1
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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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2
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Gao P, Ha-Duong T, Nicolas J. Coarse-Grained Model-Assisted Design of Polymer Prodrug Nanoparticles with Enhanced Cytotoxicity: A Combined Theoretical and Experimental Study. Angew Chem Int Ed Engl 2024; 63:e202316056. [PMID: 38345287 DOI: 10.1002/anie.202316056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Indexed: 03/12/2024]
Abstract
To achieve drug release from polymer prodrug nanoparticles, the drug-polymer linker must be accessible for cleavage to release the drug, which can occur under certain physiological conditions (e.g., presence of specific enzymes). Supramolecular organization of polymer prodrug nanoparticles is crucial as it greatly affects the location of the linker, its surface exposure/solvation and thus its cleavage to release the drug. Since experimental access to these data is not straightforward, new methodologies are critically needed to access this information and to accelerate the development of more effective polymer prodrug nanoparticles, and replace the time-consuming and resource-intensive traditional trial-and-error strategy. In this context, we reported here the use of a coarse-grained model to assist the design of polymer prodrug nanoparticles with enhanced cytotoxicity. By choosing the solvent accessible surface area as the critical parameter for predicting drug release and hence cytotoxicity of polymer prodrug nanoparticles, we developed an optimized polymer-drug linker with enhanced hydrophilicity and solvation. Our hypothesis was then experimentally validated by the synthesis of the corresponding polymer prodrugs based on two different drugs (gemcitabine and paclitaxel), which demonstrated greater performances in terms of drug release and cytotoxicity on two cancer cell lines. Interestingly, our methodology can be easily applied to other polymer prodrug structures, which would contribute to the development of more efficient drug delivery systems via in silico screening.
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Affiliation(s)
- Ping Gao
- Université Paris-Saclay, CNRS, BioCIS, Orsay, 91400, France
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, Orsay, 91400, France
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, Orsay, 91400, France
| | - Julien Nicolas
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, Orsay, 91400, France
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3
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Martins da Silva AY, Arouche TDS, Siqueira MRS, Ramalho TC, de Faria LJG, Gester RDM, Carvalho Junior RND, Santana de Oliveira M, Neto AMDJC. SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics. J Biomol Struct Dyn 2023:1-16. [PMID: 37712854 DOI: 10.1080/07391102.2023.2252930] [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: 12/27/2022] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anderson Yuri Martins da Silva
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
| | - Tiago da Silva Arouche
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
| | | | - Teodorico Castro Ramalho
- Postgraduate Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, Belém, Brazil
| | | | - Rodrigo do Monte Gester
- Institute of Exact Sciences (ICE), Federal University of the South and Southeast of Pará, Maraba, Brazil
| | - Raul Nunes de Carvalho Junior
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Engineering of Natural Resources of the Amazon, ITEC, Federal University of Pará, Belém, Brazil
- Faculty of Food Engineering ITEC, Federal University of Pará, Belém, Brazil
| | | | - Antonio Maia de Jesus Chaves Neto
- Laboratory for the Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, Belem, Brazil
- Graduated in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- Postgraduate Program in Chemical Engineering, ITEC, Federal University of Pará, Belém, Brazil
- National Professional Master's in Physics Teaching, Federal University of Pará, Belém, Brazil
- Museu Paraense Emílio Goeldi, Diretoria, Coordenação de Botânica, Rua Augusto Corrêa, Belém, Brazil
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4
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Sun B, Wu W, Narasipura EA, Ma Y, Yu C, Fenton OS, Song H. Engineering nanoparticle toolkits for mRNA delivery. Adv Drug Deliv Rev 2023; 200:115042. [PMID: 37536506 DOI: 10.1016/j.addr.2023.115042] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
The concept of using mRNA to produce its own medicine in situ in the body makes it an ideal drug candidate, holding great potential to revolutionize the way we approach medicine. The unique characteristics of mRNA, as well as its customizable biomedical functions, call for the rational design of delivery systems to protect and transport mRNA molecules. In this review, a nanoparticle toolkit is presented for the development of mRNA-based therapeutics from a drug delivery perspective. Nano-delivery systems derived from either natural systems or chemical synthesis, in the nature of organic or inorganic materials, are summarised. Delivery strategies in controlling the tissue targeting and mRNA release, as well as the role of nanoparticles in building and boosting the activity of mRNA drugs, have also been introduced. In the end, our insights into the clinical and translational development of mRNA nano-drugs are presented.
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Affiliation(s)
- Bing Sun
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Weixi Wu
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Eshan A Narasipura
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yutian Ma
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chengzhong Yu
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Owen S Fenton
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Hao Song
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia.
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5
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Zaboli A, Raissi H, Hashemzadeh H, Farzad F. Graphene Oxide Hosting a pH-Sensitive Prodrug: An In Silico Investigation of Graphene Oxide-Based Nanovehicle toward Cancer Therapy. ACS APPLIED BIO MATERIALS 2023. [PMID: 37327458 DOI: 10.1021/acsabm.3c00276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Prodrug and drug delivery systems are two effective strategies for improving the selectivity of chemotherapeutics. Herein, via molecular dynamics (MD) simulation and free energy calculation, the effectiveness of the graphene oxide (GO) decorated with the pH-sensitive prodrug (PD) molecules in cancer therapy is investigated. PEI-CA-DOX (prodrug) was loaded onto the GO surface, in which the hydrogen bonding and pi-pi stacking interactions play the main role in the stability of the GO-PD complex. Due to the strong interaction of GO and PD (about -800 kJ/mol), the GO-PD complex remains stable during the membrane penetration process. The obtained results confirm that GO is a suitable surface for hosting the prodrug and passing it through the membrane. Furthermore, the investigation of the release process shows that the PD can be released under acidic conditions. This phenomenon is due to the reduction of the contribution of electrostatic energy in the GO and PD interaction and the entry of water into the drug delivery system. Moreover, it is found that an external electrical field does not have much effect on drug release. Our results provide a deep understanding of the prodrug delivery systems, which helps the combination of nanocarriers and modified chemotherapy drugs in the future.
