1
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Li Y, Nan G, Hou X, Yan Y, Yang Y, Yang Y, Li K, Xiao Z. Non-peptidic immunoproteasome β5i-selective inhibitor as potential treatment for idiopathic pulmonary fibrosis: Virtual screening, hit evolution and lead identification. Eur J Med Chem 2023; 261:115856. [PMID: 37826934 DOI: 10.1016/j.ejmech.2023.115856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
The immunoproteasome has emerged as a potential therapeutic target for idiopathic pulmonary fibrosis (IPF). We report herein our efforts to discover novel non-peptidic immunoproteasome inhibitors as potential treatment for IPF. A structure-based virtual screening was initially performed and the hit compound VS-7 with an IC50 of 9.437 μM against β5i was identified. Hit evolution based on the interaction mode of VS-7 proceeded, and a potent β5i inhibitor 54 (IC50 = 8.463 nM) with favorable subunit-selective profiles was obtained. Compound 54 also imposed significant effects on the release of TNF-α and IL-6, the transcriptional activity of NF-κB, as well as TGF-β1 induced fibroblast proliferation, activation and collagen synthesis. Notably, when administered at 30 mg/kg in a bleomycin-induced IPF mouse model, compound 54 showed anti-fibrotic effects comparable to the clinical drug nintedanib. The results suggest that selective inhibition of immunoproteasome could be an effective approach to treat IPF.
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Affiliation(s)
- Yunxuan Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Guanglei Nan
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xianxin Hou
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yechao Yan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yajun Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ke Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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2
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Gobec M, Obreza A, Jukič M, Baumgartner A, Mihelčič N, Potočnik Š, Virant J, Mlinarič I, Stanislav R, Sosič GI. Design and synthesis of amino-substituted N-arylpiperidinyl-based inhibitors of the (immuno)proteasome. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:441-456. [PMID: 37708963 DOI: 10.2478/acph-2023-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/02/2023] [Indexed: 09/16/2023]
Abstract
The constitutive proteasome and the immunoproteasome represent validated targets for pharmacological intervention in the context of various diseases, such as cancer, inflammation, and autoimmune diseases. The development of novel chemical scaffolds of non-peptidic nature, capable of inhibiting different catalytically active subunits of both isoforms, is a viable approach against these diseases. Such compounds are also useful as leads for the development of biochemical probes that enable the studies of the roles of both isoforms in various biological contexts. Here, we present a ligand-based computational design of (immuno)proteasome inhibitors, which resulted in the amino-substituted N-arylpiperidine-based compounds that can inhibit different subunits of the (immuno)proteasome in the low micromolar range. The compounds represent a useful starting point for further structure-activity relationship studies that will, hopefully, lead to non-peptidic compounds that could be used in pharmacological and biochemical studies of both proteasomes.
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Affiliation(s)
- Martina Gobec
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Aleš Obreza
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Marko Jukič
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
- Current address: University of Maribor, Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, 2000 Maribor Slovenia
| | - Ana Baumgartner
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Nja Mihelčič
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Špela Potočnik
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Julija Virant
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Irena Mlinarič
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
| | - Raščan Stanislav
- University of Ljubljana, Faculty of Pharmacy, 1000 Ljubljana, Slovenia
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3
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Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations. Sci Rep 2022; 12:19986. [PMID: 36411383 PMCID: PMC9676757 DOI: 10.1038/s41598-022-24695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.
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4
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Ogrizek M, Janežič M, Valjavec K, Perdih A. Catalytic Mechanism of ATP Hydrolysis in the ATPase Domain of Human DNA Topoisomerase IIα. J Chem Inf Model 2022; 62:3896-3909. [PMID: 35948041 PMCID: PMC9400105 DOI: 10.1021/acs.jcim.2c00303] [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] [Indexed: 11/29/2022]
Abstract
![]()
Human DNA topoisomerase IIα is a biological nanomachine
that
regulates the topological changes of the DNA molecule and is considered
a prime target for anticancer drugs. Despite intensive research, many
atomic details about its mechanism of action remain unknown. We investigated
the ATPase domain, a segment of the human DNA topoisomerase IIα,
using all-atom molecular simulations, multiscale quantum mechanics/molecular
mechanics (QM/MM) calculations, and a point mutation study. The results
suggested that the binding of ATP affects the overall dynamics of
the ATPase dimer. Reaction modeling revealed that ATP hydrolysis favors
the dissociative substrate-assisted reaction mechanism with the catalytic
Glu87 serving to properly position and polarize the lytic water molecule.
The point mutation study complemented our computational results, demonstrating
that Lys378, part of the important QTK loop, acts as a stabilizing
residue. The work aims to pave the way to a deeper understanding of
these important molecular motors and to advance the development of
new therapeutics.
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Affiliation(s)
- Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Katja Valjavec
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI 1000 Ljubljana, Slovenia
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5
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Kisselev AF. Site-Specific Proteasome Inhibitors. Biomolecules 2021; 12:54. [PMID: 35053202 PMCID: PMC8773591 DOI: 10.3390/biom12010054] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/14/2022] Open
Abstract
Proteasome is a multi-subunit protein degradation machine, which plays a key role in the maintenance of protein homeostasis and, through degradation of regulatory proteins, in the regulation of numerous cell functions. Proteasome inhibitors are essential tools for biomedical research. Three proteasome inhibitors, bortezomib, carfilzomib, and ixazomib are approved by the FDA for the treatment of multiple myeloma; another inhibitor, marizomib, is undergoing clinical trials. The proteolytic core of the proteasome has three pairs of active sites, β5, β2, and β1. All clinical inhibitors and inhibitors that are widely used as research tools (e.g., epoxomicin, MG-132) inhibit multiple active sites and have been extensively reviewed in the past. In the past decade, highly specific inhibitors of individual active sites and the distinct active sites of the lymphoid tissue-specific immunoproteasome have been developed. Here, we provide a comprehensive review of these site-specific inhibitors of mammalian proteasomes and describe their utilization in the studies of the biology of the active sites and their roles as drug targets for the treatment of different diseases.
