1
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Moisoi N. Mitochondrial proteases modulate mitochondrial stress signalling and cellular homeostasis in health and disease. Biochimie 2024:S0300-9084(24)00141-X. [PMID: 38906365 DOI: 10.1016/j.biochi.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Maintenance of mitochondrial homeostasis requires a plethora of coordinated quality control and adaptations' mechanisms in which mitochondrial proteases play a key role. Their activation or loss of function reverberate beyond local mitochondrial biochemical and metabolic remodelling into coordinated cellular pathways and stress responses that feedback onto the mitochondrial functionality and adaptability. Mitochondrial proteolysis modulates molecular and organellar quality control, metabolic adaptations, lipid homeostasis and regulates transcriptional stress responses. Defective mitochondrial proteolysis results in disease conditions most notably, mitochondrial diseases, neurodegeneration and cancer. Here, it will be discussed how mitochondrial proteases and mitochondria stress signalling impact cellular homeostasis and determine the cellular decision to survive or die, how these processes may impact disease etiopathology, and how modulation of proteolysis may offer novel therapeutic strategies.
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Affiliation(s)
- Nicoleta Moisoi
- Leicester School of Pharmacy, Leicester Institute for Pharmaceutical Health and Social Care Innovations, Faculty of Health and Life Sciences, De Montfort University, The Gateway, Hawthorn Building 1.03, LE1 9BH, Leicester, UK.
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2
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Aduriz-Arrizabalaga J, Mercero JM, De Sancho D, Lopez X. Rules governing metal coordination in Aβ-Zn(II) complex models from quantum mechanical calculations. Phys Chem Chem Phys 2023; 25:27618-27627. [PMID: 37811710 DOI: 10.1039/d3cp02070c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Transition metals directly contribute to the neurotoxicity of the aggregates of the amyloid-forming Aβ peptide. The understanding and rationalization of the coordination modes of metals to Aβ amyloid is, therefore, of paramount importance to understand the capacity of a given metal to promote peptide aggregation. Experimentally, multiple Aβ-metal structures have been resolved, which exhibit different modes of coordination in both the monomeric and oligomeric forms of Aβ. Although Zn(II) metalloproteins are very abundant and often involve cysteine residues in the first coordination shell, in the case of Aβ-Zn(II), though, Zn(II) is coordinated by glutamic/aspartic acid and/or histidine residues exclusively, making for an interesting case study. Here we present a systematic analysis of the underlying chemistry on Aβ-Zn(II) coordination, where relative stabilities of different coordination arrangements indicate that a mixture of Glu/Asp and His residues is favored. A detailed comparison between different coordination shell geometries shows that tetrahedral coordination is generally favored in the aqueous phase. Our calculations show an interplay between dative covalent interactions and electrostatics which explains the observed trends. Multiple structures deposited in the Protein Data Bank support our findings, suggesting that the trends found in our work may be transferable to other Zn(II) metalloproteins with this type of coordination.
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Affiliation(s)
- Julen Aduriz-Arrizabalaga
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
| | - Jose M Mercero
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
| | - Xabier Lopez
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), PK 1072, 20018 Donostia-San Sebastian, Euskadi, Spain.
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3
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Nagano N, Ichihashi Y, Komatsu T, Matsuzaki H, Hata K, Watanabe T, Misawa Y, Suzuki M, Sakamoto S, Kagami Y, Kashiro A, Takeuchi K, Kanemitsu Y, Ochiai H, Watanabe R, Honda K, Urano Y. Development of fluorogenic substrates for colorectal tumor-related neuropeptidases for activity-based diagnosis. Chem Sci 2023; 14:4495-4499. [PMID: 37152255 PMCID: PMC10155908 DOI: 10.1039/d2sc07029d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
The M3 metalloproteases, neurolysin and THOP1, are neuropeptidases that are expressed in various tissues and metabolize neuropeptides, such as neurotensin. The biological roles of these enzymes are not well characterized, partially because the chemical tools to analyse their activities are not well developed. Here, we developed a fluorogenic substrate probe for neurolysin and thimet oligopeptidase 1 (THOP1), which enabled the analysis of enzymatic activity changes in tissue and plasma samples. In particular, the probe was useful for studying enzyme activities in a single-molecule enzyme assay platform, which can detect enzyme activity with high sensitivity. We detected the activity of neurolysin in plasma samples and revealed higher enzyme activity in the blood samples of patients with colorectal tumor. The result indicated that single-molecule neurolysin activity is a promising candidate for a blood biomarker for colorectal cancer diagnosis.