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Affiliation(s)
- Ameneh Zaboli
- Department of Chemistry, University of Birjand, Birjand 9717434765, Iran
| | - Heidar Raissi
- Department of Chemistry, University of Birjand, Birjand 9717434765, Iran
| | - Hassan Hashemzadeh
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Birjand University of Medical Sciences, Birjand 9717853076, Iran
| | - Farzaneh Farzad
- Department of Chemistry, University of Birjand, Birjand 9717434765, Iran
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6
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Wang Z, Hao D, Wang Y, Zhao J, Zhang J, Rong X, Zhang J, Min J, Qi W, Su R, He M. Peptidyl Virus-Like Nanovesicles as Reconfigurable "Trojan Horse" for Targeted siRNA Delivery and Synergistic Inhibition of Cancer Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204959. [PMID: 36372545 DOI: 10.1002/smll.202204959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/10/2022] [Indexed: 06/16/2023]
Abstract
The self-assembly of peptidyl virus-like nanovesicles (pVLNs) composed of highly ordered peptide bilayer membranes that encapsulate the small interfering RNA (siRNA) is reported. The targeting and enzyme-responsive sequences on the bilayer's surface allow the pVLNs to enter cancer cells with high efficiency and control the release of genetic drugs in response to the subcellular environment. By transforming its structure in response to the highly expressed enzyme matrix metalloproteinase 7 (MMP-7) in cancer cells, it helps the siRNA escape from the lysosomes, resulting in a final silencing efficiency of 92%. Moreover, the pVLNs can serve as reconfigurable "Trojan horse" by transforming into membranes triggered by the MMP-7 and disrupting the cytoplasmic structure, thereby achieving synergistic anticancer effects and 96% cancer cell mortality with little damage to normal cells. The pVLNs benefit from their biocompatibility, targeting, and enzyme responsiveness, making them a promising platform for gene therapy and anticancer therapy.
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Affiliation(s)
- Zixuan Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Dongzhao Hao
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jinwu Zhao
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Xi Rong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiaojiao Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
| | - Mingxia He
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, 300072, P. R. China
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7
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Boosted Cross-Linking and Characterization of High-Performing Self-Assembling Peptides. NANOMATERIALS 2022; 12:nano12030320. [PMID: 35159664 PMCID: PMC8838902 DOI: 10.3390/nano12030320] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/10/2022]
Abstract
Tissue engineering (TE) strategies require the design and characterization of novel biomaterials capable of mimicking the physiological microenvironments of the tissues to be regenerated. As such, implantable materials should be biomimetic, nanostructured and with mechanical properties approximating those of the target organ/tissue. Self-assembling peptides (SAPs) are biomimetic nanomaterials that can be readily synthesized and customized to match the requirements of some TE applications, but the weak interactions involved in the self-assembling phenomenon make them soft hydrogels unsuited for the regeneration of medium-to-hard tissues. In this work, we moved significant steps forward in the field of chemical cross-linked SAPs towards the goal of stiff peptidic materials suited for the regeneration of several tissues. Novel SAPs were designed and characterized to boost the 4-(N-Maleimidomethyl) cyclohexane-1-carboxylic acid 3-sulpho-N-hydroxysuccinimide ester (Sulfo-SMCC) mediated cross-linking reaction, where they reached G′ values of ~500 kPa. An additional orthogonal cross-linking was also effective and allowed to top remarkable G′ values of 840 kPa. We demonstrated that cross-linking fastened the pre-existing self-aggregated nanostructures, and at the same time, a strong presence of ß-structures is necessary for an effective cross-linking of (LKLK)3-based SAPs. Combining strong SAP design and orthogonal cross-linking reactions, we brought SAP stiffness closer to the MPa threshold, and as such, we opened the door of the regeneration of skin, muscle and lung to biomimetic SAP technology.
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8
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Sasselli IR, Syrgiannis Z, Sather NA, Palmer LC, Stupp SI. Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments. J Phys Chem B 2022; 126:650-659. [PMID: 35029997 DOI: 10.1021/acs.jpcb.1c09258] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.
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Affiliation(s)
- Ivan R Sasselli
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zois Syrgiannis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Nicholas A Sather
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Liam C Palmer
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, 11th Floor, Chicago, Illinois 60611, United States.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States.,Department of Medicine, Northwestern University, 676 N St. Clair, Chicago, Illinois 60611, United States.,Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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9
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Machado N, Bruininks BMH, Singh P, Dos Santos L, Dal Pizzol C, Dieamant GDC, Kruger O, Martin AA, Marrink SJ, Souza PCT, Favero PP. Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes. NANOSCALE 2022; 14:506-514. [PMID: 34913938 DOI: 10.1039/d1nr04610a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lipid nanoemulsions are promising nanomaterials for drug delivery applications in food, pharmaceutical and cosmetic industries. Despite the noteworthy commercial interest, little is known about their supramolecular organization, especially about how such multicomponent formulations interact with cell membranes. In the present work, coarse-grained molecular dynamics simulations have been employed to study the self-assembly of a 15-component lipid nanoemulsion droplet containing vitamins A and E for skin delivery. Our results display aspects of the unique "onion-like" agglomeration between the chemical constituents in the different layers of the lipid nanodroplet. Vitamin E molecules are more concentrated in the center of the droplet together with other hydrophobic constituents such as the triglycerides with long tails. On the other hand, vitamin A occupies an intermediate layer between the core and the co-emulsifier surface of the nanodroplet, together with lecithin phospholipids. Coarse-grained molecular dynamics simulations were also performed to provide insight into the first steps involved in absorption and penetration of the nanodroplet through skin membrane models, representing an intracellular (hair follicle infundibulum) and intercellular pathway (stratum corneum) through the skin. Our data provide a first view on the complex organization of commercial nanoemulsion and its interaction with skin membranes. We expect our results to open the way towards the rational design of such nanomaterials.
