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Kataria A, Srivastava A, Singh DD, Haque S, Han I, Yadav DK. Systematic computational strategies for identifying protein targets and lead discovery. RSC Med Chem 2024; 15:2254-2269. [PMID: 39026640 PMCID: PMC11253860 DOI: 10.1039/d4md00223g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.
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Affiliation(s)
- Arti Kataria
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan Jaipur India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University Jazan-45142 Saudi Arabia
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University Seoul 01897 Republic of Korea +82 32 820 4948
| | - Dharmendra Kumar Yadav
- Department of Biologics, College of Pharmacy, Gachon University Hambakmoeiro 191, Yeonsu-gu Incheon 21924 Republic of Korea
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2
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Leimu L, Holm P, Gąciarz A, Haavisto O, Prince S, Pesonen U, Huovinen T, Lamminmäki U. Epitope-specific antibody fragments block aggregation of AGelD187N, an aberrant peptide in gelsolin amyloidosis. J Biol Chem 2024; 300:107507. [PMID: 38944121 DOI: 10.1016/j.jbc.2024.107507] [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: 04/26/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Aggregation of aberrant fragment of plasma gelsolin, AGelD187N, is a crucial event underlying the pathophysiology of Finnish gelsolin amyloidosis, an inherited form of systemic amyloidosis. The amyloidogenic gelsolin fragment AGelD187N does not play any physiological role in the body, unlike most aggregating proteins related to other protein misfolding diseases. However, no therapeutic agents that specifically and effectively target and neutralize AGelD187N exist. We used phage display technology to identify novel single-chain variable fragments that bind to different epitopes in the monomeric AGelD187N that were further maturated by variable domain shuffling and converted to antigen-binding fragment (Fab) antibodies. The generated antibody fragments had nanomolar binding affinity for full-length AGelD187N, as evaluated by biolayer interferometry. Importantly, all four Fabs selected for functional studies efficiently inhibited the amyloid formation of full-length AGelD187N as examined by thioflavin fluorescence assay and transmission electron microscopy. Two Fabs, neither of which bound to the previously proposed fibril-forming region of AGelD187N, completely blocked the amyloid formation of AGelD187N. Moreover, no small soluble aggregates, which are considered pathogenic species in protein misfolding diseases, were formed after successful inhibition of amyloid formation by the most promising aggregation inhibitor, as investigated by size-exclusion chromatography combined with multiangle light scattering. We conclude that all regions of the full-length AGelD187N are important in modulating its assembly into fibrils and that the discovered epitope-specific anti-AGelD187N antibody fragments provide a promising starting point for a disease-modifying therapy for gelsolin amyloidosis, which is currently lacking.
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Affiliation(s)
- Laura Leimu
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Department of Life Technologies, University of Turku, Turku, Finland; Organon R&D Finland, Turku, Finland
| | - Anna Gąciarz
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Mobidiag, A Hologic Company, Espoo, Finland
| | - Oskar Haavisto
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland.
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3
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Leimu L, Haavisto O, Nesati V, Holm P, Haapalinna A, Salbo R, Pesonen U. Development of an in vitro aggregation assay for long synthetic polypeptide, amyloidogenic gelsolin fragment AGelD187N 173-242. PLoS One 2023; 18:e0290179. [PMID: 37590229 PMCID: PMC10434866 DOI: 10.1371/journal.pone.0290179] [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: 04/11/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Aggregation of the gelsolin protein fragment is the hallmark of the hereditary systemic disease gelsolin amyloidosis. As with other protein misfolding diseases, there is an urgent need for efficient disease-modifying treatment for gelsolin amyloidosis. The formation of amyloids can be reproduced by incubating the disease-causing amyloidogenic 8 kDa polypeptide, 70-residue gelsolin protein fragment, AGelD187N 173-242, in vitro and monitoring the process by thioflavin T dye. However, for screening of potential aggregation inhibitors, the required protein amounts are large and the biotechnological production of amyloidogenic proteins has many challenges. Conversely, use of shorter synthetic regions of AGelD187N 173-242 does not mimic the in vivo aggregation kinetics of full-length fragment as they have different aggregation propensity. In this study, we present an in vitro aggregation assay for full-length AGelD187N 173-242 that has been produced by solid-phase chemical synthesis and after that monomerized carefully. Chemical synthesis allows us to produce high quantities of full-length fragment efficiently and at low cost. We demonstrate that the generated aggregates are fibrillar in nature and how the purity, terminal modification, initial aggregates and seeding affect the aggregation kinetics of a synthetic gelsolin fragment. We also present sufficient quality criteria for the initial monomerized synthetic polypeptide.