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Affiliation(s)
- Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA
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6
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Zhou Y, Gou Z, Huang L, Fan Y, Zhang F, Lu L. Inhibition of immunoproteasome subunit low molecular mass polypeptide 7 with ONX-0914 improves hypoxic-ischemic brain damage via PI3K/Akt signaling. Neuroreport 2021; 32:1206-1215. [PMID: 34406990 PMCID: PMC8389355 DOI: 10.1097/wnr.0000000000001715] [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: 03/13/2021] [Accepted: 06/17/2021] [Indexed: 11/26/2022]
Abstract
The immunoproteasome subunit low molecular mass polypeptide 7 (LMP7) leads to brain injuries, such as autoimmune neuritis and ischemic stroke, by activating inflammation. However, the roles and mechanisms of LMP7 in hypoxic-ischemic brain damage (HIBD) remain unclear. This study explored these issues in a rat model of HIBD. Pathology was evaluated using hematoxylin-eosin staining. LMP7 expression was detected using western blot analysis, reverse transcription-quantitative PCR (RT-qPCR), and immunohistochemical staining. The presence of proinflammatory cytokines, including tumor necrosis factor-a, interleukin-6, and interleukin-1β, was tested using ELISA and RT-qPCR. Behavioral performance was evaluated using a short-term neurological function score and the Morris water maze test. Compared to those in the Sham group, the HIBD group exhibited obvious upregulated LMP7 and pro-inflammatory cytokine levels. HIBD rats exhibited severe pathological and behavioral damage. LMP7 inhibition with ONX-0914 reduced proinflammatory cytokine expression, attenuated pathological damage, and enhanced behavioral performance of rats with HIBD. Inhibition of phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling with LY29400 increased LMP7 expression and abolished the protective effects of ONX-0914 in HIBD rats. Our findings indicate that LMP7 aggravates brain injury by triggering inflammatory responses in HIBD rats. LMP7 inhibition with ONX-0914 exerts protective effects on HIBD rats, possibly via PI3K/Akt signaling.
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Affiliation(s)
- Yue Zhou
- Department of Pediatrics, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Zhixian Gou
- Department of Pediatrics, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Lin Huang
- Department of Pediatrics, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Yang Fan
- Department of Pediatrics, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng Zhang
- Department of Pediatrics, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Liqun Lu
- Department of Pediatrics, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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7
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Mihalovits LM, Ferenczy GG, Keserű GM. Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors. Comput Struct Biotechnol J 2021; 19:4486-4496. [PMID: 34471494 PMCID: PMC8379283 DOI: 10.1016/j.csbj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
The ubiquitin–proteasome system is responsible for the degradation of proteins and plays a critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily induced during disease processes, and its inhibition is beneficial in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were reported to selectively inhibit iPS over cPS, and the inhibitory activity of several oxathiazolones against iPS was experimentally determined. However, the detailed mechanism of the chemical reaction leading to irreversible iPS inhibition and the key selectivity drivers are unknown, and separate characterization of the noncovalent and covalent inhibition steps is not available for several compounds. Here, we investigate the chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism and to determine the rate-determining step of covalent complex formation. The modelled binding mode and reaction mechanism are in line with the selective inhibition of iPS versus cPS by oxathiazolones. The kinact value of several ligands was estimated by constructing the potential of mean force of the rate-determining step by QM/MM simulations coupled with umbrella sampling. The equilibrium constant Ki of the noncovalent complex formation was evaluated by classical force field-based thermodynamic integration. The calculated Ki and kinact values made it possible to analyse the contribution of the noncovalent and covalent steps to the overall inhibitory activity. Compounds with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS owing to subtle differences in the binding modes that slightly affect Ki, the noncovalent affinity, and importantly alter kinact, the covalent reactivity of the bound compounds. A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in designing iPS selective inhibitors with improved drug-like properties.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
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8
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A Nut for Every Bolt: Subunit-Selective Inhibitors of the Immunoproteasome and Their Therapeutic Potential. Cells 2021; 10:cells10081929. [PMID: 34440698 PMCID: PMC8394499 DOI: 10.3390/cells10081929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
At the heart of the ubiquitin-proteasome system, the 20S proteasome core particle (CP) breaks down the majority of intracellular proteins tagged for destruction. Thereby, the CP controls many cellular processes including cell cycle progression and cell signalling. Inhibitors of the CP can suppress these essential biological pathways, resulting in cytotoxicity, an effect that is beneficial for the treatment of certain blood cancer patients. During the last decade, several preclinical studies demonstrated that selective inhibition of the immunoproteasome (iCP), one of several CP variants in mammals, suppresses autoimmune diseases without inducing toxic side effects. These promising findings led to the identification of natural and synthetic iCP inhibitors with distinct chemical structures, varying potency and subunit selectivity. This review presents the most prominent iCP inhibitors with respect to possible scientific and medicinal applications, and discloses recent trends towards pan-immunoproteasome reactive inhibitors that cumulated in phase II clinical trials of the lead compound KZR-616 for chronic inflammations.
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9
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Yarza R, Bover M, Agulló-Ortuño MT, Iglesias-Docampo LC. Current approach and novel perspectives in nasopharyngeal carcinoma: the role of targeting proteasome dysregulation as a molecular landmark in nasopharyngeal cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:202. [PMID: 34154654 PMCID: PMC8215824 DOI: 10.1186/s13046-021-02010-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022]
Abstract
Nasopharyngeal carcinoma (NPC) represents a molecularly paradigmatic tumor given the complex diversity of environmental as well as host dependent factors that are closely implicated in tissue transformation and carcinogenesis. Epstein Barr Virus (EBV) plays a key role in tissue invasion, hyperplasia and malignant transformation. Therefore, EBV related oncoviral proteins such as Latent Membrane Protein family (LMP1, LMP2), Epstein Barr Nuclear Antigen 1 (EBNA1) and EBV related glycoprotein B (gB) are responsible for inducing intracellular signalling aberrations leading to sustained proliferation and further acquisition of NPC related invasive nature and metastatic potential.Dysregulation of proteasome signaling seems to be centrally implicated in oncoviral protein stabilization as well as in modulating tumor microenvironment. Different studies in vitro and in vivo suggest a potential role of proteasome inhibitors in the therapeutic setting of NPC. Furthermore, alterations affecting proteasome signalling in NPC have been associated to tumor growth and invasion, distant metastasis, immune exclusion and resistance as well as to clinical poor prognosis. So on, recent studies have shown the efficacy of immunotherapy as a suitable therapeutic approach to NPC. Nevertheless, novel strategies seem to look for combinatorial regimens aiming to potentiate immune recognition as well as to restore both primary and acquired immune resistance.In this work, our goal is to thoroughly review the molecular implications of proteasome dysregulation in the molecular pathogenesis of NPC, together with their direct relationship with EBV related oncoviral proteins and their role in promoting immune evasion and resistance. We also aim to hypothesize about the feasibility of the use of proteasome inhibitors as part of immunotherapy-including combinatorial regimens for their potential role in reversing immune resistance and favouring tumor recognition and eventual tumor death.
