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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Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 DOI: 10.3390/biom13060981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
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Affiliation(s)
- Tarsila G Castro
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristina E A Sousa
- BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Artur Cavaco-Paulo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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3
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Zhang X, Ligny R, Chewchanwuttiwong S, Hadade R, Laurent MY, Martel A, Jacquemmoz C, Lhoste J, Bricaud S, Py S, Dujardin G. δ-Valerolactamic Quaternary Amino Acid Derivatives: Enantiodivergent Synthesis and Evidence for Stereodifferentiated β-Turn-Inducing Properties. J Org Chem 2021; 86:8041-8055. [PMID: 33960779 DOI: 10.1021/acs.joc.1c00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Enantiopure (R) and (S) cyclic α,α-disubstituted amino acid derivatives displaying a δ-valerolactam side chain were prepared from a common isoxazolidine precursor. The (R)-configured δ-valerolactam 11 was converted into diastereoisomeric pseudopeptides to investigate its ability to induce secondary structures in peptidomimetics. Conformational studies of these pseudopeptides were carried out in the solid state (X-ray diffraction), in solution (NMR analyses), and in silico (computer-aided conformational analysis), which demonstrated that such quaternary amino acids induce β-turn conformations stable enough to be retained in polar media (DMSO). Incorporation of this new type of α,α-disubstituted amino acid into a representative pseudopeptidic sequence by N- then C-elongation and N-debenzylation is also described herein and could serve for the synthesis of various structured peptidomimetics.
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Affiliation(s)
- Xiaofei Zhang
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France.,Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France.,CNRS, DCM, F-38000 Grenoble, France
| | - Romain Ligny
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Sopa Chewchanwuttiwong
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France.,Prince of Songkla University, Faculty of Science and Industrial Technology Surat Thani 84000, Thailand
| | - Rawan Hadade
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Mathieu Y Laurent
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Arnaud Martel
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Corentin Jacquemmoz
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Jérôme Lhoste
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Sullivan Bricaud
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
| | - Sandrine Py
- Univ. Grenoble Alpes, DCM, F-38000 Grenoble, France.,CNRS, DCM, F-38000 Grenoble, France
| | - Gilles Dujardin
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRS-Le Mans Université, Equipe Méthodologie et Synthèse Organique, F-72085 Le Mans Cedex 09, France
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4
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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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5
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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6
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [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] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- 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, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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7
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Ruffoni A, Cavanna MV, Argentiere S, Locarno S, Pellegrino S, Gelmi ML, Clerici F. Aqueous self-assembly of short hydrophobic peptides containing norbornene amino acid into supramolecular structures with spherical shape. RSC Adv 2016. [DOI: 10.1039/c6ra17116h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The preparation and self-assembly of short hydrophobic peptides containing the non-coded norbornene amino acid is reported. The formation of a supramolecular assembly in water was assessed by TEM and DLS.
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Affiliation(s)
- Alessandro Ruffoni
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | | | | | - Silvia Locarno
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Sara Pellegrino
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Maria Luisa Gelmi
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Francesca Clerici
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
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8
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Žukauskaitė A, Moretto A, Peggion C, De Zotti M, Šačkus A, Formaggio F, De Kimpe N, Mangelinckx S. Synthesis and Conformational Study of Model Peptides ContainingN-Substituted 3-Aminoazetidine-3-carboxylic Acids. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301741] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Revilla-López G, Torras J, Nussinov R, Alemán C, Zanuy D. Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide. Phys Chem Chem Phys 2011; 13:9986-94. [PMID: 21258721 PMCID: PMC7385989 DOI: 10.1039/c0cp02572k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently a new non-coded amino acid was designed as a replacement for Arg, to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This constrained Arg analog, denoted c(5)Arg, was engineered to also promote the stability of the CREKA bioactive conformation. The conformational profile of the CREKA analog obtained by replacing Arg by c(5)Arg has been extensively investigated in this work. Two molecular dynamics simulations-based strategies have been employed: a modified simulated annealing and replica exchange. Results obtained using both techniques show that the conformational features of the new analog fulfill the purpose of its design. The new CREKA analog not only preserves the main structural attributes found for the bioactive conformation of the parent peptide but also shows lower flexibility. Moreover, the conformational profile of the mutated peptide narrows towards the most stable structures previously observed for the parent CREKA peptide.
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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
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10
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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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11
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Warren JG, Revilla-López G, Alemán C, Jiménez AI, Cativiela C, Torras J. Conformational preferences of proline analogues with a fused benzene ring. J Phys Chem B 2011; 114:11761-70. [PMID: 20722365 DOI: 10.1021/jp105456r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of indoline-2-carboxylic acid (Inc) and its α-methylated derivative (αMeInc) have been investigated using quantum mechanical calculations. Specifically, the behavior of their N-acetyl-N'-methylamide derivatives, Ac-L-Inc-NHMe and Ac-L-αMeInc-NHMe, has been explored at the B3LYP/6-31+G(d,p) level. Such amino acids are analogues of proline and (α-methyl)proline, respectively, bearing a benzene ring fused to the C(γ)-C(δ) bond of the five-membered pyrrolidine ring. The additional aromatic group has been shown to significantly restrict the conformational space available to these residues by reducing the flexibility of both the five-membered cycle and the peptide backbone. The fused benzene ring also plays a critical role in determining the cis-trans arrangement of the amide bond involving the pyrrolidine nitrogen, which is also modulated by the presence of the α-methyl group in the αMeInc derivative. Furthermore, the influence of the environment on the conformational propensities of these compounds has been evaluated by using both a self-consistent reaction field model and a recently developed interface in a hybrid QM/MM scheme, in which the solvent molecules are treated explicitly with classical mechanics while the solute is described by quantum mechanics at the density functional theory level.
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Affiliation(s)
- Javier G Warren
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
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12
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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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