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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Park J, Lee HS, Kim H, Choi JM. Conformational landscapes of artificial peptides predicted by various force fields: are we ready to simulate β-amino acids? Phys Chem Chem Phys 2023; 25:7466-7476. [PMID: 36848062 DOI: 10.1039/d2cp05998c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
With the introduction of artificial peptides as antimicrobial agents and organic catalysts, numerous efforts have been made to design foldamers with desirable structures and functions. Computational tools are a helpful proxy for revealing the dynamic structures at atomic resolution and understanding foldamer's complex structure-function relationships. However, the performance of conventional force fields in predicting the structures of artificial peptides has not been systematically evaluated. In this study, we critically assessed three popular force fields, AMBER ff14SB, CHARMM36m, and OPLS-AA/L, in predicting conformational propensities of a β-peptide foldamer at monomer and hexamer levels. Simulation results were compared to those obtained from quantum chemistry calculations and experimental data. We also utilised replica exchange molecular dynamics simulations to investigate the energy landscape of each force field and assess the similarities and differences between force fields. We compared different solvent systems in the AMBER ff14SB and CHARMM36m frameworks and confirmed the unanimous role of hydrogen bonds in shaping energy landscapes. We anticipate that our data will pave the way for further improvements to force fields and for understanding the role of solvents in peptide folding, crystallisation, and engineering.
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Affiliation(s)
- Jihye Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hee-Seung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea. .,Center for Multiscale Chiral Architectures, KAIST, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea.
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3
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Fobe TL, Walker CC, Meek GA, Shirts MR. Folding Coarse-Grained Oligomer Models with PyRosetta. J Chem Theory Comput 2022; 18:6354-6369. [PMID: 36179376 DOI: 10.1021/acs.jctc.2c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta's ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.
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Affiliation(s)
- Theodore L Fobe
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Christopher C Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Garrett A Meek
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
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4
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Szefczyk M, Ożga K, Drewniak-Świtalska M, Rudzińska-Szostak E, Hołubowicz R, Ożyhar A, Berlicki Ł. Controlling the conformational stability of coiled-coil peptides with a single stereogenic center of a peripheral β-amino acid residue. RSC Adv 2022; 12:4640-4647. [PMID: 35425498 PMCID: PMC8981378 DOI: 10.1039/d2ra00111j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
The key issue in the research on foldamers remains the understanding of the relationship between the monomers structure and conformational properties at the oligomer level. In peptidomimetic foldamers, the main goal of which is to mimic the structure of proteins, a main challenge is still better understanding of the folding of peptides and the factors that influence their conformational stability. We probed the impact of the modification of the peptide periphery with trans- and cis-2-aminocyclopentanecarboxylic acid (ACPC) on the structure and stability of the model coiled-coil using circular dichroism (CD), analytical ultracentrifugation (AUC) and two-dimensional nuclear magnetic resonance spectroscopy (2D NMR). Although, trans-ACPC and cis-ACPC-containing mutants differ by only one peripheral stereogenic center, their conformational stability is strikingly different.
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Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Magda Drewniak-Świtalska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wroclaw Poland
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5
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Wacha A, Beke‐Somfai T, Nagy T. Improved Modeling of Peptidic Foldamers Using a Quantum Chemical Parametrization Based on Torsional Minimum Energy Path Matching. Chempluschem 2019; 84:927-941. [PMID: 31423411 PMCID: PMC6686720 DOI: 10.1002/cplu.201900180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/12/2019] [Indexed: 11/11/2022]
Abstract
The increasing interest in novel foldamer constructs demands an accurate computational treatment on an extensive timescale. However, it is still a challenge to derive a force field (FF) that can reproduce the experimentally known fold while also allowing the spontaneous exploration of other structures. Here, aiming at a realistic reproduction of backbone torsional barriers, the relevant proper dihedrals of acyclic β2-, β3- and β2,3-amino acids were added to the CHARMM FF and optimized using a novel, self-consistent iterative procedure based on quantum chemical relaxed scans. The new FF was validated by molecular dynamics simulations on three acyclic peptides. While they resided most of the time in their preferred fold (>80 % in helices and >50 % in hairpin), they also visited other conformations. Owing to the CHARMM36m-consistent parametrization, the proposed extension is suitable for exploring new foldamer structures and assemblies, and their interactions with diverse biomolecules.
