,γ-Diaminocarboxylates. J Org Chem 2007; 72:8786-90. [DOI: 10.1021/jo701332v] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Loránd Kiss
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
| | - Enikó Forró
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
| | - Reijo Sillanpää
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
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Abstract
Homo- and heterochiral tetrameric gamma-peptide derivatives in which the backbone is constrained by a five-membered ring populate a bend-ribbon conformation in solution stabilized by intramolecular hydrogen bonds.
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Affiliation(s)
- Abhishek Kothari
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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