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Affiliation(s)
- Neila Machado
- Institute of Research and Development, Universidade do Vale do Paraíba, Av. Shishima Hifumi 2911, 12244-000, São José dos Campos, São Paulo, Brazil
- UFABC Universidade Federal do ABC, Avenida dos Estados, 5001, 09210-580, Santo André, São Paulo, Brazil.
| | - Bart M H Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Priyanka Singh
- Institute of Research and Development, Universidade do Vale do Paraíba, Av. Shishima Hifumi 2911, 12244-000, São José dos Campos, São Paulo, Brazil
| | - Laurita Dos Santos
- Institute of Research and Development, Universidade do Vale do Paraíba, Av. Shishima Hifumi 2911, 12244-000, São José dos Campos, São Paulo, Brazil
- Biomedical Engineering Innovation Center, Biomedical Vibrational Spectroscopy Group. Universidade Brasil UnBr, Rua Carolina Fonseca 235, 08230-030, Itaquera, São Paulo, Brazil.
| | - Carine Dal Pizzol
- Grupo Boticário, Av. Rui Barbosa, 4110, 83055-010, Parque da Fonte, São José dos Pinhais, Paraná, Brazil
| | - Gustavo de C Dieamant
- Grupo Boticário, Av. Rui Barbosa, 4110, 83055-010, Parque da Fonte, São José dos Pinhais, Paraná, Brazil
| | - Odivania Kruger
- Grupo Boticário, Av. Rui Barbosa, 4110, 83055-010, Parque da Fonte, São José dos Pinhais, Paraná, Brazil
| | - Airton A Martin
- Biomedical Engineering Innovation Center, Biomedical Vibrational Spectroscopy Group. Universidade Brasil UnBr, Rua Carolina Fonseca 235, 08230-030, Itaquera, São Paulo, Brazil.
- DermoProbes - Research, Innovation and Technological Development, Av. Cassiano Ricardo, 601, Sala 73-74, 12246-870, São José dos Campos, SP, Brazil
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France.
| | - Priscila P Favero
- Biomedical Engineering Innovation Center, Biomedical Vibrational Spectroscopy Group. Universidade Brasil UnBr, Rua Carolina Fonseca 235, 08230-030, Itaquera, São Paulo, Brazil.
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10
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Shen Y, Wang Y, Hamley IW, Qi W, Su R, He Z. Chiral self-assembly of peptides: Toward the design of supramolecular polymers with enhanced chemical and biological functions. Prog Polym Sci 2021. [DOI: 10.1016/j.progpolymsci.2021.101469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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Razavilar N, Hanna G. Molecular‐Level Insights into the Diffusion of a Hydrophobic Drug in a Disordered Block Copolymer Micelle by Molecular Dynamics Simulation. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202100060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Negin Razavilar
- Department of Chemistry University of Alberta 11227 Saskatchewan Drive Edmonton Alberta T6G 2G2 Canada
| | - Gabriel Hanna
- Department of Chemistry University of Alberta 11227 Saskatchewan Drive Edmonton Alberta T6G 2G2 Canada
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12
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Mastrobattista E. Formulation and delivery solutions for the next generation biotherapeutics. J Control Release 2021; 336:583-597. [PMID: 34174354 DOI: 10.1016/j.jconrel.2021.06.029] [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: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022]
Abstract
In 2018 I was appointed full professor of Pharmaceutical Biotechnology & Delivery at the Pharmaceutics division of the department of Pharmaceutical Sciences at Utrecht University, The Netherlands. In this contribution to the Orations - New Horizons of the Journal of Controlled Release I will introduce my research group (see also www.uu.nl/pharmaceutics) and will highlight my current and future research projects. In coming years the focus of my research will be on the administration of biotherapeutics, aiming to control their fate from the site of injection to the site of action. I will discuss issues related to formulation of biotherapeutics into nanomedicines (NMs), intracellular delivery of nucleic acids as well as protein therapeutics, and targeted delivery of biotherapeutics beyond the liver. In addition, I will provide a forward view on how current developments in the drug delivery and gene therapy field may result in sustainable and cost-effective dosing regimens for biotherapeutics.
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Affiliation(s)
- Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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13
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Alessandri R, Grünewald F, Marrink SJ. The Martini Model in Materials Science. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2008635. [PMID: 33956373 DOI: 10.1002/adma.202008635] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/15/2021] [Indexed: 06/12/2023]
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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14
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Lau CYJ, Mastrobattista E. Programming supramolecular peptide materials by modulating the intermediate steps in the complex assembly pathway: Implications for biomedical applications. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Lau CYJ, Fontana F, Mandemaker LDB, Wezendonk D, Vermeer B, Bonvin AMJJ, de Vries R, Zhang H, Remaut K, van den Dikkenberg J, Medeiros-Silva J, Hassan A, Perrone B, Kuemmerle R, Gelain F, Hennink WE, Weingarth M, Mastrobattista E. Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides. Commun Chem 2020; 3:164. [PMID: 36703336 PMCID: PMC9814929 DOI: 10.1038/s42004-020-00417-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/19/2020] [Indexed: 01/29/2023] Open
Abstract
Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.
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Affiliation(s)
- Chun Yin Jerry Lau
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Federico Fontana
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy
| | - Laurens D. B. Mandemaker
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Dennie Wezendonk
- grid.5477.10000000120346234Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Benjamin Vermeer
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Renko de Vries
- grid.4818.50000 0001 0791 5666Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Heyang Zhang
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Katrien Remaut
- grid.5342.00000 0001 2069 7798Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Joep van den Dikkenberg
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - João Medeiros-Silva
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alia Hassan
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Barbara Perrone
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- grid.481597.60000 0004 0452 3124Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Fabrizio Gelain
- grid.413503.00000 0004 1757 9135IRCCS Casa Sollievo della Sofferenza, Opera di San Pio da Pietralcina, Viale Capuccini 1, 71013 San Giovanni Rotondo, Italy ,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell’Ospedale Maggiore 3, 20162 Milan, Italy
| | - Wim E. Hennink
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Markus Weingarth
- grid.5477.10000000120346234NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Enrico Mastrobattista
- grid.5477.10000000120346234Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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16
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Mushnoori S, Lu CY, Schmidt K, Zang E, Dutt M. Peptide-based vesicles and droplets: a review. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 33:053002. [PMID: 32942264 DOI: 10.1088/1361-648x/abb995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Peptide assembly is an increasingly important field of study due to the versatility, tunability and vast design space of amino acid based biomolecular assemblies. Peptides can be precisely engineered to possess various useful properties such as the ability to form supramolecular assemblies, desired response to pH, or thermal stability. These peptide supramolecular assemblies have diverse morphologies including vesicles, nanotubes, nanorods and ribbons. Of specific interest is the domain of engineering peptides that aggregate into spherical nanostructures due to their encapsulation properties: the ability to hold, transport and release chemical payloads in a controllable manner. This is invaluable to the fields of nanomedicine and targeted drug delivery. In this review, the state of the art in the domain of peptide-based vesicles and nanospheres is summarized. Specifically, an overview of the assembly of peptides into nanovesicles and nanospheres is provided. Both aromatic as well as aliphatic side chain amino acids are discussed. The domain of aromatic side chained amino acid residues is largely dominated by phenylalanine based peptides and variants thereof. Tyrosine also demonstrates similar aggregation properties. Both experimentally and computationally driven approaches are discussed. The domain of aliphatic amino acid residues based vesicles and droplets is broader, and details multiple amino acid residues such as alanine, valine, lysine, glycine, proline, and aspartic acid. Finally, a discussion on potential future directions is provided.