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Affiliation(s)
- András Wacha
- Institute of Materials and Environmental Chemistry Research Centre for Natural SciencesHungarian Academy of SciencesH-1117Budapest, Magyar tudósok körútja 2Hungary
| | - Tamás Beke‐Somfai
- Institute of Materials and Environmental Chemistry Research Centre for Natural SciencesHungarian Academy of SciencesH-1117Budapest, Magyar tudósok körútja 2Hungary
| | - Tibor Nagy
- Institute of Materials and Environmental Chemistry Research Centre for Natural SciencesHungarian Academy of SciencesH-1117Budapest, Magyar tudósok körútja 2Hungary
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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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Drewniak M, Węglarz-Tomczak E, Ożga K, Rudzińska-Szostak E, Macegoniuk K, Tomczak JM, Bejger M, Rypniewski W, Berlicki Ł. Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics. Bioorg Chem 2018; 81:356-361. [PMID: 30195249 DOI: 10.1016/j.bioorg.2018.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/18/2023]
Abstract
De novo designed helix-loop-helix peptide foldamers containing cis-2-aminocyclopentanecarboxylic acid residues were evaluated for their conformational stability and possible use in enzyme mimetic development. The correlation between hydrogen bond network size and conformational stability was demonstrated through CD and NMR spectroscopies. Molecules incorporating a Cys/His/Glu triad exhibited enzyme-like hydrolytic activity.
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Affiliation(s)
- Magda Drewniak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Macegoniuk
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jakub M Tomczak
- Amsterdam Machine Learning Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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8
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Gopalakrishnan R, Frolov AI, Knerr L, Drury WJ, Valeur E. Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates? J Med Chem 2016; 59:9599-9621. [PMID: 27362955 DOI: 10.1021/acs.jmedchem.6b00376] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, foldamers have progressively emerged as useful architectures to mimic secondary structures of proteins. Peptidic foldamers, consisting of various amino acid based backbones, have been the most studied from a therapeutic perspective, while polyaromatic foldamers have barely evolved from their nascency and remain perplexing for medicinal chemists due to their poor drug-like nature. Despite these limitations, this compound class may still offer opportunities to study challenging targets or provide chemical biology tools. The potential of foldamer drug candidates reaching the clinic is still a stretch. Nevertheless, advances in the field have demonstrated their potential for the discovery of next generation therapeutics. In this perspective, the current knowledge of foldamers is reviewed in a drug discovery context. Recent advances in the early phases of drug discovery including hit finding, target validation, and optimization and molecular modeling are discussed. In addition, challenges and focus areas are debated and gaps highlighted.
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Affiliation(s)
- Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Department of Chemical Biology, Max Planck Institute of Molecular Physiology , Dortmund 44202, Germany
| | - Andrey I Frolov
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Laurent Knerr
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - William J Drury
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
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9
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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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10
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Uribe L, Jaschonek S, Gauss J, Diezemann G. Mechanical unfolding pathway of a model β-peptide foldamer. J Chem Phys 2015; 142:204901. [DOI: 10.1063/1.4921371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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11
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Synthesis and secondary conformations of homochiral β-oligopeptides containing aryl side chains. Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-4423-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Olajos G, Hetényi A, Wéber E, Németh LJ, Szakonyi Z, Fülöp F, Martinek TA. Induced folding of protein-sized foldameric β-sandwich models with core β-amino acid residues. Chemistry 2015; 21:6173-80. [PMID: 25677195 DOI: 10.1002/chem.201405581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 01/27/2023]
Abstract
The mimicry of protein-sized β-sheet structures with unnatural peptidic sequences (foldamers) is a considerable challenge. In this work, the de novo designed betabellin-14 β-sheet has been used as a template, and α→β residue mutations were carried out in the hydrophobic core (positions 12 and 19). β-Residues with diverse structural properties were utilized: Homologous β(3) -amino acids, (1R,2S)-2-aminocyclopentanecarboxylic acid (ACPC), (1R,2S)-2-aminocyclohexanecarboxylic acid (ACHC), (1R,2S)-2-aminocyclohex-3-enecarboxylic acid (ACEC), and (1S,2S,3R,5S)-2-amino-6,6-dimethylbicyclo[3.1.1]heptane-3-carboxylic acid (ABHC). Six α/β-peptidic chains were constructed in both monomeric and disulfide-linked dimeric forms. Structural studies based on circular dichroism spectroscopy, the analysis of NMR chemical shifts, and molecular dynamics simulations revealed that dimerization induced β-sheet formation in the 64-residue foldameric systems. Core replacement with (1R,2S)-ACHC was found to be unique among the β-amino acid building blocks studied because it was simultaneously able to maintain the interstrand hydrogen-bonding network and to fit sterically into the hydrophobic interior of the β-sandwich. The novel β-sandwich model containing 25 % unnatural building blocks afforded protein-like thermal denaturation behavior.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, 6720 Szeged (Hungary)
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