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Stael S, Sabljić I, Audenaert D, Andersson T, Tsiatsiani L, Kumpf RP, Vidal-Albalat A, Lindgren C, Vercammen D, Jacques S, Nguyen L, Njo M, Fernández-Fernández ÁD, Beunens T, Timmerman E, Gevaert K, Van Montagu M, Ståhlberg J, Bozhkov PV, Linusson A, Beeckman T, Van Breusegem F. Structure-function study of a Ca 2+-independent metacaspase involved in lateral root emergence. Proc Natl Acad Sci U S A 2023; 120:e2303480120. [PMID: 37216519 PMCID: PMC10235996 DOI: 10.1073/pnas.2303480120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Metacaspases are part of an evolutionarily broad family of multifunctional cysteine proteases, involved in disease and normal development. As the structure-function relationship of metacaspases remains poorly understood, we solved the X-ray crystal structure of an Arabidopsis thaliana type II metacaspase (AtMCA-IIf) belonging to a particular subgroup not requiring calcium ions for activation. To study metacaspase activity in plants, we developed an in vitro chemical screen to identify small molecule metacaspase inhibitors and found several hits with a minimal thioxodihydropyrimidine-dione structure, of which some are specific AtMCA-IIf inhibitors. We provide mechanistic insight into the basis of inhibition by the TDP-containing compounds through molecular docking onto the AtMCA-IIf crystal structure. Finally, a TDP-containing compound (TDP6) effectively hampered lateral root emergence in vivo, probably through inhibition of metacaspases specifically expressed in the endodermal cells overlying developing lateral root primordia. In the future, the small compound inhibitors and crystal structure of AtMCA-IIf can be used to study metacaspases in other species, such as important human pathogens, including those causing neglected diseases.
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Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Dominique Audenaert
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | | | - Liana Tsiatsiani
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | | | | | | | - Dominique Vercammen
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Silke Jacques
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Long Nguyen
- VIB Screening Core, VIB,9052Ghent, Belgium
- Centre for Bioassay Development and Screening, Ghent University,9000Ghent, Belgium
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Álvaro D. Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Tine Beunens
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Evy Timmerman
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University,9052Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007Uppsala, Sweden
| | - Anna Linusson
- Department of Chemistry, Umeå University,90187Umeå, Sweden
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University,9052Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
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Ramos-Guzmán CA, Ruiz-Pernía JJ, Zinovjev K, Tuñón I. Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1. ACS Catal 2023; 13:4348-4361. [PMID: 37066044 PMCID: PMC10088814 DOI: 10.1021/acscatal.3c00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/27/2023] [Indexed: 03/17/2023]
Abstract
Caspases are cysteine proteases in charge of breaking a peptide bond next to an aspartate residue. Caspases constitute an important family of enzymes involved in cell death and inflammatory processes. A plethora of diseases, including neurological and metabolic diseases and cancer, are associated with the poor regulation of caspase-mediated cell death and inflammation. Human caspase-1 in particular carries out the transformation of the pro-inflammatory cytokine pro-interleukin-1β into its active form, a key process in the inflammatory response and then in many diseases, such as Alzheimer's disease. Despite its importance, the reaction mechanism of caspases has remained elusive. The standard mechanistic proposal valid for other cysteine proteases and that involves the formation of an ion pair in the catalytic dyad is not supported by experimental evidence. Using a combination of classical and hybrid DFT/MM simulations, we propose a reaction mechanism for the human caspase-1 that explains experimental observations, including mutagenesis, kinetic, and structural data. In our mechanistic proposal, the catalytic cysteine, Cys285, is activated after a proton transfer to the amide group of the scissile peptide bond, a process facilitated by hydrogen-bond interactions with Ser339 and His237. The catalytic histidine does not directly participate in any proton transfer during the reaction. After formation of the acylenzyme intermediate, the deacylation step takes place through the activation of a water molecule by the terminal amino group of the peptide fragment formed during the acylation step. The overall activation free energy obtained from our DFT/MM simulations is in excellent agreement with the value derived from the experimental rate constant, 18.7 vs 17.9 kcal·mol-1, respectively. Simulations of the H237A mutant support our conclusions and agree with the reported reduced activity observed for this caspase-1 variant. We propose that this mechanism can explain the reactivity of all cysteine proteases belonging to the CD clan and that differences with respect to other clans could be related to the larger preference showed by enzymes of the CD clan for charged residues at position P1. This mechanism would avoid the free energy penalty associated with the formation of an ion pair. Finally, our structural description of the reaction process can be useful to assist in the design of inhibitors of caspase-1, a target in the treatment of several human diseases.
