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Bergasa-Caceres F, Rabitz HA. A Perspective on Interdicting in Protein Misfolding for Therapeutic Drug Design: Modulating the Formation of Nonlocal Contacts in α-Synuclein as a Strategy against Parkinson's Disease. J Phys Chem B 2024; 128:6439-6448. [PMID: 38940731 PMCID: PMC11247489 DOI: 10.1021/acs.jpcb.3c07519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
In recent work we proposed that interdiction in the earliest contact-formation events along the folding pathway of key viral proteins could provide a novel avenue for therapeutic drug design. In this Perspective we explore the potential applicability of the protein folding interdiction strategy in the realm of neurodegenerative diseases with a specific focus on synucleinopathies. In order to fulfill this goal we review the interdiction proposal and its practical challenges, and we present new results concerning design strategies for possible peptide drugs that could be useful in preventing α-synuclein aggregation.
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Affiliation(s)
| | - Herschel A. Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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2
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Odolczyk N, Marzec E, Winiewska-Szajewska M, Poznański J, Zielenkiewicz P. Native Structure-Based Peptides as Potential Protein-Protein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor. Molecules 2021; 26:2157. [PMID: 33918595 PMCID: PMC8070189 DOI: 10.3390/molecules26082157] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus that causes severe respiratory syndrome in humans, which is now referred to as coronavirus disease 2019 (COVID-19). Since December 2019, the new pathogen has rapidly spread globally, with over 65 million cases reported to the beginning of December 2020, including over 1.5 million deaths. Unfortunately, currently, there is no specific and effective treatment for COVID-19. As SARS-CoV-2 relies on its spike proteins (S) to bind to a host cell-surface receptor angiotensin-converting enzyme-2(ACE2), and this interaction is proved to be responsible for entering a virus into host cells, it makes an ideal target for antiviral drug development. In this work, we design three very short peptides based on the ACE2 sequence/structure fragments, which may effectively bind to the receptor-binding domain (RBD) of S protein and may, in turn, disrupt the important virus-host protein-protein interactions, blocking early steps of SARS-CoV-2 infection. Two of our peptides bind to virus protein with affinity in nanomolar range, and as very short peptides have great potential for drug development.
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Affiliation(s)
- Norbert Odolczyk
- Laboratory of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (E.M.); (M.W.-S.); (J.P.)
| | - Ewa Marzec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (E.M.); (M.W.-S.); (J.P.)
| | - Maria Winiewska-Szajewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (E.M.); (M.W.-S.); (J.P.)
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (E.M.); (M.W.-S.); (J.P.)
| | - Piotr Zielenkiewicz
- Laboratory of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; (E.M.); (M.W.-S.); (J.P.)
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Varma N, Singh A, Ravi VK, Thakur M, Kumar S. Deltamethrin modulates the native structure of Hen Egg White Lysozyme and induces its aggregation at physiological pH. Colloids Surf B Biointerfaces 2021; 201:111646. [PMID: 33652208 DOI: 10.1016/j.colsurfb.2021.111646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/26/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
Deltamethrin, a type II pyrethroid pesticide was initially considered as safe for human use. Recent studies have reported several pathophysiological effects of deltamethrin on human and non-human species. However, its effect on structure and function of protein leading to progressive neurodegeneration is poorly understood. In present study, we investigated the interaction of deltamethrin with Hen Egg White Lysozyme (HEWL) at physiological pH and tried to understand the effect of pesticide on structure and function of protein. Employing different biophysical techniques, we shown that deltamethrin induces in vitro aggregation of HEWL in concentration dependent manner. Interaction of pesticide with different amino acids, followed by exposure of hydrophobic regions was driving force of aggregation process. Apart from modulating the hydrophobic domain, deltamethrin is observed to reduce α-helical and promote β-sheet content of lysozyme, eventually converting the globular protein into ThT sensitive amyloid fibrils and amorphous aggregates. Our study also indicate that deltamethrin induced aggregation reduces the catalytic activity of lysozyme.
