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Huang F, Huang J, Yan J, Liu Y, Lian J, Sun Q, Ding F, Sun Y. Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin. J Chem Inf Model 2024; 64:4500-4510. [PMID: 38745385 DOI: 10.1021/acs.jcim.4c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Human calcitonin (hCT) regulates calcium-phosphorus metabolism, but its amyloid aggregation disrupts physiological activity, increases thyroid carcinoma risk, and hampers its clinical use for bone-related diseases like osteoporosis and Paget's disease. Improving hCT with targeted modifications to mitigate amyloid formation while maintaining its function holds promise as a strategy. Understanding how each residue in hCT's amyloidogenic core affects its structure and aggregation dynamics is crucial for designing effective analogues. Mutants F16L-hCT and F19L-hCT, where Phe residues in the core are replaced with Leu as in nonamyloidogenic salmon calcitonin, showed different aggregation kinetics. However, the molecular effects of these substitutions in hCT are still unclear. Here, we systematically investigated the folding and self-assembly conformational dynamics of hCT, F16L-hCT, and F19L-hCT through multiple long-time scale independent atomistic discrete molecular dynamics (DMD) simulations. Our results indicated that the hCT monomer primarily assumed unstructured conformations with dynamic helices around residues 4-12 and 14-21. During self-assembly, the amyloidogenic core of hCT14-21 converted from dynamic helices to β-sheets. However, substituting F16L did not induce significant conformational changes, as F16L-hCT exhibited characteristics similar to those of wild-type hCT in both monomeric and oligomeric states. In contrast, F19L-hCT exhibited substantially more helices and fewer β-sheets than did hCT, irrespective of their monomers or oligomers. The substitution of F19L significantly enhanced the stability of the helical conformation for hCT14-21, thereby suppressing the helix-to-β-sheet conformational conversion. Overall, our findings elucidate the molecular mechanisms underlying hCT aggregation and the effects of F16L and F19L substitutions on the conformational dynamics of hCT, highlighting the critical role of F19 as an important target in the design of amyloid-resistant hCT analogs for future clinical applications.
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Affiliation(s)
- Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Jiahui Huang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Jiangfang Lian
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Qinxue Sun
- Ningbo Institute of Innovation for Combined Medicine and Engineering, Lihuili Hospital Affiliated to Ningbo University, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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2
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Vismara A, Gautieri A. Molecular insights into nanoplastics-peptides binding and their interactions with the lipid membrane. Biophys Chem 2024; 308:107213. [PMID: 38428229 DOI: 10.1016/j.bpc.2024.107213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/15/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Micro- and nanoplastics have become a significant concern, due to their ubiquitous presence in the environment. These particles can be internalized by the human body through ingestion, inhalation, or dermal contact, and then they can interact with environmental or biological molecules, such as proteins, resulting in the formation of the protein corona. However, information on the role of protein corona in the human body is still missing. Coarse-grain models of the nanoplastics and pentapeptides were created and simulated at the microscale to study the role of protein corona. Additionally, a lipid bilayer coarse-grain model was reproduced to investigate the behavior of the coronated nanoplastics in proximity of a lipid bilayer. Hydrophobic and aromatic amino acids have a high tendency to create stable bonds with all nanoplastics. Moreover, polystyrene and polypropylene establish bonds with polar and charged amino acids. When the coronated nanoplastics are close to a lipid bilayer, different behaviors can be observed. Polyethylene creates a single polymeric chain, while polypropylene tends to break down into its single chains. Polystyrene can both separate into its individual chains and remain aggregated. The protein corona plays an important role when interacting with the nanoplastics and the lipid membrane. More studies are needed to validate the results and to enhance the complexity of the systems.