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Affiliation(s)
- Laura Leimu
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Oskar Haavisto
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Victor Nesati
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | | | - Rune Salbo
- R&D, Orion Pharma, Orion Corporation, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
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4
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Wei X, Luo P, Zhan L. Tracking the disulfide rearrangement of heated lactoglobulin by matrix-assisted laser desorption/ionization-in-source decay top-down analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4920. [PMID: 37130515 DOI: 10.1002/jms.4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 05/04/2023]
Abstract
Disulfide bond rearrangement is a common occurrence during protein analysis or treatment. A convenient and rapid method has been developed to investigate heat-induced disulfide rearrangement of lactoglobulin using matrix-assisted laser desorption/ionization-in-source decay (MALDI-ISD) technology. By analyzing heated lactoglobulin in reflectron and linear mode, we demonstrated that cysteines C66 and C160 exist as free residues other than linked ones in some protein isomers. This method provides a straightforward and expeditious way to assess the cysteine status and structural changes of proteins under heat stress.
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Affiliation(s)
- Xiaoyun Wei
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
| | - Peiqi Luo
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China
| | - Lingpeng Zhan
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
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5
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Romero-Márquez JM, Forbes-Hernández TY, Navarro-Hortal MD, Quirantes-Piné R, Grosso G, Giampieri F, Lipari V, Sánchez-González C, Battino M, Quiles JL. Molecular Mechanisms of the Protective Effects of Olive Leaf Polyphenols against Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24054353. [PMID: 36901783 PMCID: PMC10001635 DOI: 10.3390/ijms24054353] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Alzheimer's Disease (AD) is the cause of around 60-70% of global cases of dementia and approximately 50 million people have been reported to suffer this disease worldwide. The leaves of olive trees (Olea europaea) are the most abundant by-products of the olive grove industry. These by-products have been highlighted due to the wide variety of bioactive compounds such as oleuropein (OLE) and hydroxytyrosol (HT) with demonstrated medicinal properties to fight AD. In particular, the olive leaf (OL), OLE, and HT reduced not only amyloid-β formation but also neurofibrillary tangles formation through amyloid protein precursor processing modulation. Although the isolated olive phytochemicals exerted lower cholinesterase inhibitory activity, OL demonstrated high inhibitory activity in the cholinergic tests evaluated. The mechanisms underlying these protective effects may be associated with decreased neuroinflammation and oxidative stress via NF-κB and Nrf2 modulation, respectively. Despite the limited research, evidence indicates that OL consumption promotes autophagy and restores loss of proteostasis, which was reflected in lower toxic protein aggregation in AD models. Therefore, olive phytochemicals may be a promising tool as an adjuvant in the treatment of AD.