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Affiliation(s)
- Srinivas Mushnoori
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Chien Y Lu
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Kassandra Schmidt
- Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Ethan Zang
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
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17
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Abudula T, Bhatt K, Eggermont LJ, O'Hare N, Memic A, Bencherif SA. Supramolecular Self-Assembled Peptide-Based Vaccines: Current State and Future Perspectives. Front Chem 2020; 8:598160. [PMID: 33195107 PMCID: PMC7662149 DOI: 10.3389/fchem.2020.598160] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 02/01/2023] Open
Abstract
Despite the undeniable success of vaccination programs in preventing diseases, effective vaccines against several life-threatening infectious pathogens such as human immunodeficiency virus are still unavailable. Vaccines are designed to boost the body's natural ability to protect itself against foreign pathogens. To enhance vaccine-based immunotherapies to combat infections, cancer, and other conditions, biomaterials have been harnessed to improve vaccine safety and efficacy. Recently, peptides engineered to self-assemble into specific nanoarchitectures have shown great potential as advanced biomaterials for vaccine development. These supramolecular nanostructures (i.e., composed of many peptides) can be programmed to organize into various forms, including nanofibers, nanotubes, nanoribbons, and hydrogels. Additionally, they have been designed to be responsive upon exposure to various external stimuli, providing new innovations in the development of smart materials for vaccine delivery and immunostimulation. Specifically, self-assembled peptides can provide cell adhesion sites, epitope recognition, and antigen presentation, depending on their biochemical and structural characteristics. Furthermore, they have been tailored to form exquisite nanostructures that provide improved enzymatic stability and biocompatibility, in addition to the controlled release and targeted delivery of immunomodulatory factors (e.g., adjuvants). In this mini review, we first describe the different types of self-assembled peptides and resulting nanostructures that have recently been investigated. Then, we discuss the recent progress and development trends of self-assembled peptide-based vaccines, their challenges, and clinical translatability, as well as their future perspectives.
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Affiliation(s)
| | - Khushbu Bhatt
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, United States
| | - Loek J Eggermont
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - Nick O'Hare
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States
| | - Adnan Memic
- Center of Nanotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sidi A Bencherif
- Department of Chemical Engineering, Northeastern University, Boston, MA, United States.,Department of Bioengineering, Northeastern University, Boston, MA, United States.,Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States.,Sorbonne University, UTC CNRS UMR 7338, Biomechanics and Bioengineering (BMBI), University of Technology of Compiègne, Compiègne, France
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18
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Shankar S, Junaid Ur Rahim, Rai R. Self-Assembly in Peptides Containing β-and γ-amino Acids. Curr Protein Pept Sci 2020; 21:584-597. [DOI: 10.2174/1389203721666200127112244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 12/17/2022]
Abstract
The peptides containing β-and γ-amino acids as building blocks display well-defined secondary
structures with unique morphologies. The ability of such peptides to self-assemble into complex
structures of controlled geometries has been exploited in biomedical applications. Herein, we have
provided an updated overview about the peptides containing β-and γ-amino acids considering the significance
and advancement in the area of development of peptide-based biomaterials having diverse
applications.
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Affiliation(s)
- Sudha Shankar
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | - Junaid Ur Rahim
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | - Rajkishor Rai
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
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19
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El Hariri El Nokab M, van der Wel PC. Use of solid-state NMR spectroscopy for investigating polysaccharide-based hydrogels: A review. Carbohydr Polym 2020; 240:116276. [DOI: 10.1016/j.carbpol.2020.116276] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/22/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022]
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20
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Gupta S, Singh I, Sharma AK, Kumar P. Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos. Front Bioeng Biotechnol 2020; 8:504. [PMID: 32548101 PMCID: PMC7273840 DOI: 10.3389/fbioe.2020.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.