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Affiliation(s)
- Ramon Yarza
- Medical Oncology Division, Hospital Universitarioss 12 de Octubre, Avda. Córdoba s/n, E-28041, Madrid, Spain. .,Clinical and Translational Laboratory, Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain.
| | - Mateo Bover
- Medical Oncology Division, Hospital Universitarioss 12 de Octubre, Avda. Córdoba s/n, E-28041, Madrid, Spain.,Clinical and Translational Laboratory, Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain
| | - Maria Teresa Agulló-Ortuño
- Clinical and Translational Laboratory, Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain. .,Lung Cancer Group, Clinical Research Program (H12O-CNIO), Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain. .,Biomedical Research Networking Centre: Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain. .,Facultad de Fisioterapia y Enfermería, Universidad de Castilla La Mancha (UCLM), Toledo, Spain.
| | - Lara Carmen Iglesias-Docampo
- Medical Oncology Division, Hospital Universitarioss 12 de Octubre, Avda. Córdoba s/n, E-28041, Madrid, Spain.,Clinical and Translational Laboratory, Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain.,Lung Cancer Group, Clinical Research Program (H12O-CNIO), Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
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10
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Kim HR, Tagirasa R, Yoo E. Covalent Small Molecule Immunomodulators Targeting the Protease Active Site. J Med Chem 2021; 64:5291-5322. [PMID: 33904753 DOI: 10.1021/acs.jmedchem.1c00172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cells of the immune system utilize multiple proteases to regulate cell functions and orchestrate innate and adaptive immune responses. Dysregulated protease activities are implicated in many immune-related disorders; thus, protease inhibitors have been actively investigated for pharmaceutical development. Although historically considered challenging with concerns about toxicity, compounds that covalently modify the protease active site represent an important class of agents, emerging not only as chemical probes but also as approved drugs. Here, we provide an overview of technologies useful for the study of proteases with the focus on recent advances in chemoproteomic methods and screening platforms. By highlighting covalent inhibitors that have been designed to target immunomodulatory proteases, we identify opportunities for the development of small molecule immunomodulators.
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Affiliation(s)
- Hong-Rae Kim
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ravichandra Tagirasa
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Euna Yoo
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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11
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Kollár L, Gobec M, Szilágyi B, Proj M, Knez D, Ábrányi-Balogh P, Petri L, Imre T, Bajusz D, Ferenczy GG, Gobec S, Keserű GM, Sosič I. Discovery of selective fragment-sized immunoproteasome inhibitors. Eur J Med Chem 2021; 219:113455. [PMID: 33894528 DOI: 10.1016/j.ejmech.2021.113455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/14/2021] [Accepted: 04/05/2021] [Indexed: 11/26/2022]
Abstract
Proteasomes contribute to maintaining protein homeostasis and their inhibition is beneficial in certain types of cancer and in autoimmune diseases. However, the inhibition of the proteasomes in healthy cells leads to unwanted side-effects and significant effort has been made to identify inhibitors specific for the immunoproteasome, especially to treat diseases which manifest increased levels and activity of this proteasome isoform. Here, we report our efforts to discover fragment-sized inhibitors of the human immunoproteasome. The screening of an in-house library of structurally diverse fragments resulted in the identification of benzo[d]oxazole-2(3H)-thiones, benzo[d]thiazole-2(3H)-thiones, benzo[d]imidazole-2(3H)-thiones, and 1-methylbenzo[d]imidazole-2(3H)-thiones (with a general term benzoXazole-2(3H)-thiones) as inhibitors of the chymotrypsin-like (β5i) subunit of the immunoproteasome. A subsequent structure-activity relationship study provided us with an insight regarding growing vectors. Binding to the β5i subunit was shown and selectivity against the β5 subunit of the constitutive proteasome was determined. Thorough characterization of these compounds suggested that they inhibit the immunoproteasome by forming a disulfide bond with the Cys48 available specifically in the β5i active site. To obtain fragments with biologically more tractable covalent interactions, we performed a warhead scan, which yielded benzoXazole-2-carbonitriles as promising starting points for the development of selective immunoproteasome inhibitors with non-peptidic scaffolds.
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Affiliation(s)
- Levente Kollár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Martina Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia
| | - Bence Szilágyi
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Matic Proj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia
| | - Damijan Knez
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary.
| | - Izidor Sosič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI-1000, Ljubljana, Slovenia.
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12
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Synthesis of macrocyclic α-ketoamide as a selective and reversible immunoproteasome inhibitor. Med Chem Res 2021. [DOI: 10.1007/s00044-020-02678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Schiffrer ES, Proj M, Gobec M, Rejc L, Šterman A, Mravljak J, Gobec S, Sosič I. Synthesis and Biochemical Evaluation of Warhead-Decorated Psoralens as (Immuno)Proteasome Inhibitors. Molecules 2021; 26:molecules26020356. [PMID: 33445542 PMCID: PMC7826781 DOI: 10.3390/molecules26020356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/03/2021] [Accepted: 01/09/2021] [Indexed: 02/07/2023] Open
Abstract
The immunoproteasome is a multicatalytic protease that is predominantly expressed in cells of hematopoietic origin. Its elevated expression has been associated with autoimmune diseases, various types of cancer, and inflammatory diseases. Selective inhibition of its catalytic activities is therefore a viable approach for the treatment of these diseases. However, the development of immunoproteasome-selective inhibitors with non-peptidic scaffolds remains a challenging task. We previously reported 7H-furo[3,2-g]chromen-7-one (psoralen)-based compounds with an oxathiazolone warhead as selective inhibitors of the chymotrypsin-like (β5i) subunit of immunoproteasome. Here, we describe the influence of the electrophilic warhead variations at position 3 of the psoralen core on the inhibitory potencies. Despite mapping the chemical space with different warheads, all compounds showed decreased inhibition of the β5i subunit of immunoproteasome in comparison to the parent oxathiazolone-based compound. Although suboptimal, these results provide crucial information about structure–activity relationships that will serve as guidance for the further design of (immuno)proteasome inhibitors.
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Affiliation(s)
- Eva Shannon Schiffrer
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
| | - Matic Proj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
| | - Luka Rejc
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia;
| | - Andrej Šterman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
| | - Janez Mravljak
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia; (E.S.S.); (M.P.); (M.G.); (A.Š.); (J.M.); (S.G.)
- Correspondence: ; Tel.: +386-1-4769-569
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14
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Zhan W, Singh PK, Ban Y, Qing X, Ah Kioon MD, Fan H, Zhao Q, Wang R, Sukenick G, Salmon J, Warren JD, Ma X, Barrat FJ, Nathan CF, Lin G. Structure-Activity Relationships of Noncovalent Immunoproteasome β5i-Selective Dipeptides. J Med Chem 2020; 63:13103-13123. [PMID: 33095579 PMCID: PMC8086754 DOI: 10.1021/acs.jmedchem.0c01520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The immunoproteasome (i-20S) has emerged as a therapeutic target for autoimmune and inflammatory disorders and hematological malignancies. Inhibition of the chymotryptic β5i subunit of i-20S inhibits T cell activation, B cell proliferation, and dendritic cell differentiation in vitro and suppresses immune responses in animal models of autoimmune disorders and allograft rejection. However, cytotoxicity to immune cells has accompanied the use of covalently reactive β5i inhibitors, whose activity against the constitutive proteasome (c-20S) is cumulative with the time of exposure. Herein, we report a structure-activity relationship study of a class of noncovalent proteasome inhibitors with picomolar potencies and 1000-fold selectivity for i-20S over c-20S. Furthermore, these inhibitors are specific for β5i over the other five active subunits of i-20S and c-20S, providing useful tools to study the functions of β5i in immune responses. The potency of these compounds in inhibiting human T cell activation suggests that they may have therapeutic potential.