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Affiliation(s)
- Jose M. Romero-Márquez
- Department of Physiology, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18016 Armilla, Spain
| | - Tamara Y. Forbes-Hernández
- Department of Physiology, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18016 Armilla, Spain
| | - María D. Navarro-Hortal
- Department of Physiology, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18016 Armilla, Spain
| | - Rosa Quirantes-Piné
- Research and Development Functional Food Centre (CIDAF), Health Science Technological Park, Avenida del Conocimiento 37, 18016 Granada, Spain
| | - Giuseppe Grosso
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
- Center for Human Nutrition and Mediterranean Foods (NUTREA), University of Catania, 95123 Catania, Italy
| | - Francesca Giampieri
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
| | - Vivian Lipari
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico
- Department of Prohect Management, Universidade Internacional do Cuanza, Cuito 250, Bié, Angola
| | - Cristina Sánchez-González
- Department of Physiology, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18016 Armilla, Spain
- Sport and Health Research Centre, University of Granada, C/Menéndez Pelayo 32, 18016 Granada, Spain
| | - Maurizio Battino
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- International Joint Research Laboratory of Intelligent Agriculture and Agri-Products Processing, Jiangsu University, Zhenjiang 212013, China
| | - José L. Quiles
- Department of Physiology, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18016 Armilla, Spain
- Research and Development Functional Food Centre (CIDAF), Health Science Technological Park, Avenida del Conocimiento 37, 18016 Granada, Spain
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain
- Correspondence:
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6
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Determination of Conformational and Functional Stability of Potential Plague Vaccine Candidate in Formulation. Vaccines (Basel) 2022; 11:vaccines11010027. [PMID: 36679872 PMCID: PMC9865242 DOI: 10.3390/vaccines11010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Generally, protein-based vaccines are available in liquid form and are highly susceptible to instability under elevated temperature changes including freezing conditions. There is a need to create a convenient formulation of protein/peptides that can be stored at ambient conditions without loss of activity or production of adverse effects. The efficiency of naturally occurring biocompatible polymer dextran in improving the shelf-life and biological activity of a highly thermally unstable plague vaccine candidate protein called Low Calcium Response V antigen (LcrV), which can be stored at room temperature (30 ± 2 °C), has been evaluated. To determine the preferential interactions with molecular-level insight into solvent-protein interactions, analytical techniques such asspectroscopy, particle size distribution, gel electrophoresis, microscopy, and thermal analysis have been performed along with the evaluation of humoral immune response, invivo. The analytical methods demonstrate the structural stability of the LcrV protein by expressing its interaction with the excipients in the formulation. The invivo studies elicited the biological activity of the formulated antigen with a significantly higher humoral immune response (p-value = 0.047) when compared to the native, adjuvanted antigen. We propose dextran as a potential biopolymer with its co-excipient sodium chloride (NaCl) to provide protein compactness, i.e., prevent protein unfolding by molecular crowding or masking mechanism using preferential hydrophobic interaction for up to three weeks at room temperature (30 ± 2 °C).
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Bollati M, Peqini K, Barone L, Natale C, Beeg M, Gobbi M, Diomede L, Trucchi M, de Rosa M, Pellegrino S. Rational Design of a Peptidomimetic Inhibitor of Gelsolin Amyloid Aggregation. Int J Mol Sci 2022; 23:ijms232213973. [PMID: 36430461 PMCID: PMC9698219 DOI: 10.3390/ijms232213973] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Gelsolin amyloidosis (AGel) is characterized by multiple systemic and ophthalmic features resulting from pathological tissue deposition of the gelsolin (GSN) protein. To date, no cure is available for the treatment of any form of AGel. More than ten single-point substitutions in the GSN gene are responsible for the occurrence of the disease and, among them, D187N/Y is the most widespread variant. These substitutions undergo an aberrant proteolytic cascade, producing aggregation-prone peptides of 5 and 8 kDa, containing the Gelsolin Amyloidogenic Core, spanning residues 182-192 (GAC182-192). Following a structure-based approach, we designed and synthesized three novel sequence-specific peptidomimetics (LB-5, LB-6, and LB-7) built on a piperidine-pyrrolidine unnatural amino acid. LB-5 and LB-6, but not LB-7, efficiently inhibit the aggregation of the GAC182-192 amyloidogenic peptides at sub-stoichiometric concentrations. These peptidomimetics resulted also effective in vivo, in a C. elegans-based assay, in counteracting the proteotoxicity of aggregated GAC182-192. These data pave the way to a novel pharmacological strategy against AGel and also validate a toolbox exploitable in other amyloidogenic diseases.
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Affiliation(s)
- Michela Bollati
- Institute of Biophysics, National Research Council (IBF-CNR), c/o Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Kaliroi Peqini
- Department of Pharmaceutical Science, “A. Marchesini” General and Organic Chemistry Section, University of Milano, Via Venezian 21, 20133 Milano, Italy
| | - Luigi Barone
- Department of Pharmaceutical Science, “A. Marchesini” General and Organic Chemistry Section, University of Milano, Via Venezian 21, 20133 Milano, Italy
| | - Carmina Natale
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Marten Beeg
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Michelangelo Trucchi
- Institute of Biophysics, National Research Council (IBF-CNR), c/o Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Matteo de Rosa
- Institute of Biophysics, National Research Council (IBF-CNR), c/o Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
- Correspondence: (M.d.R.); (S.P.)
| | - Sara Pellegrino
- Department of Pharmaceutical Science, “A. Marchesini” General and Organic Chemistry Section, University of Milano, Via Venezian 21, 20133 Milano, Italy
- Correspondence: (M.d.R.); (S.P.)
