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Yu S, Ye Z, Roy R, Sonani RR, Pramudya I, Xian S, Xiang Y, Liu G, Flores B, Nativ-Roth E, Bitton R, Egelman EH, Webber MJ. Glucose-Triggered Gelation of Supramolecular Peptide Nanocoils with Glucose-Binding Motifs. Adv Mater 2024; 36:e2311498. [PMID: 38095904 PMCID: PMC11031314 DOI: 10.1002/adma.202311498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Indexed: 12/28/2023]
Abstract
Peptide self-assembly is a powerful tool to prepare functional materials at the nanoscale. Often, the resulting materials have high aspect-ratio, with intermolecular β-sheet formation underlying 1D fibrillar structures. Inspired by dynamic structures in nature, peptide self-assembly is increasingly moving toward stimuli-responsive designs wherein assembled structures are formed, altered, or dissipated in response to a specific cue. Here, a peptide bearing a prosthetic glucose-binding phenylboronic acid (PBA) is demonstrated to self-assemble into an uncommon nanocoil morphology. These nanocoils arise from antiparallel β-sheets, with molecules aligned parallel to the long axis of the coil. The binding of glucose to the PBA motif stabilizes and elongates the nanocoil, driving entanglement and gelation at physiological glucose levels. The glucose-dependent gelation of these materials is then explored for the encapsulation and release of a therapeutic agent, glucagon, that corrects low blood glucose levels. Accordingly, the release of glucagon from the nanocoil hydrogels is inversely related to glucose level. When evaluated in a mouse model of severe acute hypoglycemia, glucagon delivered from glucose-stabilized nanocoil hydrogels demonstrates increased protection compared to delivery of the agent alone or within a control nanocoil hydrogel that is not stabilized by glucose.
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Affiliation(s)
- Sihan Yu
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Zhou Ye
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Rajdip Roy
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Irawan Pramudya
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Sijie Xian
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Yuanhui Xiang
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Guoqiang Liu
- Integrated Biomedical Sciences Program, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Belen Flores
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
| | - Einat Nativ-Roth
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Ronit Bitton
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Matthew J Webber
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, 105 McCourtney Hall, Notre Dame, IN 46556, USA
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Zhang Y, Zhou T, Qi Y, Li Y, Zhang Y, Zhao Y, Han H, Wang Y. Engineered assemblies from isomeric pentapeptides augment dry eye treatment. J Control Release 2024; 365:521-529. [PMID: 38040342 DOI: 10.1016/j.jconrel.2023.11.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/10/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Changing positions of amino acid residues in the peptide sequence alters the peptide' s assembly behaviors, affording various nanostructures. However, it remains elusive that how subtle changes in the peptide sequence influence the in vivo bioactivity of peptide-based nanocarriers, further impacting the efficacy of the encapsulated drugs. We report here a class of isomeric pentapeptide amphiphiles that associate into filaments with different dimensions, which were further used as carriers of Diquafosol tetrasodium (DQS), for the treatment of dry eye disease. Our results suggest that subtle changes in peptide sequences resulted in dramatically different molecular packings and distinct morphologies, which were verified by molecular dynamics simulations. In vivo results show that the drug retention time could be prolonged by the peptidic nanostructures on the ocular surface but were highly morphological-dependent. The longer retention time promised better therapeutic efficacy. In terms of facile synthesis and good biocompatibility, we believe that these peptides could be used for eye disease treatments or other related areas.
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Affiliation(s)
- Yanwen Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tinglian Zhou
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310009, China
| | - Yuzhen Qi
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yijie Li
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yijing Zhang
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaxue Zhao
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Haijie Han
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, Hangzhou 310009, China.
| | - Yin Wang
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
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Thede AT, Tang JD, Cocker CE, Harold LJ, Amelung CD, Kittel AR, Taylor PA, Lampe KJ. Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments. Cells Tissues Organs 2023; 212:468-483. [PMID: 37751723 DOI: 10.1159/000534280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3-12 mm) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 mm of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.
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Affiliation(s)
- Andrew T Thede
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - James D Tang
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
| | - Clare E Cocker
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
| | - Liza J Harold
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Connor D Amelung
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Anna R Kittel
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Phillip A Taylor
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
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Mohammadi E, Joshi SY, Deshmukh SA. Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models. Biomacromolecules 2023; 24:4078-4092. [PMID: 37603467 DOI: 10.1021/acs.biomac.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Interactions between amino acids and water play an important role in determining the stability and folding/unfolding, in aqueous solution, of many biological macromolecules, which affects their function. Thus, understanding the molecular-level interactions between water and amino acids is crucial to tune their function in aqueous solutions. Herein, we have developed nonbonded interaction parameters between the coarse-grained (CG) models of 20 amino acids and the one-site CG water model. The nonbonded parameters, represented using the 12-6 Lennard Jones (LJ) potential form, have been optimized using an artificial neural network (ANN)-assisted particle swarm optimization (PSO) (ANN-assisted PSO) method. All-atom (AA) molecular dynamics (MD) simulations of dipeptides in TIP3P water molecules were performed to calculate the Gibbs hydration free energies. The nonbonded force-field (FF) parameters between CG amino acids and the one-site CG water model were developed to accurately reproduce these energies. Furthermore, to test the transferability of these newly developed parameters, we calculated the hydration free energies of the analogues of the amino acid side chains, which showed good agreement with reported experimental data. Additionally, we show the applicability of these models by performing self-assembly simulations of peptide amphiphiles. Overall, these models are transferable and can be used to study the self-assembly of various biomaterials and biomolecules to develop a mechanistic understanding of these processes.