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Affiliation(s)
- Arianna Vismara
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
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3
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Liu Y, Wang Y, Zhang Y, Zou Y, Wei G, Ding F, Sun Y. Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants. J Chem Inf Model 2023; 63:308-320. [PMID: 36456917 PMCID: PMC9839651 DOI: 10.1021/acs.jcim.2c01202] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Human calcitonin (hCT) is a polypeptide hormone that participates in calcium-phosphorus metabolism. Irreversible aggregation of 32-amino acid hCT into β-sheet-rich amyloid fibrils impairs physiological activity and increases the risk of medullary carcinoma of the thyroid. Amyloid-resistant hCT derivatives substituting critical amyloidogenic residues are of particular interest for clinical applications as therapeutic drugs against bone-related diseases. Uncovering the aggregation mechanism of hCT at the molecular level, therefore, is important for the design of amyloid-resistant hCT analogues. Here, we investigated the aggregation dynamics of hCT, non-amyloidogenic salmon calcitonin (sCT), and two hCT analogues with reduced aggregation tendency─TL-hCT and phCT─using long timescale discrete molecular dynamics simulations. Our results showed that hCT monomers mainly adopted unstructured conformations with dynamically formed helices around the central region. hCT self-assembled into helix-rich oligomers first, followed by a conformational conversion into β-sheet-rich oligomers with β-sheets formed by residues 10-30 and stabilized by aromatic and hydrophobic interactions. Our simulations confirmed that TL-hCT and phCT oligomers featured more helices and fewer β-sheets than hCT. Substitution of central aromatic residues with leucine in TL-hCT and replacing C-terminal hydrophobic residue with hydrophilic amino acid in phCT only locally suppressed β-sheet propensities in the central region and C-terminus, respectively. Having mutations in both central and C-terminal regions, sCT monomers and dynamically formed oligomers predominantly adopted helices, confirming that both central aromatic and C-terminal hydrophobic residues played important roles in the fibrillization of hCT. We also observed the formation of β-barrel intermediates, postulated as the toxic oligomers in amyloidosis, for hCT but not for sCT. Our computational study depicts a complete picture of the aggregation dynamics of hCT and the effects of mutations. The design of next-generation amyloid-resistant hCT analogues should consider the impact on both amyloidogenic regions and also take into account the amplification of transient β-sheet population in monomers upon aggregation.
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Affiliation(s)
- Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
| | - Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Yu Zhang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, P. R. China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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4
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Pizzi A, Sori L, Pigliacelli C, Gautieri A, Andolina C, Bergamaschi G, Gori A, Panine P, Grande AM, Linder MB, Baldelli Bombelli F, Soncini M, Metrangolo P. Emergence of Elastic Properties in a Minimalist Resilin-Derived Heptapeptide upon Bromination. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200807. [PMID: 35723172 DOI: 10.1002/smll.202200807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Bromination is herein exploited to promote the emergence of elastic behavior in a short peptide-SDSYGAP-derived from resilin, a rubber-like protein exerting its role in the jumping and flight systems of insects. Elastic and resilient hydrogels are obtained, which also show self-healing behavior, thanks to the promoted non-covalent interactions that limit deformations and contribute to the structural recovery of the peptide-based hydrogel. In particular, halogen bonds may stabilize the β-sheet organization working as non-covalent cross-links between nearby peptide strands. Importantly, the unmodified peptide (i.e., wild type) does not show such properties. Thus, SDSY(3,5-Br)GAP is a novel minimalist peptide elastomer.
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Affiliation(s)
- Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
| | - Lorenzo Sori
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
| | - Claudia Pigliacelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Puumiehenkuja2, Espoo, FI-00076, Finland
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, 20131, Italy
| | - Clara Andolina
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Puumiehenkuja2, Espoo, FI-00076, Finland
| | - Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR), Milan, 20131, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche - National Research Council of Italy (SCITEC-CNR), Milan, 20131, Italy
| | - Pierre Panine
- Xenocs SAS, 1-3 Allée du Nanomètre, Grenoble, 38000, France
| | - Antonio Mattia Grande
- Department of Aerospace Science and Technology, Politecnico di Milano, via La Masa 34, Milano, 20156, Italy
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, Aalto, FI-00076, Finland
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
| | - Monica Soncini
- Biomolecular Engineering Lab, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, 20131, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab)Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milan, 20131, Italy
- Hyber Center of Excellence, Department of Applied Physics, Aalto University, Puumiehenkuja2, Espoo, FI-00076, Finland
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5
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:450-463. [PMID: 35790379 DOI: 10.1134/s0006297922050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.