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Affiliation(s)
- Neelakant Varma
- Laboratory of Forensic Biology and Biotechnology, School of Forensic Science, National Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India(1)
| | - Abhishek Singh
- Laboratory of Forensic Biology and Biotechnology, School of Forensic Science, National Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India(1); Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700 053, India
| | - Vijay K Ravi
- Centre for Nanoscience and Nanotechnology, Aryabhatta Knowledge University, Mithapur, Patna, Bihar, 800 001, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700 053, India
| | - Satish Kumar
- Laboratory of Forensic Biology and Biotechnology, School of Forensic Science, National Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India(1).
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Varma N, Kukrety H, Ravi VK, Kumar S. Bacopa monnieriinhibit hen egg white lysozyme fibrillation and help in retaining its activity at acidic condition. J Biomol Struct Dyn 2019; 38:1786-1797. [DOI: 10.1080/07391102.2019.1617784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Neelakant Varma
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Himanshi Kukrety
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Vijay K. Ravi
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Satish Kumar
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
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Zhan J, Jia H, Semchenko EA, Bian Y, Zhou AM, Li Z, Yang Y, Wang J, Sarkar S, Totsika M, Blanchard H, Jen FEC, Ye Q, Haselhorst T, Jennings MP, Seib KL, Zhou Y. Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides. FASEB J 2019; 33:2095-2104. [PMID: 30260702 PMCID: PMC6338635 DOI: 10.1096/fj.201700613rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2018] [Indexed: 11/11/2022]
Abstract
Bacterial infection is one of the leading causes of death in young, elderly, and immune-compromised patients. The rapid spread of multi-drug-resistant (MDR) bacteria is a global health emergency and there is a lack of new drugs to control MDR pathogens. We describe a heretofore-unexplored discovery pathway for novel antibiotics that is based on self-targeting, structure-disrupting peptides. We show that a helical peptide, KFF- EcH3, derived from the Escherichia coli methionine aminopeptidase can disrupt secondary and tertiary structure of this essential enzyme, thereby killing the bacterium (including MDR strains). Significantly, no detectable resistance developed against this peptide. Based on a computational analysis, our study predicted that peptide KFF- EcH3 has the strongest interaction with the structural core of the methionine aminopeptidase. We further used our approach to identify peptide KFF- NgH1 to target the same enzyme from Neisseria gonorrhoeae. This peptide inhibited bacterial growth and was able to treat a gonococcal infection in a human cervical epithelial cell model. These findings present an exciting new paradigm in antibiotic discovery using self-derived peptides that can be developed to target the structures of any essential bacterial proteins.-Zhan, J., Jia, H., Semchenko, E. A., Bian, Y., Zhou, A. M., Li, Z., Yang, Y., Wang, J., Sarkar, S., Totsika, M., Blanchard, H., Jen, F. E.-C., Ye, Q., Haselhorst, T., Jennings, M. P., Seib, K. L., Zhou, Y. Self-derived structure-disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides.