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Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Pradeep K Singh
- Department of Biochemistry, Milstein Chemistry Core Facility
| | - Yi Ban
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Xiaoping Qing
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - Marie Dominique Ah Kioon
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - Hao Fan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Quanju Zhao
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Rong Wang
- NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center
| | - George Sukenick
- NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center
| | - Jane Salmon
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - J David Warren
- Department of Biochemistry, Milstein Chemistry Core Facility
| | - Xiaojing Ma
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Franck J. Barrat
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - Carl F. Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
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15
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Rožman K, Alexander EM, Ogorevc E, Bozovičar K, Sosič I, Aldrich CC, Gobec S. Psoralen Derivatives as Inhibitors of Mycobacterium tuberculosis Proteasome. Molecules 2020; 25:E1305. [PMID: 32178473 PMCID: PMC7144120 DOI: 10.3390/molecules25061305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/19/2022] Open
Abstract
Protein degradation is a fundamental process in all living organisms. An important part of this system is a multisubunit, barrel-shaped protease complex called the proteasome. This enzyme is directly responsible for the proteolysis of ubiquitin- or pup-tagged proteins to smaller peptides. In this study, we present a series of 92 psoralen derivatives, of which 15 displayed inhibitory potency against the Mycobacterium tuberculosis proteasome in low micromolar concentrations. The best inhibitors, i.e., 8, 11, 13 and 15, exhibited a mixed type of inhibition and overall good inhibitory potency in biochemical assays. N-(cyanomethyl)acetamide 8 (Ki = 5.6 µM) and carboxaldehyde-based derivative 15 (Ki = 14.9 µM) were shown to be reversible inhibitors of the enzyme. On the other hand, pyrrolidine-2,5-dione esters 11 and 13 irreversibly inhibited the enzyme with Ki values of 4.2 µM and 1.1 µM, respectively. In addition, we showed that an established immunoproteasome inhibitor, PR-957, is a noncompetitive irreversible inhibitor of the mycobacterial proteasome (Ki = 5.2 ± 1.9 µM, kinact/Ki = 96 ± 41 M-1·s-1). These compounds represent interesting hit compounds for further optimization in the development of new drugs for the treatment of tuberculosis.
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Affiliation(s)
- Kaja Rožman
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN 55455, USA; (E.M.A.); (C.C.A.)
| | - Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN 55455, USA; (E.M.A.); (C.C.A.)
| | - Eva Ogorevc
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
| | - Krištof Bozovičar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
| | - Izidor Sosič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN 55455, USA; (E.M.A.); (C.C.A.)
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
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Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease. Molecules 2020; 25:molecules25030671. [PMID: 32033280 PMCID: PMC7037493 DOI: 10.3390/molecules25030671] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
The proteasome is the central component of the main cellular protein degradation pathway. During the past four decades, the critical function of the proteasome in numerous physiological processes has been revealed, and proteasome activity has been linked to various human diseases. The proteasome prevents the accumulation of misfolded proteins, controls the cell cycle, and regulates the immune response, to name a few important roles for this macromolecular "machine." As a therapeutic target, proteasome inhibitors have been approved for the treatment of multiple myeloma and mantle cell lymphoma. However, inability to sufficiently inhibit proteasome activity at tolerated doses has hampered efforts to expand the scope of proteasome inhibitor-based therapies. With emerging new modalities in myeloma, it might seem challenging to develop additional proteasome-based therapies. However, the constant development of new applications for proteasome inhibitors and deeper insights into the intricacies of protein homeostasis suggest that proteasome inhibitors might have novel therapeutic applications. Herein, we summarize the latest advances in proteasome inhibitor development and discuss the future of proteasome inhibitors and other proteasome-based therapies in combating human diseases.
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18
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Schiffrer ES, Sosič I, Šterman A, Mravljak J, Raščan IM, Gobec S, Gobec M. A focused structure-activity relationship study of psoralen-based immunoproteasome inhibitors. MEDCHEMCOMM 2019; 10:1958-1965. [PMID: 32952997 PMCID: PMC7478164 DOI: 10.1039/c9md00365g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/08/2019] [Indexed: 12/22/2022]
Abstract
The immunoproteasome is a multicatalytic protease that is predominantly expressed in cells of hematopoietic origin. Its elevated expression has been associated with autoimmune diseases, various types of cancer, and inflammatory diseases. The development of immunoproteasome-selective inhibitors with non-peptidic scaffolds remains a challenging task. Here, we describe a focused series of psoralen-based inhibitors of the β5i subunit of the immunoproteasome with different substituents placed at position 4'. The most promising compound was further evaluated through changes at position 3 of the psoralen ring. Despite a small decrease in the inhibitory potency in comparison with the parent compound, we were able to improve the selectivity against other subunits of both the immunoproteasome and the constitutive proteasome. The most potent compounds discriminated between both proteasome types in cell lysates and also showed a decrease in cytokine secretion in peripheral blood mononuclear cells.
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Affiliation(s)
- Eva Shannon Schiffrer
- Faculty of Pharmacy , Chair of Pharmaceutical Chemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy , Chair of Pharmaceutical Chemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia
| | - Andrej Šterman
- Faculty of Pharmacy , Chair of Pharmaceutical Chemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia
| | - Janez Mravljak
- Faculty of Pharmacy , Chair of Pharmaceutical Chemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia
| | - Irena Mlinarič Raščan
- Faculty of Pharmacy , Chair of Clinical Biochemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia . ; Tel: +386 1 476 9636
| | - Stanislav Gobec
- Faculty of Pharmacy , Chair of Pharmaceutical Chemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia
| | - Martina Gobec
- Faculty of Pharmacy , Chair of Clinical Biochemistry , University of Ljubljana , Aškerčeva 7 , 1000 Ljubljana , Slovenia . ; Tel: +386 1 476 9636
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Xi J, Zhuang R, Kong L, He R, Zhu H, Zhang J. Immunoproteasome-selective inhibitors: An overview of recent developments as potential drugs for hematologic malignancies and autoimmune diseases. Eur J Med Chem 2019; 182:111646. [PMID: 31521028 DOI: 10.1016/j.ejmech.2019.111646] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/24/2019] [Accepted: 08/25/2019] [Indexed: 12/23/2022]
Abstract
The immunoproteasome, a specialized form of proteasome, is mainly expressed in lymphocytes and monocytes of jawed vertebrates and responsible for the generation of antigenic peptides for cell-mediated immunity. Overexpression of immunoproteasome have been detected in a wide range of diseases including malignancies, autoimmune and inflammatory diseases. Following the successful approval of constitutive proteasome inhibitors bortezomib, carfilzomib and Ixazomib, and with the clarification of immunoproteasome crystal structure and functions, a variety of immunoproteasome inhibitors were discovered or rationally developed. Not only the inhibitory activities, the selectivities for immunoproteasome over constitutive proteasome are essential for the clinical potential of these analogues, which has been validated by the clinical evaluation of immunoproteasome-selective inhibitor KZR-616 for the treatment of systemic lupus erythematosus. In this review, structure, function as well as the current developments of various inhibitors against immunoproteasome are going to be summarized, which help to fully understand the target for drug discovery.