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Affiliation(s)
- Seema Gupta
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Indu Singh
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashwani K. Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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21
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Sarkar D, Chakraborty I, Condorelli M, Ghosh B, Mass T, Weingarth M, Mandal AK, La Rosa C, Subramanian V, Bhunia A. Self‐Assembly and Neurotoxicity of β‐Amyloid (21–40) Peptide Fragment: The Regulatory Role of GxxxG Motifs. ChemMedChem 2019; 15:293-301. [DOI: 10.1002/cmdc.201900620] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/19/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Ipsita Chakraborty
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | | | - Baijayanti Ghosh
- Division of Molecular Medicine Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Thorben Mass
- Department of Chemistry Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Markus Weingarth
- Department of Chemistry Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Atin K Mandal
- Division of Molecular Medicine Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Carmelo La Rosa
- Department of Chemical Sciences University of Catania 95125 Catania Italy
| | | | - Anirban Bhunia
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
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22
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Jekhmane S, Prachar M, Pugliese R, Fontana F, Medeiros‐Silva J, Gelain F, Weingarth M. Design Parameters of Tissue‐Engineering Scaffolds at the Atomic Scale. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Marek Prachar
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Raffaele Pugliese
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
- ASST Grande Ospedale Metropolitano NiguardaCenter for Nanomedicine and Tissue Engineering Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
| | - João Medeiros‐Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
- ASST Grande Ospedale Metropolitano NiguardaCenter for Nanomedicine and Tissue Engineering Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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23
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Jekhmane S, Prachar M, Pugliese R, Fontana F, Medeiros-Silva J, Gelain F, Weingarth M. Design Parameters of Tissue-Engineering Scaffolds at the Atomic Scale. Angew Chem Int Ed Engl 2019; 58:16943-16951. [PMID: 31573131 PMCID: PMC6899630 DOI: 10.1002/anie.201907880] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/03/2019] [Indexed: 01/08/2023]
Abstract
Stem-cell behavior is regulated by the material properties of the surrounding extracellular matrix, which has important implications for the design of tissue-engineering scaffolds. However, our understanding of the material properties of stem-cell scaffolds is limited to nanoscopic-to-macroscopic length scales. Herein, a solid-state NMR approach is presented that provides atomic-scale information on complex stem-cell substrates at near physiological conditions and at natural isotope abundance. Using self-assembled peptidic scaffolds designed for nervous-tissue regeneration, we show at atomic scale how scaffold-assembly degree, mechanics, and homogeneity correlate with favorable stem cell behavior. Integration of solid-state NMR data with molecular dynamics simulations reveals a highly ordered fibrillar structure as the most favorable stem-cell scaffold. This could improve the design of tissue-engineering scaffolds and other self-assembled biomaterials.
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Affiliation(s)
- Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Marek Prachar
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Raffaele Pugliese
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy.,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy.,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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24
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Crowet JM, Sinnaeve D, Fehér K, Laurin Y, Deleu M, Martins JC, Lins L. Molecular Model for the Self-Assembly of the Cyclic Lipodepsipeptide Pseudodesmin A. J Phys Chem B 2019; 123:8916-8922. [PMID: 31558021 DOI: 10.1021/acs.jpcb.9b08035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Self-assembly of peptides into supramolecular structures represents an active field of research with potential applications ranging from material science to medicine. Their study typically involves the application of a large toolbox of spectroscopic and imaging techniques. However, quite often, the structural aspects remain underexposed. Besides, molecular modeling of the self-assembly process is usually difficult to handle, since a vast conformational space has to be sampled. Here, we have used an approach that combines short molecular dynamics simulations for peptide dimerization and NMR restraints to build a model of the supramolecular structure from the dimeric units. Experimental NMR data notably provide crucial information about the conformation of the monomeric units, the supramolecular assembly dimensions, and the orientation of the individual peptides within the assembly. This in silico/in vitro mixed approach enables us to define accurate atomistic models of supramolecular structures of the bacterial cyclic lipodepsipeptide pseudodesmin A.
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Affiliation(s)
- Jean-Marc Crowet
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - Davy Sinnaeve
- CNRS-Unité de Glycobiologie structurale et fonctionnelle (UGSF) UMR 8576 , 50, Avenue de Halley, Campus CNRS de la Haute Borne , 59658 Villeneuve d'Ascq , France
| | - Krisztina Fehér
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , 69118 Heidelberg , Germany
| | - Yoann Laurin
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 S4 , B-9000 Gent , Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
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25
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Sis MJ, Webber MJ. Drug Delivery with Designed Peptide Assemblies. Trends Pharmacol Sci 2019; 40:747-762. [DOI: 10.1016/j.tips.2019.08.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 12/18/2022]
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26
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Lien YH, Ram Mahato D, Hoppe-Seyler F, Fischer WB. Membrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:524-532. [PMID: 30774024 DOI: 10.1080/07391102.2019.1581660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Coarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is coupled with a protein transducing domain (PTD) of nine arginine residues (R9) at its N-terminal side as well as a peptide, pep11**, which has been shown to bind to human papilloma virus 16 (HPV16) E6 oncoprotein. A short hydrophobic stretch of the transmembrane domain (TMD) of BST-2 aggregates the fastest and inserts into a lipid membrane. An aggregate of R9-pep11** attaches to the membrane via simultaneous contact of many arginine residues. Monomers from the aggregates of the shortest of the hydrophobic TMDs dissolve into the opposing leaflet when the aggregate spans the bilayer. A 'flipping' of the individual monomeric peptides is not observed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yu-Hsien Lien
- Institute of Biophotonics, Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Dhani Ram Mahato
- Institute of Biophotonics, Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
| | | | - Wolfgang B Fischer
- Institute of Biophotonics, Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan
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27
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Qiu F, Chen Y, Tang C, Zhao X. Amphiphilic peptides as novel nanomaterials: design, self-assembly and application. Int J Nanomedicine 2018; 13:5003-5022. [PMID: 30214203 PMCID: PMC6128269 DOI: 10.2147/ijn.s166403] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Designer self-assembling peptides are a category of emerging nanobiomaterials which have been widely investigated in the past decades. In this field, amphiphilic peptides have received special attention for their simplicity in design and versatility in application. This review focuses on recent progress in designer amphiphilic peptides, trying to give a comprehensive overview about this special type of self-assembling peptides. By exploring published studies on several typical types of amphiphilic peptides in recent years, herein we discuss in detail the basic design, self-assembling behaviors and the mechanism of amphiphilic peptides, as well as how their nanostructures are affected by the peptide characteristics or environmental parameters. The applications of these peptides as potential nanomaterials for nanomedicine and nanotechnology are also summarized.
