1
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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [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: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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2
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Bellotto O, D'Andrea P, Marchesan S. Nanotubes and water-channels from self-assembling dipeptides. J Mater Chem B 2023. [PMID: 36790014 DOI: 10.1039/d2tb02643k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging.
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Affiliation(s)
- Ottavia Bellotto
- Chem. Pharm. Sc. Dept., University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy.
| | - Paola D'Andrea
- Life Sc. Dept., University of Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Silvia Marchesan
- Chem. Pharm. Sc. Dept., University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy. .,INSTM, Unit of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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3
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Mayorquín-Torres MC, Navarro-Huerta A, Maldonado-Domínguez M, Flores-Álamo M, Rodríguez-Molina B, Iglesias-Arteaga MA. Palladium-Catalyzed Generation of ortho-Quinone Methides. A Three-Component Synthesis of L-Shaped Dimeric Steroidal Scaffolds. J Org Chem 2021; 86:4112-4120. [PMID: 33594882 DOI: 10.1021/acs.joc.0c02943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of hybrid dimers having orthogonal steroidal cores bridged by a chroman ketal moiety were obtained by Pd-catalyzed three-component reactions of steroid alkynols, 2-formylestradiol 17-monoacetate, and methyl orthoformate, via ortho-quinone methide intermediates. One of the obtained L-shaped scaffolds showed an inefficient crystal packing featuring large channels within the crystal array. Monte Carlo simulations indicate that these voids preferentially allocate n-hexane, opening the way to explore further applications of similar organic crystalline materials as selective hosts for small molecules.
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Affiliation(s)
- Martha C Mayorquín-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Armando Navarro-Huerta
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Marcos Flores-Álamo
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Braulio Rodríguez-Molina
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 Ciudad de México, México
| | - Martín A Iglesias-Arteaga
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, México
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4
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Cyclo(DAA-DAA) dipeptide as a peptide linker and β-sheet inducer. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Czapla M, Freza S. Functionalized ACC molecule as an effective peptide clasp. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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6
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Light-driven topochemical polymerization under organogel conditions of a symmetrical dipeptide-diacetylene system. J Pept Sci 2016; 23:155-161. [DOI: 10.1002/psc.2941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 01/03/2023]
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7
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Crisma M, Toniolo C. Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids. Biopolymers 2016; 104:46-64. [PMID: 25363510 DOI: 10.1002/bip.22581] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/14/2014] [Accepted: 10/24/2014] [Indexed: 01/09/2023]
Abstract
The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131, Padova, Italy
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8
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Mazzier D, Carraro F, Crisma M, Rancan M, Toniolo C, Moretto A. A terminally protected dipeptide: from crystal structure and self-assembly, through co-assembly with carbon-based materials, to a ternary catalyst for reduction chemistry in water. SOFT MATTER 2016; 12:238-245. [PMID: 26463728 DOI: 10.1039/c5sm02189h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A terminally protected, hydrophobic dipeptide Boc-L-Cys(Me)-L-Leu-OMe (1) was synthesized and its 3D-structure was determined by single crystal X-ray diffraction analysis. This peptide is able to hierarchically self-assemble in a variety of superstructures, including hollow rods, ranging from the nano- to the macroscale, and organogels. In addition, 1 is able to drive fullerene (C60) or multiwalled carbon nanotubes (MWCNTs) in an organogel by co-assembling with them. A hybrid 1-C60–MWCNT organogel was prepared and converted (through a high vacuum-drying process) into a robust, high-volume, water insoluble, solid material where C60 is well dispersed over the entire superstructure. This ternary material was successfully tested as a catalyst for: (i) the reduction reaction of water-soluble azo compounds mediated by NaBH4 and UV-light with an overall performance remarkably better than that provided by C60 alone, and (ii) the NaBH4-mediated reduction of benzoic acid to benzyl alcohol. Our results suggest that the self-assembly properties of 1 might be related to the occurrence in its single crystal structure of a sixfold screw axis, a feature shared by most of the linear peptides known so far to give rise to nanotubes.