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Affiliation(s)
- Carlos A. Ramos-Guzmán
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Spain
- Instituto de Materiales Avanzados, Universitat Jaume I, 12071 Castelló, Spain
| | | | - Kirill Zinovjev
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, 46100 Burjassot, Spain
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Movilla S, Martí S, Roca M, Moliner V. Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer's Disease. J Chem Inf Model 2023; 63:950-958. [PMID: 36648276 PMCID: PMC10882967 DOI: 10.1021/acs.jcim.2c01198] [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: 01/18/2023]
Abstract
Alzheimer's disease represents one of the most ambitious challenges for biomedical sciences due to the growing number of cases worldwide in the elderly population and the lack of efficient treatments. One of the recent attempts to develop a treatment points to the cysteine protease RgpB as a promising drug target. In this attempt, several small-molecule covalent inhibitors of this enzyme have been proposed. Here, we report a computational study at the atomic level of the inhibition mechanism of the most promising reported compounds. Molecular dynamics simulations were performed on six of them, and their binding energies in the active site of the protein were computed. Contact maps and interaction energies were decomposed by residues to disclose those key interactions with the enzyme. Finally, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations were performed to evaluate the reaction mechanism by which these drug candidates lead to covalently bound complexes, inhibiting the RgpB protease. The results provide a guide for future re-design of prospective and efficient inhibitors for the treatment of Alzheimer's disease.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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IL-1 family cytokines as drivers and inhibitors of trained immunity. Cytokine 2021; 150:155773. [PMID: 34844039 DOI: 10.1016/j.cyto.2021.155773] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/20/2022]
Abstract
Trained immunity is the long-term memory of innate immune cells, characterised by increased pro-inflammatory responses towards homo- and heterologous secondary stimuli. Interleukin (IL)-1 signalling plays an essential role in the induction of trained immunity, also called innate immune memory. As such, certain anti-inflammatory members of the IL-1 family of cytokines (IL-1F) which interfere with the inflammatory process have the potential to regulate the induction of a trained phenotype. The aim of this review is to provide an update on the role of IL-1F members in the context of trained immunity, emphasising the role of anti-inflammatory cytokines from the IL-1F to inhibit the induction of trained immunity, and touching upon their potential as therapeutics in IL-1-driven inflammatory disorders.
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Movilla S, Martí S, Roca M, Moliner V. Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations. J Chem Inf Model 2021; 61:4582-4593. [PMID: 34472342 DOI: 10.1021/acs.jcim.1c00666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease represents one of the greatest medical concerns for today's population and health services. Its multifactorial inherent nature represents a challenge for its treatment and requires the development of a broad spectrum of drugs. Recently, the cysteine protease gingipain RgpB has been related to neurodegenerative diseases, including Alzheimer's disease, and its inhibition appears to be a promising neuroprotective strategy. Given these features, a computational study that integrates molecular dynamics (MD) simulations with classical and hybrid quantum mechanics/molecular mechanics (QM/MM) potentials was carried out to unravel the atomistic details of RgpB activity. First, a preliminary study based on principal component analysis (PCA), determined the protonation state of the Cys/His catalytic dyad, as well as the crucial role of a flexible loop that favors reactive interactions of the catalytic residues and the peptide in the precatalytic state in its closed conformation. Then, different mechanisms were explored by means of QM/MM MD simulations. The most favorable mechanism consists of two stages. First is an acylation stage that takes place in two steps where, initially, the sulfur atom of the C244 residue attacks the carbonylic carbon of the peptide and the proton of the C244 residue is transferred to the amino group of the peptide in a concerted manner. Subsequently, the peptide bond is broken, and a fragment of the peptide is released. After that, the deacylation stage takes place in a single step where a water molecule attacks the carbonylic carbon of the peptide and a proton of the water is transferred to the C244 residue. The free energy barrier of the rate limiting step is in very good agreement with available experimental data. The mechanism exhibits an unusual role of H211 residue compared with other cysteine proteases but a crucial role of the peptide in triggering the catalysis. Notably, the atomic and energetic particularities found represent a significant contribution to the comprehension of the reaction mechanism and a great opportunity for the design of efficient inhibitors of gingipain RgpB.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Sergio Martí