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Affiliation(s)
- Feng Qiu
- Laboratory of Anaesthesia and Critical Care Medicine, Translational Neuroscience Centre, West China Hospital, Sichuan University, Chengdu 610041, China, .,Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610041, China, ,
| | - Yongzhu Chen
- Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610041, China, , .,Periodical Press of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengkang Tang
- Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610041, China, , .,Core Facility of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaojun Zhao
- Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610041, China, ,
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28
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Saracino GAA, Fontana F, Jekhmane S, Silva JM, Weingarth M, Gelain F. Elucidating Self-Assembling Peptide Aggregation via Morphoscanner: A New Tool for Protein-Peptide Structural Characterization. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800471. [PMID: 30128255 PMCID: PMC6097002 DOI: 10.1002/advs.201800471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/11/2018] [Indexed: 05/13/2023]
Abstract
Self-assembling and molecular folding are ubiquitous in Nature: they drive the organization of systems ranging from living creatures to DNA molecules. Elucidating the complex dynamics underlying these phenomena is of crucial importance. However, a tool for the analysis of the various phenomena involved in protein/peptide aggregation is still missing. Here, an innovative software is developed and validated for the identification and visualization of b-structuring and b-sheet formation in both simulated systems and crystal structures of proteins and peptides. The novel software suite, dubbed Morphoscanner, is designed to identify and intuitively represent b-structuring and b-sheet formation during molecular dynamics trajectories, paying attention to temporary strand-strand alignment, suboligomer formation and evolution of local order. Self-assembling peptides (SAPs) constitute a promising class of biomaterials and an interesting model to study the spontaneous assembly of molecular systems in vitro. With the help of coarse-grained molecular dynamics the self-assembling of diverse SAPs is simulated into molten aggregates. When applied to these systems, Morphoscanner highlights different b-structuring schemes and kinetics related to SAP sequences. It is demonstrated that Morphoscanner is a novel versatile tool designed to probe the aggregation dynamics of self-assembling systems, adaptable to the analysis of differently coarsened simulations of a variety of biomolecules.
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Affiliation(s)
- Gloria A. A. Saracino
- Center for Nanomedicine and Tissue Engineering (CNTE)ASST Ospedale Niguarda Cà GrandaPiazza dell'Ospedale Maggiore 320162MilanItaly
| | - Federico Fontana
- IRCCS Casa Sollievo della SofferenzaOpera di San Pio da PietralcinaViale Capuccini 171013San Giovanni RotondoItaly
| | - Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - João Medeiros Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Fabrizio Gelain
- IRCCS Casa Sollievo della SofferenzaOpera di San Pio da PietralcinaViale Capuccini 171013San Giovanni RotondoItaly
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29
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Higman VA. Solid-state MAS NMR resonance assignment methods for proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:37-65. [PMID: 31047601 DOI: 10.1016/j.pnmrs.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/09/2023]
Abstract
The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D 13C-detected experiments have been used for the assignment of backbone and side-chain 13C and 15N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.
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Affiliation(s)
- Victoria A Higman
- Department of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TU, UK.
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30
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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31
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Spicer CD, Jumeaux C, Gupta B, Stevens MM. Peptide and protein nanoparticle conjugates: versatile platforms for biomedical applications. Chem Soc Rev 2018; 47:3574-3620. [PMID: 29479622 PMCID: PMC6386136 DOI: 10.1039/c7cs00877e] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peptide- and protein-nanoparticle conjugates have emerged as powerful tools for biomedical applications, enabling the treatment, diagnosis, and prevention of disease. In this review, we focus on the key roles played by peptides and proteins in improving, controlling, and defining the performance of nanotechnologies. Within this framework, we provide a comprehensive overview of the key sequences and structures utilised to provide biological and physical stability to nano-constructs, direct particles to their target and influence their cellular and tissue distribution, induce and control biological responses, and form polypeptide self-assembled nanoparticles. In doing so, we highlight the great advances made by the field, as well as the challenges still faced in achieving the clinical translation of peptide- and protein-functionalised nano-drug delivery vehicles, imaging species, and active therapeutics.
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Affiliation(s)
- Christopher D Spicer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, Stockholm, Sweden.
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32
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Rad-Malekshahi M, Fransen MF, Krawczyk M, Mansourian M, Bourajjaj M, Chen J, Ossendorp F, Hennink WE, Mastrobattista E, Amidi M. Self-Assembling Peptide Epitopes as Novel Platform for Anticancer Vaccination. Mol Pharm 2017; 14:1482-1493. [PMID: 28088862 PMCID: PMC5415879 DOI: 10.1021/acs.molpharmaceut.6b01003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/29/2016] [Accepted: 01/14/2017] [Indexed: 12/17/2022]
Abstract
The aim of the present study was to improve the immunogenicity of peptide epitope vaccines using novel nanocarriers based on self-assembling materials. Several studies demonstrated that peptide antigens in nanoparticulate form induce stronger immune responses than their soluble forms. However, several issues such as poor loading and risk of inducing T cell anergy due to premature release of antigenic epitopes have challenged the clinical success of such systems. In the present study, we developed two vaccine delivery systems by appending a self-assembling peptide (Ac-AAVVLLLW-COOH) or a thermosensitive polymer poly(N-isopropylacrylamide (pNIPAm) to the N-terminus of different peptide antigens (OVA250-264, HPV-E743-57) to generate self-assembling peptide epitopes (SAPEs). The obtained results showed that the SAPEs were able to form nanostructures with a diameter from 20 to 200 nm. The SAPEs adjuvanted with CpG induced and expanded antigen-specific CD8+ T cells in mice. Furthermore, tumor-bearing mice vaccinated with SAPEs harboring the HPV E743-57 peptide showed a delayed tumor growth and an increased survival compared to sham-treated mice. In conclusion, self-assembling peptide based systems increase the immunogenicity of peptide epitope vaccines and therefore warrants further development toward clinical use.
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Affiliation(s)
- Mazda Rad-Malekshahi
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Department
of Pharmaceutical Biomaterials and Medical Biomaterials Research Center,
Faculty of Pharmacy, Tehran University of
Medical Sciences, Tehran, Iran
| | - Marieke F. Fransen
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Małgorzata Krawczyk
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mercedeh Mansourian
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Meriem Bourajjaj
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jian Chen
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ferry Ossendorp
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Wim E. Hennink
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maryam Amidi
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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33
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Pellach M, Mondal S, Harlos K, Mance D, Baldus M, Gazit E, Shimon LJW. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure. Angew Chem Int Ed Engl 2017; 56:3252-3255. [PMID: 28191715 PMCID: PMC5412914 DOI: 10.1002/anie.201609877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Indexed: 11/29/2022]
Abstract
The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level.