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Affiliation(s)
- Daniela Mazzier
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
| | - Francesco Carraro
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Marzio Rancan
- Institute for Energetics and Interphases, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy. and Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Alessandro Moretto
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy. and Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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9
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Raghavender US, Chatterjee B, Saha I, Rajagopal A, Shamala N, Balaram P. Entrapment of a Water Wire in a Hydrophobic Peptide Channel with an Aromatic Lining. J Phys Chem B 2011; 115:9236-43. [DOI: 10.1021/jp200462h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Bhaswati Chatterjee
- Department of Physics, ‡Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Indranil Saha
- Department of Physics, ‡Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Appavu Rajagopal
- Department of Physics, ‡Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Narayanaswamy Shamala
- Department of Physics, ‡Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Padmanabhan Balaram
- Department of Physics, ‡Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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10
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Jiménez AI, Vaquero V, Cabezas C, López JC, Cativiela C, Alonso JL. The Singular Gas-Phase Structure of 1-Aminocyclopropanecarboxylic Acid (Ac3c). J Am Chem Soc 2011; 133:10621-8. [DOI: 10.1021/ja2033603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana I. Jiménez
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - Vanesa Vaquero
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cabezas
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Juan C. López
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cativiela
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - José L. Alonso
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
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11
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Revilla-López G, Rodríguez-Ropero F, Curcó D, Torras J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database. Proteins 2011; 79:1841-52. [PMID: 21491493 PMCID: PMC3092812 DOI: 10.1002/prot.23009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/22/2011] [Accepted: 01/28/2011] [Indexed: 01/16/2023]
Abstract
Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Francisco Rodríguez-Ropero
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EEI, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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12
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Dutta A, Drew M, Pramanik A. Amyloid-Like Fibrillogenesis through Supramolecular Helix-Mediated Self-Assembly of Tetrapeptides Containing Non-Coded α-Aminoisobutyric Acid (Aib) and 3-Aminobenzoic Acid (m-ABA). Helv Chim Acta 2010. [DOI: 10.1002/hlca.200900335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Revilla-López G, Torras J, Curcó D, Casanovas J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Grodzinski P, Alemán C. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. J Phys Chem B 2010; 114:7413-22. [PMID: 20455555 PMCID: PMC2896893 DOI: 10.1021/jp102092m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/ Jaume II n°69, Lleida E-25001, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Piotr Grodzinski
- Alliance for Nanotechnology in Cancer, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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14
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Alfonso I, Bru M, Burguete MI, García-Verdugo E, Luis S. Structural Diversity in the Self-Assembly of Pseudopeptidic Macrocycles. Chemistry 2010; 16:1246-55. [DOI: 10.1002/chem.200902196] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Yang Y, Xue M, Chen CF. Nanotoroidal tubule assembled from a functionalized oxacalix[4]arene. CrystEngComm 2010. [DOI: 10.1039/b927446d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Alemán C, Jiménez AI, Cativiela C, Nussinov R, Casanovas J. Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue. J Org Chem 2009; 74:7834-43. [PMID: 19772338 PMCID: PMC2771318 DOI: 10.1021/jo901594e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of the restricted phenylalanine analogue generated by including the alpha and beta carbon atoms into a cyclohexane ring (1-amino-2-phenylcyclohexanecarboxylic acid, c(6)Phe) have been determined using quantum mechanical calculations. Specifically, the conformational profile of the N-acetyl-N'-methylamide derivative of the c(6)Phe stereoisomers exhibiting either a cis or a trans relative orientation between the amino and phenyl substituents has been analyzed in different environments (gas phase, chloroform, and aqueous solutions). Calculations were performed using B3LYP, MP2, and HF methods combined with the 6-31+G(d,p) and 6-311++G(d,p) basis sets, and a self-consistent reaction-field (SCRF) method was applied to analyze the influence of the solvent. The amino acids investigated can be viewed as constrained phenylalanine analogues with a rigidly oriented aromatic side chain that may interact with the peptide backbone not only sterically but also electronically through the aromatic pi orbitals. Their conformational propensities have been found to be strongly influenced by the specific orientation of the aromatic substituent in each stereoisomer and the conformation adopted by the cyclohexane ring, as well as by the environment.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n 69, Lleida E-25001, Spain
