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Carnaroli M, Deriu MA, Tuszynski JA. Computational Search for Inhibitors of SOD1 Mutant Infectivity as Potential Therapeutics for ALS Disease. Int J Mol Sci 2025; 26:4660. [PMID: 40429802 PMCID: PMC12111112 DOI: 10.3390/ijms26104660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2025] [Revised: 05/02/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025] Open
Abstract
Familial amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by the selective degeneration of motor neurons. Among the main genetic causes of ALS, over 200 mutations have been identified in the Cu/Zn superoxide dismutase (SOD1) protein, a dimeric metalloenzyme essential for converting superoxides from cellular respiration into less toxic products. Point mutations in SOD1 monomers can induce protein misfolding, which spreads to wild-type monomers through a prion-like mechanism, leading to dysfunctions that contribute to the development of the disease. Understanding the structural and functional differences between the wild-type protein and its mutated variants, as well as developing drugs capable of inhibiting the propagation of misfolding, is crucial for identifying new therapeutic strategies. In this work, seven SOD1 mutations (A4V, G41D, G41S, D76V, G85R, G93A, and I104F) were selected, and three-dimensional models of SOD1 dimers composed of one wild-type monomer and one mutated monomer were generated, along with a control dimer consisting solely of wild-type monomers. Molecular dynamics simulations were conducted to investigate conformational differences between the dimers. Additionally, molecular docking was performed using a library of ligands to identify compounds with high affinity for the mutated dimers. The study reveals some differences in the mutated dimers following molecular dynamics simulations and in the docking of the selected ligands with the various dimers.
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Affiliation(s)
- Marco Carnaroli
- DIMEAS, Politecnico di Torino, 10129 Turin, Italy; (M.C.); (M.A.D.)
| | | | - Jack Adam Tuszynski
- DIMEAS, Politecnico di Torino, 10129 Turin, Italy; (M.C.); (M.A.D.)
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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Chen S, Cai H, Du X, Wu P, Tao X, Zhou J, Dang Z, Lu G. Adsorption behavior of hierarchical porous biochar from shrimp shell for tris(2-chloroethyl) phosphate (TCEP): Sorption experiments and DFT calculations. ENVIRONMENTAL RESEARCH 2023; 219:115128. [PMID: 36563975 DOI: 10.1016/j.envres.2022.115128] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/12/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Tris(2-chloroethyl) phosphate (TCEP) as a new type of flame retardant exists in various water environments, causing great risks to humans and the environment. In this study, shrimp shell was used to prepare an economical and environmental-friendly adsorbent for the efficient removal of TCEP. The systematic studies including characterization, removal performance, and adsorption mechanism of shrimp shell biochar toward TCEP were carried out. Adsorption kinetics and thermodynamics showed that fast equilibrium reached within 30 min, the maximum adsorption capacity qm was 108 μmol g-1 at 298 K, and the adsorption process is spontaneous and exothermic. The environmental factor, such as temperature, pH, inorganic anions and organic matter hardly affected the adsorption performance. Structural characterization indicated that the hierarchical porous structure of shrimp shell biochar is the key to excellent adsorption performance. The adsorption mechanisms were further revealed using density functional theory (DFT) calculations, and the hydrogen bond, van der Waals interactions, Cl-H interactions, and pi-H interactions were identified as potential interaction mechanisms between TCEP and specific biochar structures. The calculated binding energy between TCEP and simplified biochar structure suggested that oxygen-containing groups especially carboxyl, hydroxyl and aldehyde facilitate the adsorption. Our work not only provides a novel strategy for the quick remediation of organophosphate-contaminated water environments but also offers new opportunities for crustacean waste biomass valorization.
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Affiliation(s)
- Siyuan Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Haiming Cai
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xiaodong Du
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Peiwen Wu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xueqin Tao
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiangmin Zhou
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, South China University of Technology, Guangzhou, 510006, China
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, China.