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Affiliation(s)
- Norimichi Nagano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuki Ichihashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hiroyuki Matsuzaki
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Keisuke Hata
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toshiaki Watanabe
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yoshihiro Misawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Misa Suzuki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shingo Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yu Kagami
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Ayumi Kashiro
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
| | - Keiko Takeuchi
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
| | - Yukihide Kanemitsu
- National Cancer Center Hospital 5-1-1 Tsukiji Chuo-ku Tokyo 104-0045 Japan
| | - Hiroki Ochiai
- National Cancer Center Hospital 5-1-1 Tsukiji Chuo-ku Tokyo 104-0045 Japan
| | - Rikiya Watanabe
- Cluster for Pioneering Research, RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kazufumi Honda
- Institute for Advanced Medical Sciences, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine, Nippon Medical School 1-1-5 Sendagi Bunkyo-ku Tokyo 113-8602 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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4
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Lubbe L, Sewell BT, Woodward JD, Sturrock ED. Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization. EMBO J 2022; 41:e110550. [PMID: 35818993 PMCID: PMC9379546 DOI: 10.15252/embj.2021110550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
Hypertension (high blood pressure) is a major risk factor for cardiovascular disease, which is the leading cause of death worldwide. The somatic isoform of angiotensin I‐converting enzyme (sACE) plays a critical role in blood pressure regulation, and ACE inhibitors are thus widely used to treat hypertension and cardiovascular disease. Our current understanding of sACE structure, dynamics, function, and inhibition has been limited because truncated, minimally glycosylated forms of sACE are typically used for X‐ray crystallography and molecular dynamics simulations. Here, we report the first cryo‐EM structures of full‐length, glycosylated, soluble sACE (sACES1211). Both monomeric and dimeric forms of the highly flexible apo enzyme were reconstructed from a single dataset. The N‐ and C‐terminal domains of monomeric sACES1211 were resolved at 3.7 and 4.1 Å, respectively, while the interacting N‐terminal domains responsible for dimer formation were resolved at 3.8 Å. Mechanisms are proposed for intradomain hinging, cooperativity, and homodimerization. Furthermore, the observation that both domains were in the open conformation has implications for the design of sACE modulators.
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Affiliation(s)
- Lizelle Lubbe
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Bryan Trevor Sewell
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Jeremy D Woodward
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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5
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Nikolaeva NS, Yandulova EY, Aleksandrova YR, Starikov AS, Neganova ME. The Role of a Pathological Interaction between β-amyloid and Mitochondria in the Occurrence and Development of Alzheimer's Disease. Acta Naturae 2022; 14:19-34. [PMID: 36348714 PMCID: PMC9611857 DOI: 10.32607/actanaturae.11723] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases in existence. It is characterized by an impaired cognitive function that is due to a progressive loss of neurons in the brain. Extracellular β-amyloid (Aβ) plaques are the main pathological features of the disease. In addition to abnormal protein aggregation, increased mitochondrial fragmentation, altered expression of the genes involved in mitochondrial biogenesis, disruptions in the ER-mitochondria interaction, and mitophagy are observed. Reactive oxygen species are known to affect Aβ expression and aggregation. In turn, oligomeric and aggregated Aβ cause mitochondrial disorders. In this review, we summarize available knowledge about the pathological effects of Aβ on mitochondria and the potential molecular targets associated with proteinopathy and mitochondrial dysfunction for the pharmacological treatment of Alzheimer's disease.
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Affiliation(s)
- N. S. Nikolaeva
- Federal State Budgetary Institution of Science Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Chernogolovka, 142432 Russia
| | - E. Yu. Yandulova
- Federal State Budgetary Institution of Science Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Chernogolovka, 142432 Russia
| | - Yu. R. Aleksandrova
- Federal State Budgetary Institution of Science Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Chernogolovka, 142432 Russia
| | - A. S. Starikov
- Federal State Budgetary Institution of Science Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Chernogolovka, 142432 Russia
| | - M. E. Neganova
- Federal State Budgetary Institution of Science Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Chernogolovka, 142432 Russia
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6
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Probing the Conformational States of Thimet Oligopeptidase in Solution. Int J Mol Sci 2022; 23:ijms23137297. [PMID: 35806299 PMCID: PMC9266445 DOI: 10.3390/ijms23137297] [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: 05/23/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Thimet oligopeptidase (TOP) is a metallopeptidase involved in the metabolism of oligopeptides inside and outside cells of various tissues. It has been proposed that substrate or inhibitor binding in the TOP active site induces a large hinge-bending movement leading to a closed structure, in which the bound ligand is enclosed. The main goal of the present work was to study this conformational change, and fluorescence techniques were used. Four active TOP mutants were created, each equipped with a single-Trp residue (fluorescence donor) and a p-nitro-phenylalanine (pNF) residue as fluorescence acceptor at opposite sides of the active site. pNF was biosynthetically incorporated with high efficiency using the amber codon suppression technology. Inhibitor binding induced shorter Donor-Acceptor (D-A) distances in all mutants, supporting the view that a hinge-like movement is operative in TOP. The activity of TOP is known to be dependent on the ionic strength of the assay buffer and D-A distances were measured at different ionic strengths. Interestingly, a correlation between the D-A distance and the catalytic activity of TOP was observed: the highest activities corresponded to the shortest D-A distances. In this study for the first time the hinge-bending motion of a metallopeptidase in solution could be studied, yielding insight about the position of the equilibrium between the open and closed conformation. This information will contribute to a more detailed understanding of the mode of action of these enzymes, including therapeutic targets like neurolysin and angiotensin-converting enzyme 2 (ACE2).