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Affiliation(s)
- Jianjun Xi
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Rangxiao Zhuang
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Limin Kong
- Department of Pharmacy, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, Zhejiang Province, China
| | - Ruoyu He
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Huajian Zhu
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang Province, China
| | - Jiankang Zhang
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang Province, China.
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Discovery of Immunoproteasome Inhibitors Using Large-Scale Covalent Virtual Screening. Molecules 2019; 24:molecules24142590. [PMID: 31315311 PMCID: PMC6680723 DOI: 10.3390/molecules24142590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/19/2022] Open
Abstract
Large-scale virtual screening of boronic acid derivatives was performed to identify nonpeptidic covalent inhibitors of the β5i subunit of the immunoproteasome. A hierarchical virtual screening cascade including noncovalent and covalent docking steps was applied to a virtual library of over 104,000 compounds. Then, 32 virtual hits were selected, out of which five were experimentally confirmed. Biophysical and biochemical tests showed micromolar binding affinity and time-dependent inhibitory potency for two compounds. These results validate the computational protocol that allows the screening of large compound collections. One of the lead-like boronic acid derivatives identified as a covalent immunoproteasome inhibitor is a suitable starting point for chemical optimization.
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21
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Leonardi A, Sajevic T, Pungerčar J, Križaj I. Comprehensive Study of the Proteome and Transcriptome of the Venom of the Most Venomous European Viper: Discovery of a New Subclass of Ancestral Snake Venom Metalloproteinase Precursor-Derived Proteins. J Proteome Res 2019; 18:2287-2309. [PMID: 31017792 PMCID: PMC6727599 DOI: 10.1021/acs.jproteome.9b00120] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
nose-horned viper, its nominotypical subspecies Vipera
ammodytes ammodytes (Vaa), in particular,
is, medically, one of the most relevant snakes in Europe. The local
and systemic clinical manifestations of poisoning by the venom of
this snake are the result of the pathophysiological effects inflicted
by enzymatic and nonenzymatic venom components acting, most prominently,
on the blood, cardiovascular, and nerve systems. This venom is a very
complex mixture of pharmacologically active proteins and peptides.
To help improve the current antivenom therapy toward higher specificity
and efficiency and to assist drug discovery, we have constructed,
by combining transcriptomic and proteomic analyses, the most comprehensive
library yet of the Vaa venom proteins and peptides.
Sequence analysis of the venom gland cDNA library has revealed the
presence of messages encoding 12 types of polypeptide precursors.
The most abundant are those for metalloproteinase inhibitors (MPis),
bradykinin-potentiating peptides (BPPs), and natriuretic peptides
(NPs) (all three on a single precursor), snake C-type lectin-like
proteins (snaclecs), serine proteases (SVSPs), P-II and P-III metalloproteinases
(SVMPs), secreted phospholipases A2 (sPLA2s),
and disintegrins (Dis). These constitute >88% of the venom transcriptome.
At the protein level, 57 venom proteins belonging to 16 different
protein families have been identified and, with SVSPs, sPLA2s, snaclecs, and SVMPs, comprise ∼80% of all venom proteins.
Peptides detected in the venom include NPs, BPPs, and inhibitors of
SVSPs and SVMPs. Of particular interest, a transcript coding for a
protein similar to P-III SVMPs but lacking the MP domain was also
found at the protein level in the venom. The existence of such proteins,
also supported by finding similar venom gland transcripts in related
snake species, has been demonstrated for the first time, justifying
the proposal of a new P-IIIe subclass of ancestral SVMP precursor-derived
proteins.
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Affiliation(s)
- Adrijana Leonardi
- Department of Molecular and Biomedical Sciences , Jožef Stefan Institute , Jamova cesta 39 , SI-1000 Ljubljana , Slovenia
| | - Tamara Sajevic
- Department of Molecular and Biomedical Sciences , Jožef Stefan Institute , Jamova cesta 39 , SI-1000 Ljubljana , Slovenia
| | - Jože Pungerčar
- Department of Molecular and Biomedical Sciences , Jožef Stefan Institute , Jamova cesta 39 , SI-1000 Ljubljana , Slovenia
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences , Jožef Stefan Institute , Jamova cesta 39 , SI-1000 Ljubljana , Slovenia
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Zhang R, Jin S, Liu Q, Lin S, Yan Z. Transition Metal-Free Cross-Dehydrogenative Coupling Reaction of Coumarins with Acetonitrile or Acetone. J Org Chem 2018; 83:13030-13035. [DOI: 10.1021/acs.joc.8b01508] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rongxing Zhang
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Shengzhou Jin
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Qian Liu
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Sen Lin
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
| | - Zhaohua Yan
- Department of Chemistry, Nanchang University, No. 999, Xuefu Road, Nanchang 330031, P. R. China
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González Y, Doens D, Cruz H, Santamaría R, Gutiérrez M, Llanes A, Fernández PL. A Marine Diterpenoid Modulates the Proteasome Activity in Murine Macrophages Stimulated with LPS. Biomolecules 2018; 8:E109. [PMID: 30301161 PMCID: PMC6315684 DOI: 10.3390/biom8040109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/14/2018] [Accepted: 10/01/2018] [Indexed: 11/17/2022] Open
Abstract
The proteasome is an intracellular complex that degrades damaged or unfolded proteins and participates in the regulation of several processes. The immunoproteasome is a specialized form that is expressed in response to proinflammatory signals and is particularly abundant in immune cells. In a previous work, we found an anti-inflammatory effect in a diterpenoid extracted from the octocoral Pseudopterogorgia acerosa, here called compound 1. This compound prevented the degradation of inhibitor κB α (IκBα) and the subsequent activation of nuclear factor κB (NFκB), suggesting that this effect might be due to inhibition of the ubiquitin-proteasome system. Here we show that compound 1 inhibits the proteasomal chymotrypsin-like activity (CTL) of murine macrophages in the presence of lipopolysaccharide (LPS) but not in its absence. This effect might be due to the capacity of this compound to inhibit the activity of purified immunoproteasome. The compound inhibits the cell surface expression of major histocompatibility complex (MHC)-I molecules and the production of proinflammatory cytokines induced by LPS in vitro and in vivo, respectively. Molecular docking simulations predicted that compound 1 selectively binds to the catalytic site of immunoproteasome subunits β1i and β5i, which are responsible for the CTL activity. Taken together these findings suggest that the compound could be a selective inhibitor of the immunoproteasome, and hence could pave the way for its future evaluation as a candidate for the treatment of inflammatory disorders and autoimmune diseases.