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Dashnaw CM, Zhang AY, Gonzalez M, Koone JC, Shaw BF. Metal migration and subunit swapping in ALS-linked SOD1: Zn 2+ transfer between mutant and wild-type occurs faster than the rate of heterodimerization. J Biol Chem 2022; 298:102610. [PMID: 36265587 PMCID: PMC9667317 DOI: 10.1016/j.jbc.2022.102610] [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: 08/01/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
The heterodimerization of WT Cu, Zn superoxide dismutase-1 (SOD1), and mutant SOD1 might be a critical step in the pathogenesis of SOD1-linked amyotrophic lateral sclerosis (ALS). Rates and free energies of heterodimerization (ΔGHet) between WT and ALS-mutant SOD1 in mismatched metalation states-where one subunit is metalated and the other is not-have been difficult to obtain. Consequently, the hypothesis that under-metalated SOD1 might trigger misfolding of metalated SOD1 by "stealing" metal ions remains untested. This study used capillary zone electrophoresis and mass spectrometry to track heterodimerization and metal transfer between WT SOD1, ALS-variant SOD1 (E100K, E100G, D90A), and triply deamidated SOD1 (modeled with N26D/N131D/N139D substitutions). We determined that rates of subunit exchange between apo dimers and metalated dimers-expressed as time to reach 30% heterodimer-ranged from t30% = 67.75 ± 9.08 to 338.53 ± 26.95 min; free energies of heterodimerization ranged from ΔGHet = -1.21 ± 0.31 to -3.06 ± 0.12 kJ/mol. Rates and ΔGHet values of partially metalated heterodimers were more similar to those of fully metalated heterodimers than apo heterodimers, and largely independent of which subunit (mutant or WT) was metal-replete or metal-free. Mass spectrometry and capillary electrophoresis demonstrated that mutant or WT 4Zn-SOD1 could transfer up to two equivalents of Zn2+ to mutant or WT apo-SOD1 (at rates faster than the rate of heterodimerization). This result suggests that zinc-replete SOD1 can function as a chaperone to deliver Zn2+ to apo-SOD1, and that WT apo-SOD1 might increase the toxicity of mutant SOD1 by stealing its Zn2+.
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Peng H, Zhang S, Zhang Z, Wang X, Tian X, Zhang L, Du J, Huang Y, Jin H. Nitric oxide inhibits endothelial cell apoptosis by inhibiting cysteine-dependent SOD1 monomerization. FEBS Open Bio 2022; 12:538-548. [PMID: 34986524 PMCID: PMC8804620 DOI: 10.1002/2211-5463.13362] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/07/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Endothelial cell apoptosis is an important pathophysiology in many cardiovascular diseases. The gasotransmitter nitric oxide (NO) is known to regulate cell survival and apoptosis. However, the mechanism underlying the effect of NO remains unclear. In this research, by targeting cytosolic copper/zinc superoxide dismutase (SOD1) monomerization, we aimed to explore how NO inhibited endothelial cell apoptosis. We showed that treatment with the NO synthase (NOS) inhibitor nomega‐nitro‐l‐arginine methyl ester hydrochloride (L‐NAME) significantly decreased the endogenous NO content of endothelial cells, facilitated the formation of SOD1 monomers, inhibited dismutase activity, and promoted reactive oxygen species (ROS) accumulation in human umbilical vein endothelial cells (HUVECs); by contrast, supplementation with the NO donor sodium nitroprusside (SNP) upregulated NO content, prevented the formation of SOD1 monomers, enhanced dismutase activity, and reduced ROS accumulation in L‐NAME‐treated HUVECs. Mechanistically, tris(2‐carboxyethyl) phosphine hydrochloride (TCEP), a specific reducer of cysteine thiol, increased SOD1 monomer formation, thus preventing the NO‐induced increase in dismutase activity and the decrease in ROS. Furthermore, SNP inhibited HUVEC apoptosis caused by the decrease in endogenous NO, whereas TCEP abolished this protective effect of SNP. In summary, our data reveal that NO protects endothelial cells against apoptosis by inhibiting cysteine‐dependent SOD1 monomerization to enhance SOD1 activity and inhibit oxidative stress.