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Affiliation(s)
- Michal Pellach
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
| | - Karl Harlos
- Division of Structural BiologyWellcome Trust Centre for Human GeneticsUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUK
| | - Deni Mance
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Ehud Gazit
- Department of Molecular Microbiology and BiotechnologyGeorge S. Wise Faculty of Life SciencesTel Aviv UniversityRamat Aviv69978Israel
- Department of Materials Science and EngineeringIby and Aladar Fleischman Faculty of EngineeringTel Aviv UniversityRamat Aviv69978Israel
| | - Linda J. W. Shimon
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovot76100Israel
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34
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Pellach M, Mondal S, Harlos K, Mance D, Baldus M, Gazit E, Shimon LJW. A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michal Pellach
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Karl Harlos
- Division of Structural Biology; Wellcome Trust Centre for Human Genetics; University of Oxford; Roosevelt Drive Oxford OX3 7BN UK
| | - Deni Mance
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Ramat Aviv 69978 Israel
- Department of Materials Science and Engineering; Iby and Aladar Fleischman Faculty of Engineering; Tel Aviv University; Ramat Aviv 69978 Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support; Weizmann Institute of Science; Rehovot 76100 Israel
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35
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Ekiz MS, Cinar G, Khalily MA, Guler MO. Self-assembled peptide nanostructures for functional materials. NANOTECHNOLOGY 2016; 27:402002. [PMID: 27578525 DOI: 10.1088/0957-4484/27/40/402002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.
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Affiliation(s)
- Melis Sardan Ekiz
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800 Turkey
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36
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Jia Z, Whitaker SK, Tomich JM, Chen J. Organization and Structure of Branched Amphipathic Oligopeptide Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9883-91. [PMID: 27584835 PMCID: PMC5039110 DOI: 10.1021/acs.langmuir.6b02421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A class of self-assembling branched amphiphilic peptide capsules (BAPCs) was recently developed that could serve as a new drug delivery vehicle. BAPCs can encapsulate solutes up to ∼12 kDa during assembly, are unusually stable, and are readily taken up by cells with low cytotoxicity. Coarse-grained simulations have supported that BAPCs are defined by bilayers that resemble those formed by diacyl phospholipids. Here, atomistic simulations were performed to characterize the structure and organization of bilayers formed by three branched amphiphilic peptides (BAPs): bis(Ac-FLIVIGSII)-K-K4-CO-NH2, bis(Ac-CHA-LIVIGSII)-K-K4-CO-NH2, and bis(Ac-FLIVI)-K-K4-CO-NH2. The results show BAPs form a network of intra- and intermolecular backbone hydrogen bonds within the same leaflet in addition to hydrophobic side-chain interactions. The terminal residues of two leaflets form an interdigitation region locking two leaflets together. The phenyl groups in bis(Ac-FLIVIGSII)-K-K4-CO-NH2 and bis(Ac-FLIVI)-K-K4-CO-NH2 are tightly packed near the bilayer center but do not formed ordered structures with specific π-π stacking. Replacing phenyl groups with the cyclohexane side chain only slightly increases the level of disorder in bilayer structures and thus should not significantly affect the stability, consistent with experimental results on bis(Ac-CHA-LIVIGSII)-K-K4-CO-NH2 BAPCs. Self-assembly simulations further suggest that leaflet interdigitation likely occurs at early stages of BAPC formation. Atomistic simulations also reveal that the BAPC bilayers are highly permeable to water. This prediction was validated using fluorescence measurements of encapsulated self-quenching dye upon transferring BAPCs to buffers with different salt concentrations. Improved understanding of the organization and structure of BAPC bilayers at the atomic level will provide a basis for future rational modifications of BAP sequence to improve BAPC properties as a new class of delivery vehicle.
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Affiliation(s)
| | | | | | - Jianhan Chen
- Corresponding Author: Phone: (785) 532-2518; Fax: (785) 532-7278;
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37
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Lee J, Choe IR, Kim NK, Kim WJ, Jang HS, Lee YS, Nam KT. Water-Floating Giant Nanosheets from Helical Peptide Pentamers. ACS NANO 2016; 10:8263-8270. [PMID: 27583783 DOI: 10.1021/acsnano.6b00646] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of the important challenges in the development of protein-mimetic materials is understanding the sequence-specific assembly behavior and dynamic folding change. Conventional strategies for constructing two-dimensional (2D) nanostructures from peptides have been limited to using β-sheet forming sequences as building blocks due to their natural tendency to form sheet-like aggregations. We have identified a peptide sequence (YFCFY) that can form dimers via a disulfide bridge, fold into a helix, and assemble into macroscopic flat sheets at the air/water interface. Due to the large driving force for 2D assembly and high elastic modulus of the resulting sheet, the peptide assembly induces flattening of the initially round water droplet. Additionally, we found that stabilization of the helix by dimerization is a key determinant for maintaining macroscopic flatness over a few tens of centimeters even with a uniform thickness of <10 nm. Furthermore, the ability to transfer the sheets from a water droplet to another substrate allows for multiple stacking of 2D peptide nanostructures, suggesting possible applications in biomimetic catalysis, biosensors, and 2D related electronic devices.
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Affiliation(s)
| | | | - Nak-Kyoon Kim
- Korea Advanced Analysis Center, Korea Institute of Science and Technology (KIST) , Seoul, 136-791, Korea
| | - Won-Je Kim
- Korea Advanced Analysis Center, Korea Institute of Science and Technology (KIST) , Seoul, 136-791, Korea
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38
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Barros SM, Whitaker SK, Sukthankar P, Avila LA, Gudlur S, Warner M, Beltrão EIC, Tomich JM. A review of solute encapsulating nanoparticles used as delivery systems with emphasis on branched amphipathic peptide capsules. Arch Biochem Biophys 2016; 596:22-42. [PMID: 26926258 PMCID: PMC4841695 DOI: 10.1016/j.abb.2016.02.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Abstract
Various strategies are being developed to improve delivery and increase the biological half-lives of pharmacological agents. To address these issues, drug delivery technologies rely on different nano-sized molecules including: lipid vesicles, viral capsids and nano-particles. Peptides are a constituent of many of these nanomaterials and overcome some limitations associated with lipid-based or viral delivery systems, such as tune-ability, stability, specificity, inflammation, and antigenicity. This review focuses on the evolution of bio-based drug delivery nanomaterials that self-assemble forming vesicles/capsules. While lipid vesicles are preeminent among the structures; peptide-based constructs are emerging, in particular peptide bilayer delimited capsules. The novel biomaterial-Branched Amphiphilic Peptide Capsules (BAPCs) display many desirable properties. These nano-spheres are comprised of two branched peptides-bis(FLIVI)-K-KKKK and bis(FLIVIGSII)-K-KKKK, designed to mimic diacyl-phosphoglycerides in molecular architecture. They undergo supramolecular self-assembly and form solvent-filled, bilayer delineated capsules with sizes ranging from 20 nm to 2 μm depending on annealing temperatures and time. They are able to encapsulate different fluorescent dyes, therapeutic drugs, radionuclides and even small proteins. While sharing many properties with lipid vesicles, the BAPCs are much more robust. They have been analyzed for stability, size, cellular uptake and localization, intra-cellular retention and, bio-distribution both in culture and in vivo.