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Affiliation(s)
- Yisett González
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP),Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
| | - Deborah Doens
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP),Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
| | - Héctor Cruz
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP),Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
- Facultad de Ciencias de la Salud Dr. William C. Gorgas, Universidad Latina de Panamá, 0801 Panamá, Panamá.
| | - Ricardo Santamaría
- Centro de Biodiversidad y Descubrimiento de Drogas, INDICASAT AIP, Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, INDICASAT AIP, Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
| | - Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP),Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
| | - Patricia L Fernández
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP),Edificio 219, Ciudad del Saber, 0801 Panamá, Panamá.
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Ogorevc E, Schiffrer ES, Sosič I, Gobec S. A patent review of immunoproteasome inhibitors. Expert Opin Ther Pat 2018; 28:517-540. [PMID: 29865878 DOI: 10.1080/13543776.2018.1484904] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The ubiquitin-proteasome system is responsible for maintaining protein homeostasis and regulating a variety of cellular processes. The constitutive proteasome is expressed in all cells while the immunoproteasome (IP) is predominantly found in cells of hematopoietic origin. In other cells, the expression of IP can be induced under the influence of cytokines released by T cells during acute immune and stress responses. Inhibitors of IP are of significant interest, because it is expected that selective inhibition of the IP would cause fewer adverse effects. AREAS COVERED There is a considerable interest on patenting IP-specific inhibitors. Relevant patents and patent applications disclosing IP inhibitors are summarized and divided into two parts according to the chemical characteristics of compounds. We also briefly report on the biochemical methods used in the patents to profile the characteristics of IP inhibitors. EXPERT OPINION Several selective inhibitors of IP with a promising ability to address autoimmune and inflammatory diseases are being developed. Peptidic compounds are prevalent and the most advanced IP-selective compounds to date, ONX-0914 and KZR-616, are tripeptide epoxyketone-based molecules. However, some patents disclose that IP-selective inhibition is possible with compounds possessing non-peptidic scaffolds indicating countless possibilities to address inhibition of IP in the future.
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Affiliation(s)
- Eva Ogorevc
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | | | - Izidor Sosič
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Stanislav Gobec
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
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Borišek J, Pintar S, Ogrizek M, Turk D, Perdih A, Novič M. A Water-Assisted Catalytic Mechanism in Glycoside Hydrolases Demonstrated on the Staphylococcus aureus Autolysin E. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sara Pintar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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26
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Villoutreix BO, Khatib AM, Cheng Y, Miteva MA, Maréchal X, Vidal J, Reboud-Ravaux M. Blockade of the malignant phenotype by β-subunit selective noncovalent inhibition of immuno- and constitutive proteasomes. Oncotarget 2018; 8:10437-10449. [PMID: 28060729 PMCID: PMC5354670 DOI: 10.18632/oncotarget.14428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/13/2016] [Indexed: 01/04/2023] Open
Abstract
A structure-based virtual screening of over 400,000 small molecules against the constitutive proteasome activity followed by in vitro assays led to the discovery of a family of proteasome inhibitors with a sulfonyl piperazine scaffold. Some members of this family of small non-peptidic inhibitors were found to act selectively on the β2 trypsin-like catalytic site with a preference for the immunoproteasome β2i over the constitutive proteasome β2c, while some act on the β5 site and post-acid site β1 of both, the immunoproteasome and the constitutive proteasome. Anti-proliferative and anti-invasive effects on tumor cells were investigated and observed for two compounds. We report novel chemical inhibitors able to interfere with the three types of active centers of both, the immuno- and constitutive proteasomes. Identifying and analyzing a novel scaffold with decorations able to shift the binders’ active site selectivity is essential to design a future generation of proteasome inhibitors able to distinguish the immunoproteasome from the constitutive proteasome.
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Affiliation(s)
| | | | - Yan Cheng
- Sorbonne Universités, UPMC Université Paris 6, UMR 8256, ERL U1164, B2A, IBPS, Paris, France
| | - Maria A Miteva
- INSERM, U 973, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Xavier Maréchal
- Sorbonne Universités, UPMC Université Paris 6, UMR 8256, ERL U1164, B2A, IBPS, Paris, France
| | - Joëlle Vidal
- Institut des Sciences Chimiques de Rennes, Université de Rennes 1, UMR-CNRS 6226, Rennes, France
| | - Michèle Reboud-Ravaux
- Sorbonne Universités, UPMC Université Paris 6, UMR 8256, ERL U1164, B2A, IBPS, Paris, France
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27
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Richy N, Sarraf D, Maréchal X, Janmamode N, Le Guével R, Genin E, Reboud-Ravaux M, Vidal J. Structure-based design of human immuno- and constitutive proteasomes inhibitors. Eur J Med Chem 2018; 145:570-587. [PMID: 29339252 DOI: 10.1016/j.ejmech.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 12/20/2022]
Abstract
Starting from the X-ray structure of our previous tripeptidic linear mimics of TMC-95A in complex with yeast 20S proteasome, we introduced new structural features to induce a differential inhibition between human constitutive and immunoproteasome 20S particles. Libraries of 24 tripeptidic and 6 dipeptidic derivatives were synthesized. The optimized preparation of 3-hydroxyoxindolyl alanine residues from tryptophan and their incorporation in peptides were described. Several potent inhibitors of human constitutive proteasome and immunoproteasome acting at the nanomolar level (IC50 = 7.1 nM against the chymotrypsin-like activity for the best inhibitor) were obtained. A cytotoxic effect at the submicromolar level was observed against 6 human cancer cell lines.
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Affiliation(s)
- Nicolas Richy
- Université Rennes 1, Institut des Sciences Chimiques de Rennes, CNRS UMR 6226, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes, Cedex, France
| | - Daad Sarraf
- Université Rennes 1, Institut des Sciences Chimiques de Rennes, CNRS UMR 6226, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes, Cedex, France
| | - Xavier Maréchal
- Sorbonne Universités, UPMC Univ Paris 06-CNRS, IBPS, UMR 8256, Inserm ERL1164, B2A, 7 Quai Saint Bernard, F75005 Paris, France
| | - Naëla Janmamode
- Université Rennes 1, Institut des Sciences Chimiques de Rennes, CNRS UMR 6226, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes, Cedex, France
| | - Rémy Le Guével
- Université Rennes 1, Technology Platform ImPACcell, SFR UMS CNRS 3480, INSERM 018, Bâtiment 8, Campus de Villejean, 35043 Rennes, Cedex, France
| | - Emilie Genin
- Université Rennes 1, Institut des Sciences Chimiques de Rennes, CNRS UMR 6226, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes, Cedex, France
| | - Michèle Reboud-Ravaux
- Sorbonne Universités, UPMC Univ Paris 06-CNRS, IBPS, UMR 8256, Inserm ERL1164, B2A, 7 Quai Saint Bernard, F75005 Paris, France.
| | - Joëlle Vidal
- Université Rennes 1, Institut des Sciences Chimiques de Rennes, CNRS UMR 6226, Bâtiment 10A, Campus de Beaulieu, 35042 Rennes, Cedex, France.