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7
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Esfahani SH, Abbruscato TJ, Trippier PC, Karamyan VT. Small molecule neurolysin activators, potential multi-mechanism agents for ischemic stroke therapy. Expert Opin Ther Targets 2022; 26:401-404. [PMID: 35543670 DOI: 10.1080/14728222.2022.2077190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Shiva Hadi Esfahani
- Department of Pharmaceutical Sciences, Texas Tech University Health Sciences Center, Amarillo, TX, USA
| | - Thomas J Abbruscato
- Department of Pharmaceutical Sciences, Texas Tech University Health Sciences Center, Amarillo, TX, USA.,Center for Blood Brain Barrier Research, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
| | - Paul C Trippier
- Center for Drug Discovery, University of Nebraska Medical Center, Omaha, NE, USA
| | - Vardan T Karamyan
- Department of Pharmaceutical Sciences, Texas Tech University Health Sciences Center, Amarillo, TX, USA.,Center for Blood Brain Barrier Research, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA
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8
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Xiang X, Bao R, Wu Y, Luo Y. Targeting Mitochondrial Proteases for Therapy of Acute Myeloid Leukemia. Br J Pharmacol 2022; 179:3268-3282. [PMID: 35352341 DOI: 10.1111/bph.15844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Targeting cancer metabolism has emerged as an attractive approach to improve therapeutic regimens in acute myeloid leukemia (AML). Mitochondrial proteases are closely related to cancer metabolism, but their biological functions have not been well characterized in AML. According to different catogory, we comprehensively reviewed the role of mitochondrial proteases in AML. This review highlights some 'powerful' mitochondrial protease targets, including their biological function, chemical modulators, and applicative prospect in AML.
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Affiliation(s)
- Xinrong Xiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Rui Bao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Wu
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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9
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Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. EPMA J 2022; 13:149-175. [PMID: 35013687 PMCID: PMC8732965 DOI: 10.1007/s13167-021-00267-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022]
Abstract
Aims The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein–protein interface. Results Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike “boat-shaped” receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the “stern” or “bow” regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the “hull” region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00267-w.
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Abstract
Peptidases generate bioactive peptides that can regulate cell signaling and mediate intercellular communication. While the processing of peptide precursors is initiated intracellularly, some modifications by peptidases may be conducted extracellularly. Thimet oligopeptidase (TOP) is a peptidase that processes neuroendocrine peptides with roles in mood, metabolism, and immune responses, among other functions. TOP also hydrolyzes angiotensin I to angiotensin 1–7, which may be involved in the pathophysiology of COVID-19 infection. Although TOP is primarily cytosolic, it can also be associated with the cell plasma membrane or secreted to the extracellular space. Recent work indicates that membrane-associated TOP can be released with extracellular vesicles (EVs) to the extracellular space. Here we briefly summarize the enzyme’s classical function in extracellular processing of neuroendocrine peptides, as well as its more recently understood role in intracellular processing of various peptides that impact human diseases. Finally, we discuss new findings of EV-associated TOP in the extracellular space.