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Warsi MS, Habib S, Talha M, Khan S, Singh P, Mir AR, Abidi M, Ali A. 4-Chloro-1,2-phenylenediamine induced structural perturbation and genotoxic aggregation in human serum albumin. Front Chem 2022; 10:1016354. [PMID: 36199663 PMCID: PMC9527296 DOI: 10.3389/fchem.2022.1016354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
4-Chloro-1,2-phenylenediamine (4-Cl-OPD) is a halogenated aromatic diamine used as a precursor in permanent hair color production. Despite its well-documented mutagenic and carcinogenic effects in various in vitro and in vivo models, its role in fibrillar aggregate formation and their genotoxic effect in therapeutic proteins has received less attention. The significance of human serum albumin (HSA) arises from its involvement in bio-regulatory and transport processes. HSA misfolding and aggregation are responsible for some of the most frequent neurodegenerative disorders. We used various complementary approaches to track the formation of amyloid fibrils and their genotoxic effect. Molecular dynamics study demonstrated the complex stability. The impact of 4-Cl-OPD on the structural dynamics of HSA was confirmed by Raman spectroscopy, X-ray diffraction, HPLC and SDS-PAGE. Fibrilllar aggregates were investigated using Congo red assay, DLS, and SEM. The genotoxic nature of 4-Cl-OPD was confirmed using plasmid nicking assay and DAPI staining, which revealed DNA damage and cell apoptosis. 4-Cl-OPD provides a model system for studying fibrillar aggregation and their genotoxic potential in the current investigation. Future studies should investigate the inhibition of the aggregation/fibrillation process, which may yield valuable clinical insights.
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Affiliation(s)
- Mohd Sharib Warsi
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Safia Habib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Mohd Talha
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Shifa Khan
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Priyam Singh
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Minhal Abidi
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
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9
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Aggregation of gelsolin wild-type and G167K/R, N184K, and D187N/Y mutant peptides and inhibition. Mol Cell Biochem 2021; 476:2393-2408. [PMID: 33598831 DOI: 10.1007/s11010-021-04085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Gelsolin, an actin-binding protein, is localized intra- and extracellularly in the bloodstream and throughout the body. Gelsolin amyloidosis is a disease characterized by several point mutations that lead to cleavage and fibrillization of gelsolin. The D187 mutation to N or Y leads to aggregation of peptide fragments with shortest aggregating peptide identified as 182SFNNGDCFILD192. Recently, G167 has also been identified as relevant gelsolin mutation, which leads to gelsolin deposits in kidneys, but its aggregation is much less understood. Hence, we systematically investigated in vitro the aggregation propensities of the following gelsolin peptides: 167GRRVV171 (1), 161RLFQVKG167 (2), 184NNGDCFILDL193 (3), 188CFILDL193 (4), 187DCFILDL193 (5), and their respective mutants (G167K, G167R, N184K, D187Y, D187N), by using spectroscopic methods [fluorescence Proteostat, Thioflavin T (ThT), turbidity assay, and Dynamic Light Scattering (DLS)], and Transmission Electron Microscopy (TEM). The (non) mutant peptides containing CFILDL sequence aggregated into fibrillar networks, while G167R mutation promoted aggregation compared to the wild-type sequence. In the presence of inhibitors, Methylene Blue (MB) and epigallocatechin gallate (EGCG), the gelsolin peptide (3-5) aggregation was reduced with the IC50 values in the 2-13 µM range. We discovered that inhibitors have dual functionality, as aggregation inhibitors and disaggregation promoters, potentially allowing for the prevention and reversal of gelsolin amyloidosis. Such therapeutic strategies may improve outcomes related to other amyloidogenic diseases of the heart, brain, and eye.