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Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 2009; 49:1623-9. [PMID: 19548653 DOI: 10.1021/ci9001487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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18
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Revilla-López G, Torras J, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue. J Org Chem 2009; 74:2403-12. [PMID: 19236034 PMCID: PMC2682113 DOI: 10.1021/jo802704h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of the nonproteinogenic amino acids constructed by incorporating the arginine side chain in the beta position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated by using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c(5)Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N'-methylamide derivatives of cis- and trans-c(5)Arg have been examined in the gas phase and in solution by using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
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Di Giacomo M, Vinci V, Serra M, Colombo L. New fast and practical method for the enantioselective synthesis of α-vinyl, α-alkyl quaternary α-amino acids. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2007.12.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Nagarkar RP, Schneider JP. Synthesis and primary characterization of self-assembled peptide-based hydrogels. Methods Mol Biol 2008; 474:61-77. [PMID: 19031061 PMCID: PMC2650242 DOI: 10.1007/978-1-59745-480-3_5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Hydrogels based on peptide self-assembly form an important class of biomaterials that find application in tissue engineering and drug delivery. It is essential to prepare peptides with high purity to achieve batch-to-batch consistency affording hydrogels with reproducible properties. Automated solid-phase peptide synthesis coupled with optimized Fmoc (9-fluorenylmethoxy-carbonyl) chemistry to obtain peptides in high yield and purity is discussed. Details of isolating a desired peptide from crude synthetic mixtures and assessment of the peptide's final purity by high-performance liquid chromatography and mass spectrometry are provided. Beyond the practical importance of synthesis and primary characterization, techniques used to investigate the properties of hydrogels are briefly discussed.
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Affiliation(s)
- Radhika P Nagarkar
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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Biron E, Voyer N. Towards sequence selective DNA binding: design, synthesis and DNA binding studies of novel bis-porphyrin peptidic nanostructures. Org Biomol Chem 2008; 6:2507-15. [DOI: 10.1039/b803281e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Maity P, König B. Enantio- and diastereoselective syntheses of cyclic Cα-tetrasubstituted α-amino acids and their use to induce stable conformations in short peptides. Biopolymers 2007; 90:8-27. [DOI: 10.1002/bip.20902] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Baillargeon P, Bernard S, Gauthier D, Skouta R, Dory YL. Efficient Synthesis and Astonishing Supramolecular Architectures of Several Symmetric Macrolactams. Chemistry 2007; 13:9223-35. [PMID: 17886846 DOI: 10.1002/chem.200700522] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The synthesis of four C(n) symmetric macrocyclic lactams cyclo-[NH-CH(2)-CH=CH-CH(2)-CO](n) (1, n=2; 2, n=3; 3, n=4) and cyclo-[NH-CH(2)-CH(2)-CH=CH-CO](3) (4) has been achieved by two approaches. A linear route leads to precursors that are subsequently macrocyclized in a separate step. The second, convergent approach relies on the symmetry of the targets: it includes suitably activated subunits, which are subjected to macrocyclization conditions. The subunits first oligomerize, then cyclize to form either pure macrolactams or mixtures. The macrolactam units 1, 2 and 4 stack on top each other through weak interactions (hydrogen bond and van der Waals), to form endless square, rectangular and triangular prisms, respectively. These stacks are further packed side by side in crystals grown from isotropic media. The overall dipoles in the crystals from lactams 1 and 4, which result mostly from the alignment of amide groups, are zero and large, respectively. Macrolactam 2 displays an astonishing isomorphism when allowed to cool down in anisotropic liquid crystal solutions. Large hollow hexagonal tubes are then obtained through a fractal process. Contrary to the three previous rings, 3 yields crystals where prisms of any shape are absent.
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Affiliation(s)
- Pierre Baillargeon
- Laboratoire de Synthèse Supramoléculaire, Département de Chimie, Institut de Pharmacologie, Université de Sherbooke, Québec, Canada
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