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28
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Kovacs D, Phipps D, Orthaber A, Borbas KE. Highly luminescent lanthanide complexes sensitised by tertiary amide-linked carbostyril antennae. Dalton Trans 2018; 47:10702-10714. [DOI: 10.1039/c8dt01270a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The replacement of the secondary amide linker that carries the sensitizing carbostyril antenna with a tertiary amide in luminescent Eu and Tb complexes dramatically increases the lanthanide emission quantum yields.
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Affiliation(s)
- Daniel Kovacs
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
| | - Dulcie Phipps
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
| | - Andreas Orthaber
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
| | - K. Eszter Borbas
- Department of Chemistry
- Ångström Laboratory
- Uppsala University
- Uppsala
- Sweden
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29
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Nikitina N, Ivashko E, Tchernykh A. Congestion game scheduling for virtual drug screening optimization. J Comput Aided Mol Des 2017; 32:363-374. [PMID: 29264790 DOI: 10.1007/s10822-017-0093-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/15/2017] [Indexed: 12/19/2022]
Abstract
In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screening hits in a short time. To this end, we propose a mathematical model of task scheduling for virtual drug screening in high-performance computational systems as a congestion game between computational nodes to find the equilibrium solutions for best balancing the number of interim hits with their chemical diversity. The model considers the heterogeneous environment with workload uncertainty, processing time uncertainty, and limited knowledge about the input dataset structure. We perform computational experiments and evaluate the performance of the developed approach considering organic molecules database GDB-9. The used set of molecules is rich enough to demonstrate the feasibility and practicability of proposed solutions. We compare the algorithm with two known heuristics used in practice and observe that game-based scheduling outperforms them by the hit discovery rate and chemical diversity at earlier steps. Based on these results, we use a social utility metric for assessing the efficiency of our equilibrium solutions and show that they reach greatest values.
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Affiliation(s)
- Natalia Nikitina
- Institute of Applied Mathematical Research, Karelian Research Center, Russian Academy of Sciences, 11 Pushkinskaya str., 185910, Petrozavodsk, Russia.
| | - Evgeny Ivashko
- Institute of Applied Mathematical Research, Karelian Research Center, Russian Academy of Sciences, 11 Pushkinskaya str., 185910, Petrozavodsk, Russia
| | - Andrei Tchernykh
- Computer Science Department, CICESE Research Center, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Código Postal 22860, Apdo. Postal 360, Ensenada, Baja California, Mexico
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30
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Winter MB, La Greca F, Arastu-Kapur S, Caiazza F, Cimermancic P, Buchholz TJ, Anderl JL, Ravalin M, Bohn MF, Sali A, O'Donoghue AJ, Craik CS. Immunoproteasome functions explained by divergence in cleavage specificity and regulation. eLife 2017; 6. [PMID: 29182146 PMCID: PMC5705213 DOI: 10.7554/elife.27364] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/11/2017] [Indexed: 12/16/2022] Open
Abstract
The immunoproteasome (iP) has been proposed to perform specialized roles in MHC class I antigen presentation, cytokine modulation, and T cell differentiation and has emerged as a promising therapeutic target for autoimmune disorders and cancer. However, divergence in function between the iP and the constitutive proteasome (cP) has been unclear. A global peptide library-based screening strategy revealed that the proteasomes have overlapping but distinct substrate specificities. Differing iP specificity alters the quantity of production of certain MHC I epitopes but does not appear to be preferentially suited for antigen presentation. Furthermore, iP specificity was found to have likely arisen through genetic drift from the ancestral cP. Specificity differences were exploited to develop isoform-selective substrates. Cellular profiling using these substrates revealed that divergence in regulation of the iP balances its relative contribution to proteasome capacity in immune cells, resulting in selective recovery from inhibition. These findings have implications for iP-targeted therapeutic development.
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Affiliation(s)
- Michael B Winter
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Florencia La Greca
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Shirin Arastu-Kapur
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Onyx Pharmaceuticals, Inc., an Amgen subsidiary, San Francisco, United States
| | - Francesco Caiazza
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Peter Cimermancic
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Tonia J Buchholz
- Onyx Pharmaceuticals, Inc., an Amgen subsidiary, San Francisco, United States
| | - Janet L Anderl
- Onyx Pharmaceuticals, Inc., an Amgen subsidiary, San Francisco, United States
| | - Matthew Ravalin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Markus F Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
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31
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Karabuva S, Lukšić B, Brizić I, Latinović Z, Leonardi A, Križaj I. Ammodytin L is the main cardiotoxic component of the Vipera ammodytes ammodytes venom. Toxicon 2017; 139:94-100. [PMID: 29030107 DOI: 10.1016/j.toxicon.2017.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/08/2017] [Accepted: 10/08/2017] [Indexed: 11/15/2022]
Abstract
Venom of the nose-horned viper (V. a. ammodytes) as also venoms of some related European viperids can induce also cardiotoxic effects in mammals. In this work we demonstrated that the protein in the V. a. ammodytes venom acting on heart is a myotoxic secreted phospholipase A2 analogue ammodytin L (AtnL). In the isolated perfused rat heart AtnL induced significant and irreversible cardiotoxicity characterized by atrioventricular (AV) blockade. This venom protein induced appearance of high levels of creatine kinase, lactate dehydrogenase, aspartate aminotransferase and troponin I in the sinus effluent of the isolated heart, indicative for myocardial damage, which is obviously the primary cause of its cardiotoxic action. Gel filtration chromatography subfractions C1 and C2 of the V. a. ammodytes venom harboured most of the venom cardiotoxicity. As we showed, just these two subfractions contained also AtnL. Subfraction C1 in the final CF concentration 11.3 μg/mL (containing 3.1 μg/mL AtnL) induced a complete cardiac arrest while subfraction C2 in the final CF concentration 6.0 μg/mL (containing 0.8 μg/mL AtnL) and the pure AtnL (1.0 μg/mL) did not. Contrary to AtnL, subfraction C1 at 11.3 μg/mL was not able to induce the AV blockade. This exposed the only other cardiotoxic subfractions-specific venom protein, a cysteine-rich secretory protein (CRISP), as an additional venom component potentially involved in modulation of the heart activity. Cardiotoxicity reported in some cases of the adder (V. berus) venom and the asp viper (V. aspis) venom poisonings may be assigned to AtnL in these venoms.
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Affiliation(s)
- Svjetlana Karabuva
- Clinical Department of Infectious Diseases, University Hospital of Split, Šoltanska 1, Split, Croatia.
| | - Boris Lukšić
- Clinical Department of Infectious Diseases, University Hospital of Split, Šoltanska 1, Split, Croatia; University of Split School of Medicine, Šoltanska 2, Split, Croatia.
| | - Ivica Brizić
- Department of Pharmacology, Mostar University School of Medicine, Bijeli brijeg bb, Mostar, Bosnia and Herzegovina.
| | - Zorica Latinović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, Slovenia.
| | - Adrijana Leonardi
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia.
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia.