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11
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Rahman MS, Kumari S, Esfahani SH, Nozohouri S, Jayaraman S, Kinarivala N, Kocot J, Baez A, Farris D, Abbruscato TJ, Karamyan VT, Trippier PC. Discovery of First-in-Class Peptidomimetic Neurolysin Activators Possessing Enhanced Brain Penetration and Stability. J Med Chem 2021; 64:12705-12722. [PMID: 34436882 DOI: 10.1021/acs.jmedchem.1c00759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptidase neurolysin (Nln) is an enzyme that functions to cleave various neuropeptides. Upregulation of Nln after stroke has identified the enzyme as a critical endogenous cerebroprotective mechanism and validated target for the treatment of ischemic stroke. Overexpression of Nln in a mouse model of stroke results in dramatic improvement of stroke outcomes, while pharmacological inhibition aggravates them. Activation of Nln has therefore emerged as an intriguing target for drug discovery efforts for ischemic stroke. Herein, we report the discovery and hit-to-lead optimization of first-in-class Nln activators based on histidine-containing dipeptide hits identified from a virtual screen. Adopting a peptidomimetic approach provided lead compounds that retain the pharmacophoric histidine moiety and possess single-digit micromolar potency over 40-fold greater than the hit scaffolds. These compounds exhibit 5-fold increased brain penetration, significant selectivity over highly homologous peptidases, greater than 65-fold increase in mouse brain stability, and 'drug-like' fraction unbound in the brain.
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Affiliation(s)
- Md Shafikur Rahman
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Shikha Kumari
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Shiva Hadi Esfahani
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Saeideh Nozohouri
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Srinidhi Jayaraman
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Nihar Kinarivala
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Joanna Kocot
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Andrew Baez
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Delaney Farris
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Thomas J Abbruscato
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States.,Center for Blood Brain Barrier Research, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Vardan T Karamyan
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States.,Center for Blood Brain Barrier Research, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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12
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Autophagy and Mitophagy-Related Pathways at the Crossroads of Genetic Pathways Involved in Familial Sarcoidosis and Host-Pathogen Interactions Induced by Coronaviruses. Cells 2021; 10:cells10081995. [PMID: 34440765 PMCID: PMC8393644 DOI: 10.3390/cells10081995] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/16/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Sarcoidosis is a multisystem disease characterized by the development and accumulation of granulomas, the hallmark of an inflammatory process induced by environmental and/or infectious and or genetic factors. This auto-inflammatory disease mainly affects the lungs, the gateway to environmental aggressions and viral infections. We have shown previously that genetic predisposition to sarcoidosis occurring in familial cases is related to a large spectrum of pathogenic variants with, however, a clustering around mTOR (mammalian Target Of Rapamycin)-related pathways and autophagy regulation. The context of the COVID-19 pandemic led us to evaluate whether such genetic defects may increase the risk of a severe course of SARS-CoV2 infection in patients with sarcoidosis. We extended a whole exome screening to 13 families predisposed to sarcoidosis and crossed the genes sharing mutations with the list of genes involved in the SARS-CoV2 host-pathogen protein-protein interactome. A similar analysis protocol was applied to a series of 100 healthy individuals. Using ENRICH.R, a comprehensive gene set enrichment web server, we identified the functional pathways represented in the set of genes carrying deleterious mutations and confirmed the overrepresentation of autophagy- and mitophagy-related functions in familial cases of sarcoidosis. The same protocol was applied to the set of genes common to sarcoidosis and the SARS-CoV2-host interactome and found a significant enrichment of genes related to mitochondrial factors involved in autophagy, mitophagy, and RIG-I-like (Retinoic Acid Inducible Gene 1) Receptor antiviral response signaling. From these results, we discuss the hypothesis according to which sarcoidosis is a model for studying genetic abnormalities associated with host response to viral infections as a consequence of defects in autophagy and mitophagy processes.
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13
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Mirali S, Botham A, Voisin V, Xu C, St-Germain J, Sharon D, Hoff FW, Qiu Y, Hurren R, Gronda M, Jitkova Y, Nachmias B, MacLean N, Wang X, Arruda A, Minden MD, Horton TM, Kornblau SM, Chan SM, Bader GD, Raught B, Schimmer AD. The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplex formation and is necessary for AML viability. Sci Transl Med 2021; 12:12/538/eaaz8264. [PMID: 32269163 DOI: 10.1126/scitranslmed.aaz8264] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 03/09/2020] [Indexed: 12/18/2022]
Abstract
Neurolysin (NLN) is a zinc metallopeptidase whose mitochondrial function is unclear. We found that NLN was overexpressed in almost half of patients with acute myeloid leukemia (AML), and inhibition of NLN was selectively cytotoxic to AML cells and stem cells while sparing normal hematopoietic cells. Mechanistically, NLN interacted with the mitochondrial respiratory chain. Genetic and chemical inhibition of NLN impaired oxidative metabolism and disrupted the formation of respiratory chain supercomplexes (RCS). Furthermore, NLN interacted with the known RCS regulator, LETM1, and inhibition of NLN disrupted LETM1 complex formation. RCS were increased in patients with AML and positively correlated with NLN expression. These findings demonstrate that inhibiting RCS formation selectively targets AML cells and stem cells and highlights the therapeutic potential of pharmacologically targeting NLN in AML.
