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Sasselli IR, Coluzza I. Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly. J Chem Theory Comput 2024; 20:224-238. [PMID: 38113378 PMCID: PMC10782451 DOI: 10.1021/acs.jctc.3c01015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.
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Affiliation(s)
- Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Ivan Coluzza
- Ikerbasque,
Basque Foundation for Science, Plaza de Euskadi 5, 48009 Bilbao, Spain
- BCMaterials,
Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, 48940 Leioa, Spain
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2
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Du Y, Struppe J, Perrone B, Hassan A, Codina A, Su Y. Efficient analysis of pharmaceutical drug substances and products using a solid-state NMR CryoProbe. Analyst 2023; 148:724-734. [PMID: 36722866 DOI: 10.1039/d2an01903e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is a high-resolution and versatile spectroscopic tool for characterizing pharmaceutical solids. However, the inherent low sensitivity of NMR remains a significant challenge in the analysis of natural abundance drug substances and products. Here, we report, for the first time, the application of a CPMAS CryoProbe™ to improve the sensitivity of 13C and 15N detection by approximately 5 to 6 times for solid-state analysis of a commercial pharmaceutical drug posaconazole (POSA). The sensitivity enhancement enables two-dimensional (2D) 13C-13C and 1H-15N correlation experiments, which are otherwise time-prohibitive using regular MAS probes, for resonance assignment and structural elucidation. These polarization transfer and correlation experiments reveal drug-drug and drug-polymer interactions in amorphous POSA and its amorphous solid dispersion formulation. Our results demonstrated that the CPMAS CryoProbe™ can be widely applied for routine pharmaceutical analysis and advanced structural investigations with significantly enhanced efficiency and throughput.
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Affiliation(s)
- Yong Du
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | | | | | - Alia Hassan
- Bruker Switzerland AG, 8117 Faellanden, Switzerland
| | | | - Yongchao Su
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ 07065, USA.
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3
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Lau CYJ, Benne N, Lou B, Braake DT, Bosman E, van Kronenburg N, Fens M, Broere F, Hennink WE, Mastrobattista E. Tuning surface charges of peptide nanofibers for induction of antigen-specific immune tolerance: an introductory study. J Pharm Sci 2022; 111:1004-1011. [PMID: 35120963 DOI: 10.1016/j.xphs.2022.01.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022]
Abstract
Induction of antigen-specific immune tolerance has emerged as the next frontier in treating autoimmune disorders, including atherosclerosis and graft-vs-host reactions during transplantation. Nanostructures are under investigation as a platform for the coordinated delivery of critical components, i.e., the antigen epitope combined with tolerogenic agents, to the target immune cells and subsequently induce tolerance. In the present study, the utility of supramolecular peptide nanofibers to induce antigen-specific immune tolerance was explored. To study the influence of surface charges of the nanofibers towards the extent of the induced immune response, the flanking charge residues at both ends of the amphipathic fibrillization peptide sequences were varied. Dexamethasone, an immunosuppressive glucocorticoid drug, and the ovalbumin-derived OVA323-339 peptide that binds to I-A(d) MHC Class II were covalently linked at either end of the peptide sequences. It was shown that the functional extensions did not alter the structural integrity of the supramolecular nanofibers. Furthermore, the surface charges of the nanofibers were modulated by the inclusion of charged residues. Dendritic cell culture assays suggested that nanofiber of less negative ζ-potential can augment the antigen-specific tolerogenic response. Our findings illustrate a molecular approach to calibrate the tolerogenic response induced by peptide nanofibers, which pave the way for better design of future tolerogenic immunotherapies.
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Affiliation(s)
- Chun Yin Jerry Lau
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Naomi Benne
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Bo Lou
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands; Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, #08-01, MD6 Centre for Translational Medicine, 14 Medical Drive, 117599, Singapore
| | - Daniëlle Ter Braake
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Esmeralda Bosman
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Nicky van Kronenburg
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Marcel Fens
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Femke Broere
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Wim E Hennink
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Enrico Mastrobattista
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands.
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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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