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32
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Cromm PM, Crews CM. The Proteasome in Modern Drug Discovery: Second Life of a Highly Valuable Drug Target. ACS CENTRAL SCIENCE 2017; 3:830-838. [PMID: 28852696 PMCID: PMC5571462 DOI: 10.1021/acscentsci.7b00252] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 06/07/2023]
Abstract
As the central figure of the cellular protein degradation machinery, the proteasome is critical for cell survival. Having been extensively targeted for inhibition, the constitutive proteasome has proven its role as a highly valuable drug target. However, recent advances in the protein homeostasis field suggest that additional chapters can be added to this successful story. For example, selective immunoproteasome inhibition promises high clinical efficacy for autoimmune disorders and inflammation, and proteasome inhibitors might serve as novel therapeutics for malaria or other microorganisms. Furthermore, utilizing the destructive force of the proteasome for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Thus, the field of proteasome drug discovery still holds exciting questions to be answered and does not simply end with inhibiting the constitutive proteasome.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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33
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Cui H, Baur R, Le Chapelain C, Dubiella C, Heinemeyer W, Huber EM, Groll M. Structural Elucidation of a Nonpeptidic Inhibitor Specific for the Human Immunoproteasome. Chembiochem 2017; 18:523-526. [PMID: 28098422 DOI: 10.1002/cbic.201700021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Indexed: 12/30/2022]
Abstract
Selective inhibition of the immunoproteasome is a promising approach towards the development of immunomodulatory drugs. Recently, a class of substituted thiazole compounds that combine a nonpeptidic scaffold with the absence of an electrophile was reported in a patent. Here, we investigated the mode of action of the lead compound by using a sophisticated chimeric yeast model of the human immunoproteasome for structural studies. The inhibitor adopts a unique orientation perpendicular to the β5i substrate-binding channel. Distinct interactions between the inhibitor and the subpockets of the human immunoproteasome account for its isotype selectivity.
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Affiliation(s)
- Haissi Cui
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Regina Baur
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Camille Le Chapelain
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Christian Dubiella
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Wolfgang Heinemeyer
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Eva M Huber
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany
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34
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Rožman K, Lešnik S, Brus B, Hrast M, Sova M, Patin D, Barreteau H, Konc J, Janežič D, Gobec S. Discovery of new MurA inhibitors using induced-fit simulation and docking. Bioorg Med Chem Lett 2017; 27:944-949. [DOI: 10.1016/j.bmcl.2016.12.082] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/26/2016] [Accepted: 12/29/2016] [Indexed: 11/15/2022]
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35
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Takahashi T, Masui H, Ohkawa E, Kitahara R, Wanibuchi K. One-Pot, Diversity-Oriented Synthesis of Aryl-Substituted Benzoxacycles Including Benzofuran, Coumarin, and Benzoxazepine. HETEROCYCLES 2017. [DOI: 10.3987/com-17-13791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Singh PK, Fan H, Jiang X, Shi L, Nathan CF, Lin G. Immunoproteasome β5i-Selective Dipeptidomimetic Inhibitors. ChemMedChem 2016; 11:2127-2131. [PMID: 27561172 PMCID: PMC5760267 DOI: 10.1002/cmdc.201600384] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 12/22/2022]
Abstract
N,C-capped dipeptides belong to a class of noncovalent proteasome inhibitors. Herein we report that the insertion of a β-amino acid into N,C-capped dipeptides markedly decreases their inhibitory potency against human constitutive proteasome β5c, while maintaining potent inhibitory activity against human immunoproteasome β5i, thereby achieving thousands-fold selectivity for β5i over β5c. Structure-activity relationship studies revealed that β5c does not tolerate the β-amino acid based dipeptidomimetics as does β5i. In vitro, one such compound was found to inhibit human T cell proliferation. Compounds of this class may have potential as therapeutics for autoimmune and inflammatory diseases with less mechanism-based cytotoxicity than agents that also inhibit the constitutive proteasome.
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Affiliation(s)
- Pradeep K Singh
- Department of Biochemistry, The Abby and Howard Milstein Synthetic Chemistry Core Facility, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Hao Fan
- Department of Microbiology & Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, NY, 10065, USA
| | - Xiuju Jiang
- Department of Microbiology & Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, NY, 10065, USA
| | - Lei Shi
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Carl F Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, NY, 10065, USA
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medical College, 1300 York Avenue, Box 62, New York, NY, 10065, USA.
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37
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Latinović Z, Leonardi A, Šribar J, Sajevic T, Žužek MC, Frangež R, Halassy B, Trampuš-Bakija A, Pungerčar J, Križaj I. Venomics of Vipera berus berus to explain differences in pathology elicited by Vipera ammodytes ammodytes envenomation: Therapeutic implications. J Proteomics 2016; 146:34-47. [PMID: 27327134 DOI: 10.1016/j.jprot.2016.06.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 01/12/2023]
Abstract
UNLABELLED Vipera berus berus (Vbb) is the most widely distributed and Vipera ammodytes ammodytes (Vaa) the most venomous viper in Europe. In particular areas of the Old continent their toxic bites constitute a considerable public health problem. To make the current envenomation therapy more effective we have analysed the proteome of Vbb venom and compared it with that of Vaa. We found the proteome of Vbb to be much less complex and to contain smaller levels of particularly snaclecs and sPLA2s. Snaclecs are probably responsible for thrombocytopenia. The neurotoxic sPLA2s, ammodytoxins, are responsible for the most specific feature of the Vaa venom poisoning - induction of signs of neurotoxicity in patients. These molecules were not found in Vbb venom. Both venoms induce haemorrhage and coagulopathy in man. As Vaa and Vbb venoms possess homologous P-III snake venom metalloproteinases, the main haemorrhagic factors, the severity of the haemorrhage is dictated by concentration and specific activity of these molecules. The much greater anticoagulant effect of Vaa venom than that of Vbb venom lies in its higher extrinsic pathway coagulation factor-proteolysing activity and content of ammodytoxins which block the prothrombinase complex formation. BIOLOGICAL SIGNIFICANCE Envenomations by venomous snakes constitute a considerable public health problem worldwide, and also in Europe. In the submitted work we analysed the venom proteome of Vipera berus berus (Vbb), the most widely distributed venomous snake in Europe and compared it with the venom proteome of the most venomous viper in Europe, Vipera ammodytes ammodytes (Vaa). We have offered a possible explanation, at the molecular level, for the differences in clinical pictures inflicted by the Vbb and Vaa venoms. We have provided an explanation for the effectiveness of treatment of Vbb envenomation by Vaa antiserum and explained why full protection of Vaa venom poisoning by Vbb antiserum should not be always expected, especially not in cases of severe poisoning. The latter makes a strong case for Vaa antiserum production as we are faced with its shortage due to ceasing of production of two most frequently used products.
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Affiliation(s)
- Zorica Latinović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Adrijana Leonardi
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Jernej Šribar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Tamara Sajevic
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Monika C Žužek
- Institute of Physiology, Pharmacology and Toxicology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert Frangež
- Institute of Physiology, Pharmacology and Toxicology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Beata Halassy
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Croatia
| | | | - Jože Pungerčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
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