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universidad Jaume I, 12071, Castellón, Spain
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Tang Y, Feng B, Wang Y, Sun H, You Y, Yu J, Chen B, Xu C, Ruan Y, Cui S, Hu G, Hou T, Chen Z. Structure-based discovery of CZL80, a caspase-1 inhibitor with therapeutic potential for febrile seizures and later enhanced epileptogenic susceptibility. Br J Pharmacol 2020; 177:3519-3534. [PMID: 32346861 DOI: 10.1111/bph.15076] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND PURPOSE Febrile seizures (FS), the most common seizures in childhood and often accompanied by later epileptogenesis, are not well controlled. Inflammatory processes have been implicated in the pathophysiology of epilepsy. However, whether caspase-1 is involved in FS generation and could be a target for the treatment of FS is still unclear. EXPERIMENTAL APPROACH By using pharmacological and gene intervention methods in C57BL/6J mice, we assessed the role of caspase-1 in FS generation. We used structural virtual screening against the active site of caspase-1, to screen compounds for druggable and safe low MW inhibitors of caspase-1 in vitro. One compound was chosen to test in vivo for therapeutic potential, using FS models in neonatal mice and epileptogenesis in adult mice. KEY RESULTS In mice, levels of cleaved caspase-1 increased prior to FS onset. Caspase-1-/- mice were resistant to FS and showed lower neuronal excitability than wild-type littermates. Conversely, overexpression of caspase-1 using in utero electroporation increased neuronal excitability and enhanced susceptibility to FS. The structural virtual screening, using molecular docking approaches for the active site of caspase-1 of over 1 million compounds yielded CZL80, a brain-penetrable, low MW inhibitor of caspase-1. In neonatal mice, CZL80 markedly reduced neuronal excitability and incidence of FS generation, and, in adult mice, relieved later enhanced epileptogenic susceptibility. CZL80 was devoid of acute diazepam-like respiratory depression and chronic liver toxicity. CONCLUSION AND IMPLICATIONS Caspase-1 is essential for FS generation. CZL80 is a promising low MW inhibitor of FS and later enhanced epileptogenic susceptibility.
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Affiliation(s)
- Yangshun Tang
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bo Feng
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yi Wang
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Huiyong Sun
- Department of Pharmachemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yi You
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jie Yu
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bin Chen
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Cenglin Xu
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yeping Ruan
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sunliang Cui
- Department of Pharmachemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Gang Hu
- Department of Pharmacology, School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingjun Hou
- Department of Pharmachemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhong Chen
- Institute of Pharmacology and Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
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Pang H, Wang N, Chai J, Wang X, Zhang Y, Bi Z, Wu W, He G. Discovery of novel TNNI3K inhibitor suppresses pyroptosis and apoptosis in murine myocardial infarction injury. Eur J Med Chem 2020; 197:112314. [PMID: 32344181 DOI: 10.1016/j.ejmech.2020.112314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023]
Abstract
Myocardial infarction (MI) injury is a highly lethal syndrome that has, until recently, suffered from a lack of clinically efficient targeted therapeutics. The cardiac troponin I interacting kinase (TNNI3K) exacerbates ischemia-reperfusion (IR) injury via oxidative stress, thereby promoting cardiomyocyte death. In this current study, we designed and synthesized 35 novel TNNI3K inhibitors with a pyrido[4,5]thieno[2,3-d] pyrimidine scaffold. In vitro results indicated that some of the inhibitors exhibited sub-micromolar TNNI3K inhibitory capacity and good kinase selectivity, as well as cytoprotective activity, in an oxygen-glucose deprivation (OGD) injury cardiomyocyte model. Furthermore, investigation of the mechanism of the representative derivative compound 6o suggested it suppresses pyroptosis and apoptosis in cardiomyocytes by interfering with p38MAPK activation, which was further confirmed in a murine myocardial infarction injury model. In vivo results indicate that compound 6o can markedly reduce myocardial infarction size and alleviate cardiac tissue damage in rats. In brief, our results provide the basis for further development of novel TNNI3K inhibitors for targeted MI therapy.
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Affiliation(s)
- Haiying Pang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Ning Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Jinlong Chai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Xiaoyun Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Yuehua Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Zhiang Bi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China
| | - Wenbin Wu
- Department of Neurology, Chongzhou People's Hospital, Chengdu, 611230, PR China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 610041, PR China.
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