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Affiliation(s)
- Hanlin Peng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Shangyue Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Zaifeng Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiuli Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoyu Tian
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Lulu Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Junbao Du
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Key Laboratory of Molecular Cardiology, Ministry of Education, Beijing, China
| | - Yaqian Huang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hongfang Jin
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Sakanyan V, Hulin P, Alves de Sousa R, Silva VAO, Hambardzumyan A, Nedellec S, Tomasoni C, Logé C, Pineau C, Roussakis C, Fleury F, Artaud I. Activation of EGFR by small compounds through coupling the generation of hydrogen peroxide to stable dimerization of Cu/Zn SOD1. Sci Rep 2016; 6:21088. [PMID: 26883293 PMCID: PMC4756678 DOI: 10.1038/srep21088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/14/2016] [Indexed: 11/09/2022] Open
Abstract
Activation of cell signaling by reactive chemicals and pollutants is an important issue for human health. It has been shown that lipophilic nitro-benzoxadiazole (NBD) compounds rapidly move across the plasma membrane and enhance Epidermal Growth Factor Receptor (EGFR) tyrosine phosphorylation in cancer cells. Unlike ligand-dependent activation, the mechanism of this induction relies on the generation of hydrogen peroxide, which is involved in the activation of the catalytic site of the receptor and the inactivation of protein tyrosine phosphatase PTP-1B. Production of H2O2 during redox transformation of NBD compounds is associated with the transition of a monomeric form of Cu/Zn superoxide dismutase 1 (SOD1) to stable dimers. The highly stable and functionally active SOD1 dimer, in the absence of adequate activities in downstream reactions, promotes the disproportionate production and accumulation of intracellular hydrogen peroxide shortly after exposure to NBD compounds. The intrinsic fluorescence of small compounds was used to demonstrate their binding to SOD1. Our data indicate that H2O2 and concomitantly generated electrophilic intermediates behave as independent entities, but all contribute to the biological reactivity of NBD compounds. This study opens a promising path to identify new biomarkers of oxidative/electrophilic stress in the progression of cancer and other diseases.
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Affiliation(s)
- Vehary Sakanyan
- IICiMed EA-1155, Faculté de Pharmacie, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France.,ProtNeteomix, 29 rue de Provence, 44700 Orvault, France
| | - Philippe Hulin
- Plate-forme MicroPICell SFR Santé F. Bonamy-FED 4203/Inserm UMS016/CNRS UMS3556, 44007 Nantes, France
| | - Rodolphe Alves de Sousa
- UMR 8601, CNRS, Université Paris Descartes, PRES Paris cité, 45 rue des Saints-Pères, 75270 Paris Cedex06, France
| | - Viviane A O Silva
- UFIP CNRS UMR 6286, Mechanism and Regulation of DNA Repair team, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France
| | | | - Steven Nedellec
- Plate-forme MicroPICell SFR Santé F. Bonamy-FED 4203/Inserm UMS016/CNRS UMS3556, 44007 Nantes, France
| | - Christophe Tomasoni
- IICiMed EA-1155, Faculté de Pharmacie, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France
| | - Cédric Logé
- IICiMed EA-1155, Faculté de Pharmacie, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France
| | - Charles Pineau
- Protim, Inserm U1085-Irset, Campus de Beaulieu, 35042 Rennes, France
| | - Christos Roussakis
- IICiMed EA-1155, Faculté de Pharmacie, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France
| | - Fabrice Fleury
- UFIP CNRS UMR 6286, Mechanism and Regulation of DNA Repair team, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France
| | - Isabelle Artaud
- UMR 8601, CNRS, Université Paris Descartes, PRES Paris cité, 45 rue des Saints-Pères, 75270 Paris Cedex06, France
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