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Admane N, Srivastava A, Jamal S, Kundu B, Grover A. Protective Effects of a Neurohypophyseal Hormone Analogue on Prion Aggregation, Cellular Internalization, and Toxicity. ACS Chem Neurosci 2020; 11:2422-2430. [PMID: 31407881 DOI: 10.1021/acschemneuro.9b00299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Herein, we report novel neuroprotective activity of the neurohypophyseal hormone analogue desmopressin (DDAVP) against toxic conformations of human prion protein. Systematic analysis using biophysical techniques in conjunction with surface plasmon resonance, high-end microscopy, conformational antibodies, and cell-based assays demonstrated DDAVP's specific binding and potent antiaggregating effects on prion protein (rPrPres). In addition to subjugating conformational conversion of rPrPres into oligomeric forms, DDAVP also exhibits potent fibril modulatory effects. It eventually ameliorated neuronal toxicity of rPrPres oligomers by significantly reducing their cellular internalization. Molecular dynamics simulations showed that DDAVP prevents β-sheet transitions in the N-terminal amyloidogenic region of prion and induces antagonistic mobilities in its α2-α3 and β2-α2 loop regions. Collectively, our data proposes DDAVP as a new structural motif for rational drug discovery against prion diseases.
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Affiliation(s)
- Nikita Admane
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Ankit Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Salma Jamal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
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11
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Specific keratinase derived designer peptides potently inhibit Aβ aggregation resulting in reduced neuronal toxicity and apoptosis. Biochem J 2019; 476:1817-1841. [DOI: 10.1042/bcj20190183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Compelling evidence implicates self-assembly of amyloid-β (Aβ1–42) peptides into soluble oligomers and fibrils as a major underlying event in Alzheimer's disease (AD) pathogenesis. Herein, we employed amyloid-degrading keratinase (kerA) enzyme as a key Aβ1–42-binding scaffold to identify five keratinase-guided peptides (KgPs) capable of interacting with and altering amyloidogenic conversion of Aβ1–42. The KgPs showed micromolar affinities with Aβ1–42 and abolished its sigmoidal amyloidogenic transition, resulting in abrogation of fibrillogenesis. Comprehensive assessment using dynamic light scattering (DLS), atomic force microscopy (AFM) and Fourier-transform infrared (FTIR) spectroscopy showed that KgPs induced the formation of off-pathway oligomers comparatively larger than the native Aβ1–42 oligomers but with a significantly reduced cross-β signature. These off-pathway oligomers exhibited low immunoreactivity against oligomer-specific (A11) and fibril-specific (OC) antibodies and rescued neuronal cells from Aβ1–42 oligomer toxicity as well as neuronal apoptosis. Structural analysis using molecular docking and molecular dynamics (MD) simulations showed two preferred KgP binding sites (Lys16–Phe20 and Leu28–Val39) on the NMR ensembles of monomeric and fibrillar Aβ1–42, indicating an interruption of crucial hydrophobic and aromatic interactions. Overall, our results demonstrate a new approach for designing potential anti-amyloid molecules that could pave way for developing effective therapeutics against AD and other amyloid diseases.
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12
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Srivastava A, Singh J, Singh Yadav SP, Arya P, Kalim F, Rose P, Ashish, Kundu B. The Gelsolin Pathogenic D187N Mutant Exhibits Altered Conformational Stability and Forms Amyloidogenic Oligomers. Biochemistry 2018; 57:2359-2372. [DOI: 10.1021/acs.biochem.8b00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ankit Srivastava
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Jasdeep Singh
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | | | - Prabha Arya
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Fouzia Kalim
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Pooja Rose
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, IIT Delhi, New Delhi 110016, India
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13
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Expression, purification, and characterization of recombinant 8 kDa gelsolin fragment. Protein Expr Purif 2017; 135:33-36. [DOI: 10.1016/j.pep.2017.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022]
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14
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Gautam S, Karmakar S, Batra R, Sharma P, Pradhan P, Singh J, Kundu B, Chowdhury PK. Polyphenols in combination with β-cyclodextrin can inhibit and disaggregate α-synuclein amyloids under cell mimicking conditions: A promising therapeutic alternative. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:589-603. [DOI: 10.1016/j.bbapap.2017.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 02/17/2017] [Accepted: 02/22/2017] [Indexed: 01/16/2023]
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15
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Singh J, Srivastava A, Sharma P, Pradhan P, Kundu B. DNA intercalators as amyloid assembly modulators: mechanistic insights. RSC Adv 2017. [DOI: 10.1039/c6ra26313e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA intercalators modulate amyloid assembly of proteins through specific hetero-aromatic interactions diverting them to form amorphous aggregates.