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Affiliation(s)
- Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Bioinformatics Institute, Saint Petersburg, 197342, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
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6
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Bergamaschi G, Musicò A, Frigerio R, Strada A, Pizzi A, Talone B, Ghezzi J, Gautieri A, Chiari M, Metrangolo P, Vanna R, Baldelli Bombelli F, Cretich M, Gori A. Composite Peptide-Agarose Hydrogels for Robust and High-Sensitivity 3D Immunoassays. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4811-4822. [PMID: 35060693 DOI: 10.1021/acsami.1c18466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Canonical immunoassays rely on highly sensitive and specific capturing of circulating biomarkers by interacting biomolecular baits. In this frame, bioprobe immobilization in spatially discrete three-dimensional (3D) spots onto analytical surfaces by hydrogel encapsulation was shown to provide relevant advantages over conventional two-dimensional (2D) platforms. Yet, the broad application of 3D systems is still hampered by hurdles in matching their straightforward fabrication with optimal functional properties. Herein, we report on a composite hydrogel obtained by combining a self-assembling peptide (namely, Q3 peptide) with low-temperature gelling agarose that is proved to have simple and robust application in the fabrication of microdroplet arrays, overcoming hurdles and limitations commonly associated with 3D hydrogel assays. We demonstrate the real-case scenario feasibility of our 3D system in the profiling of Covid-19 patients' serum IgG immunoreactivity, which showed remarkably improved signal-to-noise ratio over canonical assays in the 2D format and exquisite specificity. Overall, the new two-component hydrogel widens the perspectives of hydrogel-based arrays and represents a step forward towards their routine use in analytical practices.
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Affiliation(s)
- Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Angelo Musicò
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Roberto Frigerio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Strada
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Benedetta Talone
- Physics Department, Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Jacopo Ghezzi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dept. Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Renzo Vanna
- Istituto di Fotonica e Nanotecnologie─National Research Council of Italy (IFN-CNR), 20133 Milan, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Marina Cretich
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
| | - Alessandro Gori
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"─National Research Council of Italy (SCITEC-CNR), 20131 Milan, Italy
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Yu P, Liu Y, Xie J, Li J. Spatiotemporally controlled calcitonin delivery: Long-term and targeted therapy of skeletal diseases. J Control Release 2021; 338:486-504. [PMID: 34481022 DOI: 10.1016/j.jconrel.2021.08.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 02/05/2023]
Abstract
Bone is a connective tissue that support the entire body and protect the internal organs. However, there are great challenges on curing intractable skeletal diseases such as hypercalcemia, osteoporosis and osteoarthritis. To address these issues, calcitonin (CT) therapy is an effective treatment alternative to regulate calcium metabolism and suppress inflammation response, which are closely related to skeletal diseases. Traditional calcitonin formulation requires frequent administration due to the low bioavailability resulting from the short half-life and abundant calcitonin receptors distributed through the whole body. Therefore, long-term and targeted calcitonin delivery systems (LCDS and TCDS) have been widely explored as the popular strategies to overcome the intrinsic limitations of calcitonin and improve the functions of calcium management and inflammation inhibition in recent years. In this review, we first explain the physiological effects of calcitonin on bone remodeling: (i) inhibitory effects on osteoclasts and (ii) facilitated effects on osteoblasts. Then we summarized four strategies for spatiotemporally controlled delivery of calcitonin: micro-/nanomedicine (e.g. inorganic micro-/nanomedicine, polymeric micro-/nanomedicine and supramolecular assemblies), hydrogels (especially thermosensitive hydrogels), prodrug (PEGylation and targeting design) and hybrid biomaterials. Subsequently, we discussed the application of LCDS and TCDS in treating hypercalcemia, osteoporosis, and arthritis. Understanding and analyzing these advanced calcitonin delivery applications are essential for future development of calcitonin therapies toward skeletal diseases with superior efficacy in clinic.