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Affiliation(s)
- Jian Zhan
- Institute for Glycomics, Griffith University, Queensland, Australia
| | - Husen Jia
- Institute for Glycomics, Griffith University, Queensland, Australia
| | | | - Yunqiang Bian
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Amy M. Zhou
- Queensland Academies–Health Sciences, Southport, Queensland, Australia
| | - Zhixiu Li
- Indiana University School of Informatics, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Yuedong Yang
- Institute for Glycomics, Griffith University, Queensland, Australia
| | - Jihua Wang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Sohinee Sarkar
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Helen Blanchard
- Institute for Glycomics, Griffith University, Queensland, Australia
| | - Freda E.-C. Jen
- Institute for Glycomics, Griffith University, Queensland, Australia
| | - Qizhuang Ye
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- School of Medicine, Shenzhen University, Shenzhen, China
| | | | | | - Kate L. Seib
- Institute for Glycomics, Griffith University, Queensland, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Queensland, Australia
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Indiana University School of Informatics, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, USA
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Varma N, Singh I, Dahiya MS, Ravi VK, Kumar S. Structural perturbation by arsenic triggers the aggregation of hen egg white lysozyme by promoting oligomers formation. Int J Biol Macromol 2017; 109:1108-1114. [PMID: 29153291 DOI: 10.1016/j.ijbiomac.2017.11.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Abstract
Arsenic trioxide is one of the most common metallic pollutants entering the food chain both by human activities and nature. Its entry inside the living organism through food, air and water results into the accumulation of heavy metal in several tissues which manifest several metabolic or hormonal disorders. Till now the effect of arsenic trioxide on protein misfolding and aggregation culminating into several neurodegenerative disorders is poorly understood. In the present study, we reveal the aggregation process of Hen Egg White Lysozyme (HEWL) in presence of arsenic trioxide (As2O3) at physiological conditions. We show that As2O3 promote the in vitro aggregation of HEWL in concentration dependent manner. Early phase of aggregation is observed to be induced by exposure of hydrophobic surfaces which later reorganized to promote further self-association leading to β sheet structure. Presence of lower ordered oligomers after two days and higher ordered oligomers along with amorphous aggregates after week long incubation indicate that As2O3 drives the self-assembly of lysozyme towards oligomeric form.
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Affiliation(s)
- Neelakant Varma
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India
| | - Inderbhan Singh
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India
| | - Mohinder Singh Dahiya
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India
| | - Vijay Kumar Ravi
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613 401, India
| | - Satish Kumar
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, 382 007, India.
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Mapping Protein-Protein Interactions of the Resistance-Related Bacterial Zeta Toxin-Epsilon Antitoxin Complex (ε₂ζ₂) with High Affinity Peptide Ligands Using Fluorescence Polarization. Toxins (Basel) 2016; 8:toxins8070222. [PMID: 27438853 PMCID: PMC4963854 DOI: 10.3390/toxins8070222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/29/2016] [Accepted: 07/05/2016] [Indexed: 01/01/2023] Open
Abstract
Toxin–antitoxin systems constitute a native survival strategy of pathogenic bacteria and thus are potential targets of antibiotic drugs. Here, we target the Zeta–Epsilon toxin–antitoxin system, which is responsible for the stable maintenance of certain multiresistance plasmids in Gram-positive bacteria. Peptide ligands were designed on the basis of the ε2ζ2 complex. Three α helices of Zeta forming the protein–protein interaction (PPI) site were selected and peptides were designed conserving the residues interacting with Epsilon antitoxin while substituting residues binding intramolecularly to other parts of Zeta. Designed peptides were synthesized with an N-terminal fluoresceinyl-carboxy-residue for binding assays and provided active ligands, which were used to define the hot spots of the ε2ζ2 complex. Further shortening and modification of the binding peptides provided ligands with affinities <100 nM, allowing us to determine the most relevant PPIs and implement a robust competition binding assay.
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Identification of the folding inhibitors of hen-egg lysozyme: gathering the right tools. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:911-9. [PMID: 19326112 DOI: 10.1007/s00249-009-0441-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 03/03/2009] [Accepted: 03/09/2009] [Indexed: 10/21/2022]
Abstract
The unfolded state of proteins displays a surprisingly rich amount of local native structure, which appears to be critical for driving the protein to its native state. Peptides with the same sequence of the corresponding structured segments can be used to interfere with the correct folding of the protein. Using model simulations, we investigate the folding of hen-egg lysozyme, identifying its key segments. Activity assays, NMR and circular dichroism experiments are used to screen the peptides which are able to inhibit the folding of lysozyme. Few peptides, corresponding to the segments of the protein which are structured in the unfolded state, are identified to have significant inhibitory effects.
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