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Affiliation(s)
- Esmat Mohammadi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Li Z, Joshi SY, Wang Y, Deshmukh SA, Matson JB. Supramolecular Peptide Nanostructures Regulate Catalytic Efficiency and Selectivity. Angew Chem Int Ed Engl 2023; 62:e202303755. [PMID: 37194941 PMCID: PMC10330506 DOI: 10.1002/anie.202303755] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 05/18/2023]
Abstract
We report three constitutionally isomeric tetrapeptides, each comprising one glutamic acid (E) residue, one histidine (H) residue, and two lysine (KS ) residues functionalized with side-chain hydrophobic S-aroylthiooxime (SATO) groups. Depending on the order of amino acids, these amphiphilic peptides self-assembled in aqueous solution into different nanostructures:nanoribbons, a mixture of nanotoroids and nanoribbons, or nanocoils. Each nanostructure catalyzed hydrolysis of a model substrate, with the nanocoils exhibiting the greatest rate enhancement and the highest enzymatic efficiency. Coarse-grained molecular dynamics simulations, analyzed with unsupervised machine learning, revealed clusters of H residues in hydrophobic pockets along the outer edge of the nanocoils, providing insight for the observed catalytic rate enhancement. Finally, all three supramolecular nanostructures catalyzed hydrolysis of the l-substrate only when a pair of enantiomeric Boc-l/d-Phe-ONp substrates were tested. This study highlights how subtle molecular-level changes can influence supramolecular nanostructures, and ultimately affect catalytic efficiency.
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Affiliation(s)
- Zhao Li
- Department of Chemistry, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
| | - Soumil Y Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
| | - Yin Wang
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sanket A Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
| | - John B Matson
- Department of Chemistry, Virginia Tech, Blacksburg, VA-24061, USA
- Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA-24061, USA
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Guan T, Li J, Chen C, Liu Y. Self-Assembling Peptide-Based Hydrogels for Wound Tissue Repair. Adv Sci (Weinh) 2022; 9:e2104165. [PMID: 35142093 PMCID: PMC8981472 DOI: 10.1002/advs.202104165] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/23/2021] [Indexed: 05/02/2023]
Abstract
Wound healing is a long-term, multistage biological process that includes hemostasis, inflammation, proliferation, and tissue remodeling and requires intelligent designs to provide comprehensive and convenient treatment. The complexity of wounds has led to a lack of adequate wound treatment materials, which must systematically regulate unique wound microenvironments. Hydrogels have significant advantages in wound treatment due to their ability to provide spatiotemporal control over the wound healing process. Self-assembling peptide-based hydrogels are particularly attractive due to their innate biocompatibility and biodegradability along with additional advantages including ligand-receptor recognition, stimulus-responsive self-assembly, and the ability to mimic the extracellular matrix. The ability of peptide-based materials to self-assemble in response to the physiological environment, resulting in functionalized microscopic structures, makes them conducive to wound treatment. This review introduces several self-assembling peptide-based systems with various advantages and emphasizes recent advances in self-assembling peptide-based hydrogels that allow for precise control during different stages of wound healing. Moreover, the development of multifunctional self-assembling peptide-based hydrogels that can regulate and remodel the wound immune microenvironment in wound therapy with spatiotemporal control has also been summarized. Overall, this review sheds light on the future clinical and practical applications of self-assembling peptide-based hydrogels.
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Affiliation(s)
- Tong Guan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology of ChinaBeijing100190P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
| | - Jiayang Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology of ChinaBeijing100190P. R. China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology of ChinaBeijing100190P. R. China
- University of Chinese Academy of SciencesBeijing100049P. R. China
- GBA National Institute for Nanotechnology InnovationGuangdong510700P. R. China
| | - Ying Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology of ChinaBeijing100190P. R. China
- GBA National Institute for Nanotechnology InnovationGuangdong510700P. R. China
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Abstract
The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.
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Affiliation(s)
- Riccardo Alessandri
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747AG, The Netherlands
| | - Fabian Grünewald
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747AG, The Netherlands
| | - Siewert J Marrink
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747AG, The Netherlands
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