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Affiliation(s)
- Peng Yu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yanpeng Liu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, PR China
| | - Jing Xie
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, PR China.
| | - Jianshu Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, PR China; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, PR China; Med-X Center for Materials, Sichuan University, Chengdu 610041, PR China.
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8
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Bono N, Coloma Smith B, Moreschi F, Redaelli A, Gautieri A, Candiani G. In silico prediction of the in vitro behavior of polymeric gene delivery vectors. NANOSCALE 2021; 13:8333-8342. [PMID: 33900339 DOI: 10.1039/d0nr09052b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-viral gene delivery vectors have increasingly come under the spotlight, but their performaces are still far from being satisfactory. Therefore, there is an urgent need for forecasting tools and screening methods to enable the development of ever more effective transfectants. Here, coarse-grained (CG) models of gold standard transfectant poly(ethylene imine)s (PEIs) have been profitably used to investigate and highlight the effect of experimentally-relevant parameters, namely molecular weight (2 vs. 10 kDa) and topologies (linear vs. branched), protonation state, and ammine-to-phosphate ratios (N/Ps), on the complexation and the gene silencing efficiency of siRNA molecules. The results from the in vitro screening of cationic polymers and conditions were used to validate the in silico platform that we developed, such that the hits which came out of the CG models were of high practical relevance. We show that our in silico platform enables to foresee the most suitable conditions for the complexation of relevant siRNA-polycation assemblies, thereby providing a reliable predictive tool to test bench transfectants in silico, and foster the design and development of gene delivery vectors.
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Affiliation(s)
- Nina Bono
- GenT LΛB, Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131 Milan, Italy.
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9
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Alıcı H, Demir K. Investigation of the stability and the helix-tail interaction of sCT and its various charged mutants based on comparative molecular dynamics simulations. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2020.111057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Takamatsu Y, Ho G, Wada R, Inoue S, Hashimoto M. Adiponectin paradox as a therapeutic target of the cancer evolvability in aging. Neoplasia 2021; 23:112-117. [PMID: 33310207 PMCID: PMC7726259 DOI: 10.1016/j.neo.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023]
Abstract
Recent study suggests that protofibril-formation of amyloidogenic proteins (APs) might be involved in evolvability, an epigenetic inheritance of multiple stresses, in various biological systems. In cancer, evolvability of multiple APs, such as p53, γ-synuclein and the members of the calcitonin family of peptides, might be involved in various features, including increased cell proliferation, metastasis and medical treatment resistance. In this context, the objective of this paper is to explore the potential therapeutic benefits of reduced APs evolvability against cancer. Notably, the same APs are involved in the pathogenesis of neurodegenerative disease and cancer. Given the unsatisfactory outcomes of recent clinical trial of Aβ immunotherapy in Alzheimer's disease, it is possible that suppressing the aggregation of individual APs might also be not effective in cancer. As such, we highlight the adiponectin (APN) paradox that might be positioned upstream of AP aggregation in both neurodegenerative disease and cancer, as a common therapeutic target in both disease types. Provided that the APN paradox due to APN resistance under the diabetic conditions might promote AP aggregation, suppressing the APN paradox combined with antidiabetic treatments might be effective for the therapy of both neurodegenerative disease and cancer.
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Affiliation(s)
- Yoshiki Takamatsu
- Laboratory for Parkinson's disease, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Gilbert Ho
- PCND Neuroscience Research Institute, Poway, CA, USA
| | - Ryoko Wada
- Laboratory for Parkinson's disease, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan; Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Makoto Hashimoto
- Laboratory for Parkinson's disease, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan.