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Affiliation(s)
- Jasdeep Singh
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi
- India
| | - Ankit Srivastava
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi
- India
| | - Pankaj Sharma
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi
- India
| | - Prashant Pradhan
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi
- India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences
- Indian Institute of Technology Delhi
- New Delhi
- India
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16
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Modulation of prion polymerization and toxicity by rationally designed peptidomimetics. Biochem J 2016; 474:123-147. [DOI: 10.1042/bcj20160737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 11/17/2022]
Abstract
Misfolding and aggregation of cellular prion protein is associated with a large array of neurological disorders commonly called the transmissible spongiform encephalopathies. Designing inhibitors against prions has remained a daunting task owing to limited information about mechanism(s) of their pathogenic self-assembly. Here, we explore the anti-prion properties of a combinatorial library of bispidine-based peptidomimetics (BPMs) that conjugate amino acids with hydrophobic and aromatic side chains. Keeping the bispidine unit unaltered, a series of structurally diverse BPMs were synthesized and tested for their prion-modulating properties. Administration of Leu- and Trp-BPMs delayed and completely inhibited the amyloidogenic conversion of human prion protein (HuPrP), respectively. We found that each BPM induced the HuPrP to form unique oligomeric nanostructures differing in their biophysical properties, cellular toxicities and response to conformation-specific antibodies. While Leu-BPMs were found to stabilize the oligomers, Trp-BPMs effected transient oligomerization, resulting in the formation of non-toxic, non-fibrillar aggregates. Yet another aromatic residue, Phe, however, accelerated the aggregation process in HuPrP. Molecular insights obtained through MD (molecular dynamics) simulations suggested that each BPM differently engages a conserved Tyr 169 residue at the α2–β2 loop of HuPrP and affects the stability of α2 and α3 helices. Our results demonstrate that this new class of molecules having chemical scaffolds conjugating hydrophobic/aromatic residues could effectively modulate prion aggregation and toxicity.
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17
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Siddiqi MK, Alam P, Chaturvedi SK, Khan RH. Anti-amyloidogenic behavior and interaction of Diallylsulfide with Human Serum Albumin. Int J Biol Macromol 2016; 92:1220-1228. [DOI: 10.1016/j.ijbiomac.2016.08.035] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 11/30/2022]
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18
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Garg DK, Kundu B. Clues for divergent, polymorphic amyloidogenesis through dissection of amyloid forming steps of bovine carbonic anhydrase and its critical amyloid forming stretch. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:794-804. [PMID: 27045222 DOI: 10.1016/j.bbapap.2016.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/12/2016] [Accepted: 03/31/2016] [Indexed: 01/23/2023]
Abstract
Certain amino acid stretches are considered 'critical' to trigger amyloidogenesis in a protein. Synthetic peptides corresponding to these stretches are often used as experimental mimics for studying the amyloidogenesis of their parent protein. Here we provide evidence that such simple extrapolation is misleading. We scrutinized each step of amyloid progression of full length bovine carbonic anhydrase (BCA) and compared it with the amyloidogenic process of its critical peptide stretch 201-227 (PepB). We found that under similar solution conditions amyloidogenesis of BCA followed surface-catalyzed secondary nucleation, whereas, that of PepB followed classical nucleation-dependent pathway. AFM images showed that while BCA formed short, thick and branched fibrils, PepB formed thin, long and unbranched fibrils. Structural information obtained by ATR-FTIR spectroscopy suggested parallel arrangement of intermolecular β-sheet in BCA amyloids in contrast to PepB amyloids which arranged into antiparallel β sheets. Amyloids formed by BCA were unable to seed the fibrillation of PepB and vice versa. Even the intermediates formed during lag phase revealed contrasting FTIR and far UV CD signature, hydrophobicity, morphology and cell cytotoxicity. Thus, we propose that sequences other than critical amyloidogenic stretches may significantly influence the initiation, polymerization and final fibrillar morphology of amyloid forming protein. The results have been discussed in light of primary sequence mediated amyloid polymorphism and its importance in the rational design of amyloid nanomaterials possessing desired physico-chemical properties.