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Affiliation(s)
- Sara Mirali
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Aaron Botham
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | - Changjiang Xu
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
| | | | - David Sharon
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Fieke W Hoff
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen 9700 RB, Netherlands.,Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rose Hurren
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Marcela Gronda
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Yulia Jitkova
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Boaz Nachmias
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Neil MacLean
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Xiaoming Wang
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Andrea Arruda
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Terzah M Horton
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven M Chan
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Gary D Bader
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada. .,Institute of Medical Science, University of Toronto, Toronto M5S 1A8, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
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14
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Qi J, Yao L. Modulators of neurolysin: promising agents for the treatment of tumor and neurological diseases. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Karamyan VT. Between two storms, vasoactive peptides or bradykinin underlie severity of COVID-19? Physiol Rep 2021; 9:e14796. [PMID: 33687143 PMCID: PMC7941673 DOI: 10.14814/phy2.14796] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to be a world-wide pandemic with overwhelming socioeconomic impact. Since inflammation is one of the major causes of COVID-19 complications, the associated molecular mechanisms have been the focus of many studies to better understand this disease and develop improved treatments for patients contracting SARS-CoV-2. Among these, strong emphasis has been placed on pro-inflammatory cytokines, associating severity of COVID-19 with so-called "cytokine storm." More recently, peptide bradykinin, its dysregulated signaling or "bradykinin storm," has emerged as a primary mechanism to explain COVID-19-related complications. Unfortunately, this important development may not fully capture the main molecular players that underlie the disease severity. To this end, in this focused review, several lines of evidence are provided to suggest that in addition to bradykinin, two closely related vasoactive peptides, substance P and neurotensin, are also likely to drive microvascular permeability and inflammation, and be responsible for development of COVID-19 pathology. Furthermore, based on published experimental observations, it is postulated that in addition to ACE and neprilysin, peptidase neurolysin (Nln) is also likely to contribute to accumulation of bradykinin, substance P and neurotensin, and progression of the disease. In conclusion, it is proposed that "vasoactive peptide storm" may underlie severity of COVID-19 and that simultaneous inhibition of all three peptidergic systems could be therapeutically more advantageous rather than modulation of any single mechanism alone.
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Affiliation(s)
- Vardan T. Karamyan
- Department of Pharmaceutical Sciences and Center for Blood Brain Barrier ResearchSchool of PharmacyTTUHSCAmarilloTXUSA
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16
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Abstract
Current experimental stroke research has evolved to focus on detailed understanding of the brain’s self-protective and restorative mechanisms, and harness this knowledge for development of new therapies. In this context, the role of peptidases and neuropeptides is of growing interest. In this focused review, peptidase neurolysin (Nln) and its extracellular peptide substrates are briefly discussed in relation to pathophysiology of ischemic stroke. Upregulation of Nln following stroke is viewed as a compensatory cerebroprotective mechanism in the acute phase of stroke, because the main neuropeptides inactivated by Nln are neuro/cerebrotoxic (bradykinin, substance P, neurotensin, angiotensin II, hemopressin), whereas the peptides generated by Nln are neuro/cerebroprotective (angiotensin-(1–7), Leu-/Met-enkephalins). This notion is confirmed by experimental studies documenting aggravation of stroke outcomes in mice after inhibition of Nln following stroke, and dramatic improvement of stroke outcomes in mice overexpressing Nln in the brain. The role of Nln in the (sub)chronic phase of stroke is less clear and it is likely, that this peptidase does not have a major role in neural repair mechanisms. This is because, the substrates of Nln are less uniform in modulating neurorestorative mechanisms in one direction, some appearing to have neural repair enhancing/stimulating potential, whereas others doing the opposite. Future studies focusing on the role of Nln in pathophysiology of stroke should determine its potential as a cerebroprotective target for stroke therapy, because its unique ability to modulate multiple neuropeptide systems critically involved in brain injury mechanisms is likely advantageous over modulation of one pathogenic pathway for stroke pharmacotherapy.
