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Paul S, Paul S. Controlling the self-assembly of human calcitonin: a theoretical approach using molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:14496-14510. [PMID: 34184696 DOI: 10.1039/d1cp00825k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human calcitonin (hCT) is a 32-residue amino acid poly-peptide hormone which is secreted by the C-cells (also known as parafollicular cells) of thyroid glands. It acts to inhibit osteoclast cell hormones by reducing the cell function and regulating calcium and phosphate in blood. hCT has a high tendency to assemble into protofilaments with β-sheet conformations. Amyloid fibril formation of hCT reduces its bio-activity and limits its application as a therapeutic drug. Salmon calcitonin (sCT), which also carries the same disulfide bridge at the N and C-terminus, but differs at the 16 residue position from hCT, has less propensity to aggregate than hCT. Human calcitonin has much higher bio-activity than sCT if its aggregation propensity is reduced. Substituting the key residues which are responsible for the aggregation of hCT, is one of the ways to reduce its aggregation and fibril formation. hCT analogues with less aggregation tendency can be exploited as therapeutic drugs. In this work, we study the amyloidogenic behavior of hCT and its peptide based derivatives i.e., sCT, phCT, N17H hCT, Y12L hCT and DM hCT, through classical molecular dynamics (MD) simulations. Our study reveals that sCT is the least aggregation prone derivative, and the double mutation at position 12 and 17 can reduce the aggregation propensity of this peptide. Also, we have applied these mutant variants of hCT as peptide inhibitors in the self-aggregation of hCT. This study could help in understanding and preparing peptide-based inhibitors for hCT fibrillation and their applications as therapeutic drugs.
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Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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Fraczyk A, Janczewski L, Wasko J, Rozniakowski K, Galecki K, Kaminski ZJ, Kolesinska B. Non-Aggregating Amylin Fragments as an Inhibitors of the Aggregation Process of Susceptible to Aggregation Fragments 18-22, 23-27, and 33-37 of Hormone. Chem Biodivers 2021; 18:e2100034. [PMID: 33687147 DOI: 10.1002/cbdv.202100034] [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: 01/16/2021] [Accepted: 02/18/2021] [Indexed: 11/10/2022]
Abstract
Amylin aggregation is one of the factors in the development of diabetes mellitus, which is classified as a civilization disease. The aim of this research was to find whether non-aggregating fragments 1-7, 8-12, 13-17 and 28-32 of amylin would inhibit the aggregation of the amyloidogenic cores 18-22, 23-27, 33-37 of hormone. In the study of the inhibitory potential of non-aggregating amylin fragments, a set of independent methods were used to study aggregation properties (spectroscopic and fluorescence studies with the use of indicators, microscopic studies, circular dichroism studies) and the method of prediction of aggregation properties. The performed research allowed to select the cyclic fragment (1-7) H-KCNTATC-OH with disulfide bond as an inhibitor capable of inhibiting the aggregation of all amyloidogenic cores 18-22, 23-27, 33-37 of the hormone. Additionally, it was found that this peptide inhibits insulin hot spot aggregation, which may indicate its universal utility in inhibiting the process of aggregation of hormones regulating carbohydrate metabolism directly related to the development of diabetes. Research on the possibility of the extensive use of the cyclic fragment (1-7) of H-KCNTATC-OH as a peptide inhibitor of the polypeptide/protein aggregation process is ongoing.
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Affiliation(s)
- Andrzej Fraczyk
- Institute of Applied Computer Science, Lodz University of Technology, Stefanowskiego Łódź, 18/22, 90-537, Lodz, Poland
| | - Lukasz Janczewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Joanna Wasko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Kamil Rozniakowski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Krystian Galecki
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
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Mitra A, Sarkar N. Sequence and structure-based peptides as potent amyloid inhibitors: A review. Arch Biochem Biophys 2020; 695:108614. [PMID: 33010227 DOI: 10.1016/j.abb.2020.108614] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Misfolded and natively disordered globular proteins tend to aggregate together in an interwoven fashion to form fibrous, proteinaceous deposits referred to as amyloid fibrils. Formation and deposition of such insoluble fibrils are the characteristic features of a broad group of diseases, known as amyloidosis. Some of these proteins are known to cause several degenerative disorders in humans, such as Amyloid-Beta (Aβ) in Alzheimer's disease (AD), human Islet Amyloid Polypeptide (hIAPP, amylin) in type 2 diabetes, α-synuclein (α-syn) in Parkinson's disease (PD) and so on. The fact that these proteins do not share any significant sequence or structural homology in their native states make therapy quite challenging. However, it is observed that aggregation-prone proteins and peptides tend to adopt a similar type of secondary structure during the formation of fibrils. Rationally designed peptides can be a potent inhibitor that has been shown to disrupt the fibril structure by binding specifically to the amyloidogenic region(s) within a protein. The following review will analyze the inhibitory potency of both sequence-based and structure-based small peptides that have been shown to inhibit amyloidogenesis of proteins such as Aβ, human amylin, and α-synuclein.
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Affiliation(s)
- Amit Mitra
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, 769008, Odisha, India.
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Lao Z, Chen Y, Tang Y, Wei G. Molecular Dynamics Simulations Reveal the Inhibitory Mechanism of Dopamine against Human Islet Amyloid Polypeptide (hIAPP) Aggregation and Its Destabilization Effect on hIAPP Protofibrils. ACS Chem Neurosci 2019; 10:4151-4159. [PMID: 31436406 DOI: 10.1021/acschemneuro.9b00393] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The aberrant self-assembly of human islet amyloid polypeptide (hIAPP) into toxic oligomers, protofibrils, and mature fibrils is associated with the pathogenesis of type 2 diabetes (T2D). Inhibition of hIAPP aggregation and destabilization of preformed hIAPP fibrils are considered as two major therapeutic strategies for treating T2D. Previous experimental studies reported that dopamine prevented the formation of hIAPP oligomers and fibrils. However, the underlying inhibitory mechanism at the atomic level remains elusive. Herein we investigated the conformational ensembles of hIAPP dimer with and without dopamine using replica-exchange molecular dynamics simulations. The simulations demonstrated that dopamine preferentially bound to R11, L12, F15, H18, F23, I26, L27, and Y37 residues, inhibited the formation of β-sheets in the amyloidogenic regions spanning residues 11RLANFLVH18, 22NFGAIL27, and 30TNVGSNT36, and resulted in more disordered hIAPP dimers, thus hindering the amyloid formation of hIAPP. Protonated and deprotonated dopamine molecules displayed distinct binding capabilities but bound to similar residue sites on hIAPP. Additional microsecond molecular dynamics simulations showed that dopamine mainly bound to the β1 and turn regions of hIAPP protofibril and destabilized the protofibril structure. This study not only revealed the molecular mechanism of dopamine toward the inhibition of hIAPP aggregation but also demonstrated the protofibril-destabilizing effects of dopamine, which may be helpful for the design of drug candidates to treat T2D.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
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