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Affiliation(s)
- Dushyant Kumar Garg
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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19
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Dutta C, Yang M, Long F, Shahbazian-Yassar R, Tiwari A. Preformed Seeds Modulate Native Insulin Aggregation Kinetics. J Phys Chem B 2015; 119:15089-99. [DOI: 10.1021/acs.jpcb.5b07221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Colina Dutta
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Mu Yang
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Fei Long
- Department
of Mechanical Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Reza Shahbazian-Yassar
- Department
of Mechanical Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
- Department
of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ashutosh Tiwari
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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20
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Gelsolin Amyloidogenesis Is Effectively Modulated by Curcumin and Emetine Conjugated PLGA Nanoparticles. PLoS One 2015; 10:e0127011. [PMID: 25996685 PMCID: PMC4440822 DOI: 10.1371/journal.pone.0127011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/09/2015] [Indexed: 11/19/2022] Open
Abstract
Small molecule based therapeutic intervention of amyloids has been limited by their low solubility and poor pharmacokinetic characteristics. We report here, the use of water soluble poly lactic-co-glycolic acid (PLGA)-encapsulated curcumin and emetine nanoparticles (Cm-NPs and Em-NPs, respectively), as potential modulators of gelsolin amyloidogenesis. Using the amyloid-specific dye Thioflavin T (ThT) as an indicator along with electron microscopic imaging we show that the presence of Cm-NPs augmented amyloid formation in gelsolin by skipping the pre-fibrillar assemblies, while Em-NPs induced non-fibrillar aggregates. These two types of aggregates differed in their morphologies, surface hydrophobicity and secondary structural signatures, confirming that they followed distinct pathways. In spite of differences, both these aggregates displayed reduced toxicity against SH-SY5Y human neuroblastoma cells as compared to control gelsolin amyloids. We conclude that the cytotoxicity of gelsolin amyloids can be reduced by either stalling or accelerating its fibrillation process. In addition, Cm-NPs increased the fibrillar bulk while Em-NPs defibrillated the pre-formed gelsolin amyloids. Moreover, amyloid modulation happened at a much lower concentration and at a faster rate by the PLGA encapsulated compounds as compared to their free forms. Thus, besides improving pharmacokinetic and biocompatible properties of curcumin and emetine, PLGA conjugation elevates the therapeutic potential of both small molecules against amyloid fibrillation and toxicity.
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21
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Bhatia NK, Srivastava A, Katyal N, Jain N, Khan MAI, Kundu B, Deep S. Curcumin binds to the pre-fibrillar aggregates of Cu/Zn superoxide dismutase (SOD1) and alters its amyloidogenic pathway resulting in reduced cytotoxicity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:426-36. [PMID: 25666897 DOI: 10.1016/j.bbapap.2015.01.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 12/25/2014] [Accepted: 01/31/2015] [Indexed: 12/13/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects motor neurons. Unfortunately, effective therapeutics against this disease is still not available. Almost 20% of familial ALS (fALS) is suggested to be associated with pathological deposition of superoxide dismutase (SOD1). Evidences suggest that SOD1-containing pathological inclusions in ALS exhibit amyloid like properties. An effective strategy to combat ALS may be to inhibit amyloid formation of SOD1 using small molecules. In the present study, we observed the fibrillation of one of the premature forms of SOD1 (SOD1 with reduced disulfide) in the presence of curcumin. Using ThT binding assay, AFM, TEM images and FTIR, we demonstrate that curcumin inhibits the DTT-induced fibrillation of SOD1 and favors the formation of smaller and disordered aggregates of SOD1. The enhancement in curcumin fluorescence on the addition of oligomers and pre-fibrillar aggregates of SOD1 suggests binding of these species to curcumin. Docking studies indicate that putative binding site of curcumin may be the amyloidogenic regions of SOD1. Further, there is a significant increase in SOD1 mediated toxicity in the regime of pre-fibrillar and fibrillar aggregates which is not evident in curcumin containing samples. All these data suggest that curcumin reduces toxicity by binding to the amyloidogenic regions of the species on the aggregation pathway and blocking the formation of the toxic species. Nanoparticles of curcumin with higher aqueous solubility show similar aggregation control as that of curcumin bulk. This suggests a potential role for curcumin in the treatment of ALS.
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Affiliation(s)
- Nidhi K Bhatia
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Ankit Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Nidhi Jain
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - M Ashhar I Khan
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India.
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