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Affiliation(s)
- Vardan T Karamyan
- Department of Pharmaceutical Sciences and Center for Blood Brain Barrier Research, School of Pharmacy, TTUHSC, Amarillo, TX, USA
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17
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Kücükköse C, Taskin AA, Marada A, Brummer T, Dennerlein S, Vögtle FN. Functional coupling of presequence processing and degradation in human mitochondria. FEBS J 2021; 288:600-613. [PMID: 32491259 DOI: 10.1111/febs.15358] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/31/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022]
Abstract
The mitochondrial proteome is built and maintained mainly by import of nuclear-encoded precursor proteins. Most of these precursors use N-terminal presequences as targeting signals that are removed by mitochondrial matrix proteases. The essential mitochondrial processing protease MPP cleaves presequences after import into the organelle thereby enabling protein folding and functionality. The cleaved presequences are subsequently degraded by peptidases. While most of these processes have been discovered in yeast, characterization of the human enzymes is still scarce. As the matrix presequence peptidase PreP has been reported to play a role in Alzheimer's disease, analysis of impaired peptide turnover in human cells is of huge interest. Here, we report the characterization of HEK293T PreP knockout cells. Loss of PreP causes severe defects in oxidative phosphorylation and changes in nuclear expression of stress response marker genes. The mitochondrial defects upon lack of PreP result from the accumulation of presequence peptides that trigger feedback inhibition of MPP and accumulation of nonprocessed precursor proteins. Also, the mitochondrial intermediate peptidase MIP that cleaves eight residues from a subset of precursors after MPP processing is compromised upon loss of PreP suggesting that PreP also degrades MIP generated octapeptides. Investigation of the PrePR183Q patient mutation associated with neurological disorders revealed that the mutation destabilizes the protein making it susceptible to enhanced degradation and aggregation upon heat shock. Taken together, our data reveal a functional coupling between precursor processing by MPP and MIP and presequence degradation by PreP in human mitochondria that is crucial to maintain a functional organellar proteome.
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Affiliation(s)
- Cansu Kücükköse
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
- Faculty of Biology, University of Freiburg, Germany
| | - Asli Aras Taskin
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
| | - Adinarayana Marada
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
| | - Tilman Brummer
- Faculty of Medicine, Institute of Molecular Medicine and Cell Research, University of Freiburg, Germany
- Centre for Biological Signalling Studies BIOSS, University of Freiburg, Germany
- Comprehensive Cancer Centre Freiburg, University of Freiburg, Germany
- DKTK Partner Site Freiburg and DKFZ, Heidelberg, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - Friederike-Nora Vögtle
- Faculty of Medicine, Institute of Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany
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18
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Proteomic Characterization of Synaptosomes from Human Substantia Nigra Indicates Altered Mitochondrial Translation in Parkinson's Disease. Cells 2020; 9:cells9122580. [PMID: 33276480 PMCID: PMC7761546 DOI: 10.3390/cells9122580] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 12/25/2022] Open
Abstract
The pathological hallmark of Parkinson's disease (PD) is the loss of neuromelanin-containing dopaminergic neurons within the substantia nigra pars compacta (SNpc). Additionally, numerous studies indicate an altered synaptic function during disease progression. To gain new insights into the molecular processes underlying the alteration of synaptic function in PD, a proteomic study was performed. Therefore, synaptosomes were isolated by density gradient centrifugation from SNpc tissue of individuals at advanced PD stages (N = 5) as well as control subjects free of pathology (N = 5) followed by mass spectrometry-based analysis. In total, 362 proteins were identified and assigned to the synaptosomal core proteome. This core proteome comprised all proteins expressed within the synapses without regard to data analysis software, gender, age, or disease. The differential analysis between control subjects and PD cases revealed that CD9 antigen was overrepresented and fourteen proteins, among them Thymidine kinase 2 (TK2), mitochondrial, 39S ribosomal protein L37, neurolysin, and Methionine-tRNA ligase (MARS2) were underrepresented in PD suggesting an alteration in mitochondrial translation within synaptosomes.
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19
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Vögtle F. Open questions on the mitochondrial unfolded protein response. FEBS J 2020; 288:2856-2869. [DOI: 10.1111/febs.15569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/28/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Friederike‐Nora Vögtle
- Institute of Biochemistry and Molecular Biology ZBMZ Faculty of Medicine University of Freiburg Germany
- CIBSS ‐ Centre for Integrative Biological Signalling Studies University of Freiburg Germany
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20
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Mirali S, Schimmer AD. The role of mitochondrial proteases in leukemic cells and leukemic stem cells. Stem Cells Transl Med 2020; 9:1481-1487. [PMID: 32761807 PMCID: PMC7695628 DOI: 10.1002/sctm.20-0142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/18/2020] [Accepted: 05/30/2020] [Indexed: 12/13/2022] Open
Abstract
The biological function of most mitochondrial proteases has not been well characterized. Moreover, most of the available information on the normal function of these proteases has been derived from studies in model organisms. Recently, the mitochondrial proteases caseinolytic protease P (CLPP) and neurolysin (NLN) have been identified as therapeutic targets in acute myeloid leukemia (AML). Both proteases are overexpressed in approximately 40% of AML patients. Mechanistically, CLPP and NLN maintain the integrity of the mitochondrial respiratory chain: CLPP cleaves defective respiratory chain proteins, while NLN promotes the formation of respiratory chain supercomplexes. In this review, we highlight the functional consequences of inhibiting and activating mitochondrial proteases and discuss their potential as therapeutic targets in AML.