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Affiliation(s)
- Sheila M Barros
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA; Department of Biochemistry, Federal University of Pernambuco-UFPE, Recife, Pernambuco, 50670-901, Brazil
| | - Susan K Whitaker
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Pinakin Sukthankar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - L Adriana Avila
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Sushanth Gudlur
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Matt Warner
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Eduardo I C Beltrão
- Department of Biochemistry, Federal University of Pernambuco-UFPE, Recife, Pernambuco, 50670-901, Brazil
| | - John M Tomich
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.
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39
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Min KI, Yun G, Jang Y, Kim KR, Ko YH, Jang HS, Lee YS, Kim K, Kim DP. Covalent Self-Assembly and One-Step Photocrosslinking of Tyrosine-Rich Oligopeptides to Form Diverse Nanostructures. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kyoung-Ik Min
- National Centre of Applied Microfluidic Chemistry; Department of Chemical Engineering; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Gyeongwon Yun
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
| | - Yoonjung Jang
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
- Department of Chemistry; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Kyung-Rok Kim
- National Centre of Applied Microfluidic Chemistry; Department of Chemical Engineering; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Young Ho Ko
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
| | - Hyung-Seok Jang
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-742 Republic of Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-742 Republic of Korea
| | - Kimoon Kim
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
- Department of Chemistry; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Dong-Pyo Kim
- National Centre of Applied Microfluidic Chemistry; Department of Chemical Engineering; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
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40
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Min KI, Yun G, Jang Y, Kim KR, Ko YH, Jang HS, Lee YS, Kim K, Kim DP. Covalent Self-Assembly and One-Step Photocrosslinking of Tyrosine-Rich Oligopeptides to Form Diverse Nanostructures. Angew Chem Int Ed Engl 2016; 55:6925-8. [DOI: 10.1002/anie.201601675] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/22/2016] [Indexed: 01/31/2023]
Affiliation(s)
- Kyoung-Ik Min
- National Centre of Applied Microfluidic Chemistry; Department of Chemical Engineering; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Gyeongwon Yun
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
| | - Yoonjung Jang
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
- Department of Chemistry; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Kyung-Rok Kim
- National Centre of Applied Microfluidic Chemistry; Department of Chemical Engineering; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Young Ho Ko
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
| | - Hyung-Seok Jang
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-742 Republic of Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul 151-742 Republic of Korea
| | - Kimoon Kim
- Center for Self-Assembly and Complexity (CSC); Institute for Basic Science (IBS); Pohang 790-784 Republic of Korea
- Department of Chemistry; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
| | - Dong-Pyo Kim
- National Centre of Applied Microfluidic Chemistry; Department of Chemical Engineering; POSTECH (Pohang University of Science and Technology); Pohang 790-784 Republic of Korea
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Sigg SJ, Postupalenko V, Duskey JT, Palivan CG, Meier W. Stimuli-Responsive Codelivery of Oligonucleotides and Drugs by Self-Assembled Peptide Nanoparticles. Biomacromolecules 2016; 17:935-45. [PMID: 26871486 DOI: 10.1021/acs.biomac.5b01614] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ever more emerging combined treatments exploiting synergistic effects of drug combinations demand smart, responsive codelivery carriers to reveal their full potential. In this study, a multifunctional stimuli-responsive amphiphilic peptide was designed and synthesized to self-assemble into nanoparticles capable of co-bearing and -releasing hydrophobic drugs and antisense oligonucleotides for combined therapies. The rational design was based on a hydrophobic l-tryptophan-d-leucine repeating unit derived from a truncated sequence of gramicidin A (gT), to entrap hydrophobic cargo, which is combined with a hydrophilic moiety of histidines to provide electrostatic affinity to nucleotides. Stimuli-responsiveness was implemented by linking the hydrophobic and hydrophilic sequence through an artificial amino acid bearing a disulfide functional group (H3SSgT). Stimuli-responsive peptides self-assembled in spherical nanoparticles in sizes (100-200 nm) generally considered as preferable for drug delivery applications. Responsive peptide nanoparticles revealed notable nucleotide condensing abilities while maintaining the ability to load hydrophobic cargo. The disulfide cleavage site introduced in the peptide sequence induced responsiveness to physiological concentrations of reducing agent, serving to release the incorporated molecules. Furthermore, the peptide nanoparticles, singly loaded or coloaded with boron-dipyrromethene (BODIPY) and/or antisense oligonucleotides, were efficiently taken up by cells. Such amphiphilic peptides that led to noncytotoxic, reduction-responsive nanoparticles capable of codelivering hydrophobic and nucleic acid payloads simultaneously provide potential toward combined treatment strategies to exploit synergistic effects.
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Affiliation(s)
- Severin J Sigg
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Viktoriia Postupalenko
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Jason T Duskey
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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42
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Rad-Malekshahi M, Lempsink L, Amidi M, Hennink WE, Mastrobattista E. Biomedical Applications of Self-Assembling Peptides. Bioconjug Chem 2015; 27:3-18. [DOI: 10.1021/acs.bioconjchem.5b00487] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mazda Rad-Malekshahi
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Ludwijn Lempsink
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Maryam Amidi
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
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