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11
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Kawasaki T, Yamaguchi Y, Ueda T, Ishikawa Y, Yaji T, Ohta T, Tsukiyama K, Idehara T, Saiki M, Tani M. Irradiation effect of a submillimeter wave from 420 GHz gyrotron on amyloid peptides in vitro. BIOMEDICAL OPTICS EXPRESS 2020; 11:5341-5351. [PMID: 33014618 PMCID: PMC7510884 DOI: 10.1364/boe.395218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
On using the far-infrared radiation system, whether the irradiation effect is thermal or non-thermal is controversial. We irradiated amyloid peptides that are causal factors for amyloidosis by using a submillimeter wave from 420 GHz gyrotron. Fluorescence reagent assay, optical and electron microscopies, and synchrotron-radiation infrared microscopy showed that the irradiation increased the fibrous conformation of peptides at room temperature for 30 min. The temperature increase on the sample was only below 5 K, and a simple heating up to 318 K hardly induced the fibril formation. Therefore, the amyloid aggregation was driven by the far-infrared radiation with little thermal effect.
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Affiliation(s)
- Takayasu Kawasaki
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuusuke Yamaguchi
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Tomomi Ueda
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Yuya Ishikawa
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Toyonari Yaji
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higasi, Kusatsu, Shiga 525-8577, Japan
| | - Toshiaki Ohta
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higasi, Kusatsu, Shiga 525-8577, Japan
| | - Koichi Tsukiyama
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Toshitaka Idehara
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Masatoshi Saiki
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
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A ratiometric electrochemiluminescent immunoassay for calcitonin by using N-(aminobutyl)-N-(ethylisoluminol) and graphite-like carbon nitride. Mikrochim Acta 2019; 186:771. [DOI: 10.1007/s00604-019-3934-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/12/2019] [Indexed: 02/07/2023]
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13
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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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14
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The Anti-Amyloidogenic Action of Doxycycline: A Molecular Dynamics Study on the Interaction with Aβ42. Int J Mol Sci 2019; 20:ijms20184641. [PMID: 31546787 PMCID: PMC6769662 DOI: 10.3390/ijms20184641] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
The pathological aggregation of amyloidogenic proteins is a hallmark of many neurological diseases, including Alzheimer’s disease and prion diseases. We have shown both in vitro and in vivo that doxycycline can inhibit the aggregation of Aβ42 amyloid fibrils and disassemble mature amyloid fibrils. However, the molecular mechanisms of the drug’s anti-amyloidogenic property are not understood. In this study, a series of molecular dynamics simulations were performed to explain the molecular mechanism of the destabilization of Aβ42 fibrils by doxycycline and to compare the action of doxycycline with those of iododoxorubicin (a toxic structural homolog of tetracyclines), curcumin (known to have anti-amyloidogenic activity) and gentamicin (an antibiotic with no experimental evidence of anti-amyloidogenic properties). We found that doxycycline tightly binds the exposed hydrophobic amino acids of the Aβ42 amyloid fibrils, partly leading to destabilization of the fibrillar structure. Clarifying the molecular determinants of doxycycline binding to Aβ42 may help devise further strategies for structure-based drug design for Alzheimer’s disease.
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15
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Molecular dynamics investigation of halogenated amyloidogenic peptides. J Mol Model 2019; 25:124. [PMID: 31020417 DOI: 10.1007/s00894-019-4012-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
Abstract
Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the β-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity. Graphical abstract Molecular dynamics investigation of halogenated amyloidogenic peptides.
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16
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Vasilescu A, Ye R, Boulahneche S, Lamraoui S, Jijie R, Medjram MS, Gáspár S, Singh SK, Kurungot S, Melinte S, Boukherroub R, Szunerits S. Porous reduced graphene oxide modified electrodes for the analysis of protein aggregation. Part 2: Application to the analysis of calcitonin containing pharmaceutical formulation. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.02.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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