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Affiliation(s)
- Sara Mirali
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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21
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The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity. Biomolecules 2020; 10:biom10020321. [PMID: 32079362 PMCID: PMC7072564 DOI: 10.3390/biom10020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Thimet oligopeptidase (EC 3.4.24.15; EP24.15; THOP1) is a potential therapeutic target, as it plays key biological functions in processing biologically functional peptides. The structural conformation of THOP1 provides a unique restriction regarding substrate size, in that it only hydrolyzes peptides (optimally, those ranging from eight to 12 amino acids) and not proteins. The proteasome activity of hydrolyzing proteins releases a large number of intracellular peptides, providing THOP1 substrates within cells. The present study aimed to investigate the possible function of THOP1 in the development of diet-induced obesity (DIO) and insulin resistance by utilizing a murine model of hyperlipidic DIO with both C57BL6 wild-type (WT) and THOP1 null (THOP1−/−) mice. After 24 weeks of being fed a hyperlipidic diet (HD), THOP1−/− and WT mice ingested similar chow and calories; however, the THOP1−/− mice gained 75% less body weight and showed neither insulin resistance nor non-alcoholic fatty liver steatosis when compared to WT mice. THOP1−/− mice had increased adrenergic-stimulated adipose tissue lipolysis as well as a balanced level of expression of genes and microRNAs associated with energy metabolism, adipogenesis, or inflammation. Altogether, these differences converge to a healthy phenotype of THOP1−/− fed a HD. The molecular mechanism that links THOP1 to energy metabolism is suggested herein to involve intracellular peptides, of which the relative levels were identified to change in the adipose tissue of WT and THOP1−/− mice. Intracellular peptides were observed by molecular modeling to interact with both pre-miR-143 and pre-miR-222, suggesting a possible novel regulatory mechanism for gene expression. Therefore, we successfully demonstrated the previously anticipated relevance of THOP1 in energy metabolism regulation. It was suggested that intracellular peptides were responsible for mediating the phenotypic differences that are described herein by a yet unknown mechanism of action.
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22
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Dalio FM, Machado MFM, Marcondes MF, Juliano MA, Chagas JR, Cunha RLOR, Oliveira V. CPP-Ala-Ala-Tyr-PABA inhibitor analogs with improved selectivity for neurolysin or thimet oligopeptidase. Biochem Biophys Res Commun 2020; 522:368-373. [PMID: 31761323 DOI: 10.1016/j.bbrc.2019.11.097] [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: 11/01/2019] [Accepted: 11/15/2019] [Indexed: 11/15/2022]
Abstract
Thimet oligopeptidase (TOP, EC 3.4.24.15) and neurolysin (NEL, EC 3.4.24.16) are closely related zinc-dependent metalo-oligopeptidases, which take part in the metabolism of oligopeptides (from 5 to 17 amino acid residues) inside and outside cells. Both peptidases are ubiquitously distributed in tissues. TOP is one of the main intracellular peptide-processing enzymes being important for the antigen selection in the MHC Class I presentation route, while NEL function has been more associated with the extracellular degradation of neurotensin. Despite efforts being made to develop specific inhibitors for these peptidases, the most used are: CPP-Ala-Ala-Tyr-PABA, described by Orlowski et al. in 1988, and CPP-Ala-Aib-Tyr-PABA (JA-2) that is an analog more resistant to proteolysis, which development was made by Shrimpton et al. in 2000. In the present work, we describe other analogs of these compounds but, with better discriminatory capacity to inhibit specifically NEL or TOP. The modifications introduced in these new analogs were based on a key difference existent in the extended binding sites of NEL and TOP: the negatively charged Glu469 residue of TOP corresponds to the positively charged Arg470 residue of NEL. These residues are in position to interact with the residue at the P1' and/or P2' of their substrates (mimicked by the Ala-Ala/P1'-P2' residues of the CPP-Ala-Ala-Tyr-PABA). Therefore, exploring this single difference, the following compounds were synthesized: CPP-Asp-Ala-Tyr-PABA, CPP-Arg-Ala-Tyr-PABA, CPP-Ala-Asp-Tyr-PABA, CPP-Ala-Arg-Tyr-PABA. Confirming the predictions, the replacement of each non-charged residue of the internal portion Ala-Ala by a charged residue Asp or Arg resulted in compounds with higher selectivity for NEL or TOP, especially due to the electrostatic attraction or repulsion by the NEL Arg470 or TOP Glu469 residue. The CPP-Asp-Ala-Tyr-PABA and CPP-Ala-Asp-Tyr-PABA presented higher affinities for NEL, and, the CFP-Ala-Arg-Tyr-PABA showed higher affinity for TOP.
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Affiliation(s)
- Fernanda M Dalio
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020, São Paulo, SP, Brazil
| | - Maurício F M Machado
- Centro Interdisciplinar de Investigação Bioquímica (CIIB), Universidade de Mogi das Cruzes, 08780-911, Mogi das Cruzes, SP, Brazil
| | - Marcelo F Marcondes
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020, São Paulo, SP, Brazil
| | - Maria A Juliano
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020, São Paulo, SP, Brazil
| | - Jair R Chagas
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020, São Paulo, SP, Brazil
| | - Rodrigo L O R Cunha
- Laboratório de Biologia Química, Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC, 09210-170, Santo André, SP, Brazil
| | - Vitor Oliveira
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020, São Paulo, SP, Brazil.
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23
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Ghifari AS, Huang S, Murcha MW. The peptidases involved in plant mitochondrial protein import. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6005-6018. [PMID: 31738432 DOI: 10.1093/jxb/erz365] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/08/2019] [Indexed: 05/17/2023]
Abstract
The endosymbiotic origin of the mitochondrion and the subsequent transfer of its genome to the host nucleus has resulted in intricate mechanisms of regulating mitochondrial biogenesis and protein content. The majority of mitochondrial proteins are nuclear encoded and synthesized in the cytosol, thus requiring specialized and dedicated machinery for the correct targeting import and sorting of its proteome. Most proteins targeted to the mitochondria utilize N-terminal targeting signals called presequences that are cleaved upon import. This cleavage is carried out by a variety of peptidases, generating free peptides that can be detrimental to organellar and cellular activity. Research over the last few decades has elucidated a range of mitochondrial peptidases that are involved in the initial removal of the targeting signal and its sequential degradation, allowing for the recovery of single amino acids. The significance of these processing pathways goes beyond presequence degradation after protein import, whereby the deletion of processing peptidases induces plant stress responses, compromises mitochondrial respiratory capability, and alters overall plant growth and development. Here, we review the multitude of plant mitochondrial peptidases that are known to be involved in protein import and processing of targeting signals to detail how their activities can affect organellar protein homeostasis and overall plant growth.
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Affiliation(s)
- Abi S Ghifari
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Perth WA, Australia
| | - Shaobai Huang
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Perth WA, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth WA, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Perth WA, Australia
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24
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Moss S, Subramanian V, Acharya KR. Crystal structure of peptide-bound neprilysin reveals key binding interactions. FEBS Lett 2019; 594:327-336. [PMID: 31514225 DOI: 10.1002/1873-3468.13602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022]
Abstract
Neprilysin (NEP) is a promiscuous zinc metalloprotease with broad substrate specificity and cleaves a remarkable diversity of substrates through endopeptidase action. Two of these - amyloid-β and natriuretic peptides - implicate the enzyme in both Alzheimer's disease and cardiovascular disease, respectively. Here, we report the creation of a catalytically inactive NEP (E584D) to determine the first peptide-bound crystal structure at 2.6 Å resolution. The structure reveals key interactions involved in substrate binding which we have identified to be conserved in other known zinc metalloproteases. In addition, the structure provides evidence for a potential exosite within the central cavity that may play a critical role in substrate positioning. Together, these results contribute to our understanding of the molecular function of NEP.
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Affiliation(s)
- Stephen Moss
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
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25
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Popov LD. Mitochondrial peptides—appropriate options for therapeutic exploitation. Cell Tissue Res 2019; 377:161-165. [DOI: 10.1007/s00441-019-03049-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022]
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26
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The serum protease network—one key to understand complex regional pain syndrome pathophysiology. Pain 2019; 160:1402-1409. [DOI: 10.1097/j.pain.0000000000001503] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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27
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Neurolysin: From Initial Detection to Latest Advances. Neurochem Res 2018; 43:2017-2024. [DOI: 10.1007/s11064-018-2624-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/20/2023]
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