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Loy CA, Trader DJ. Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement. Molecules 2024; 29:3356. [PMID: 39064934 PMCID: PMC11279888 DOI: 10.3390/molecules29143356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Protein homeostasis is a tightly conserved process that is regulated through the ubiquitin proteasome system (UPS) in a ubiquitin-independent or ubiquitin-dependent manner. Over the past two decades, the proteasome has become an excellent therapeutic target through inhibition of the catalytic core particle, inhibition of subunits responsible for recognizing and binding ubiquitinated proteins, and more recently, through targeted protein degradation using proteolysis targeting chimeras (PROTACs). The majority of the developed inhibitors of the proteasome's core particle rely on gaining selectivity through binding interactions within the unprimed substrate channel. Although this has allowed for selective inhibitors and chemical probes to be generated for the different proteasome isoforms, much remains unknown about the interactions that could be harnessed within the primed substrate channel to increase potency or selectivity. Herein, we discuss small molecules that interact with the primed substrate pocket and how their differences may give rise to altered activity. Taking advantage of additional interactions with the primed substrate pocket of the proteasome could allow for the generation of improved chemical tools for perturbing or monitoring proteasome activity.
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Affiliation(s)
| | - Darci J. Trader
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92617, USA;
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2
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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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3
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Fukuyama Y, Kubo M, Harada K. Neurotrophic Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2024; 123:1-473. [PMID: 38340248 DOI: 10.1007/978-3-031-42422-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Neurotrophins (NGF, BDNF, NT3, NT4) can decrease cell death, induce differentiation, as well as sustain the structure and function of neurons, which make them promising therapeutic agents for the treatment of neurodegenerative disorders. However, neurotrophins have not been very effective in clinical trials mostly because they cannot pass through the blood-brain barrier owing to being high-molecular-weight proteins. Thus, neurotrophin-mimic small molecules, which stimulate the synthesis of endogenous neurotrophins or enhance neurotrophic actions, may serve as promising alternatives to neurotrophins. Small-molecular-weight natural products, which have been used in dietary functional foods or in traditional medicines over the course of human history, have a great potential for the development of new therapeutic agents against neurodegenerative diseases such as Alzheimer's disease. In this contribution, a variety of natural products possessing neurotrophic properties such as neurogenesis, neurite outgrowth promotion (neuritogenesis), and neuroprotection are described, and a focus is made on the chemistry and biology of several neurotrophic natural products.
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Affiliation(s)
- Yoshiyasu Fukuyama
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, 770-8514, Japan.
| | - Miwa Kubo
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, 770-8514, Japan
| | - Kenichi Harada
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, 770-8514, Japan
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4
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Bicev RN, de Souza Degenhardt MF, de Oliveira CLP, da Silva ER, Degrouard J, Tresset G, Ronsein GE, Demasi M, da Cunha FM. Glucose restriction in Saccharomyces cerevisiae modulates the phosphorylation pattern of the 20S proteasome and increases its activity. Sci Rep 2023; 13:19383. [PMID: 37938622 PMCID: PMC10632367 DOI: 10.1038/s41598-023-46614-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Caloric restriction is known to extend the lifespan and/or improve diverse physiological parameters in a vast array of organisms. In the yeast Saccharomyces cerevisiae, caloric restriction is performed by reducing the glucose concentration in the culture medium, a condition previously associated with increased chronological lifespan and 20S proteasome activity in cell extracts, which was not due to increased proteasome amounts in restricted cells. Herein, we sought to investigate the mechanisms through which glucose restriction improved proteasome activity and whether these activity changes were associated with modifications in the particle conformation. We show that glucose restriction increases the ability of 20S proteasomes, isolated from Saccharomyces cerevisiae cells, to degrade model substrates and whole proteins. In addition, threonine 55 and/or serine 56 of the α5-subunit, were/was consistently found to be phosphorylated in proteasomes isolated from glucose restricted cells, which may be involved in the increased proteolysis capacity of proteasomes from restricted cells. We were not able to observe changes in the gate opening nor in the spatial conformation in 20S proteasome particles isolated from glucose restricted cells, suggesting that the changes in activity were not accompanied by large conformational alterations in the 20S proteasome but involved allosteric activation of proteasome catalytic site.
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Affiliation(s)
- Renata Naporano Bicev
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | | | | | - Emerson Rodrigo da Silva
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405, Orsay, France
| | - Guillaume Tresset
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405, Orsay, France
| | - Graziella Eliza Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Marilene Demasi
- Laboratório de Bioquímica, Instituto Butantan, São Paulo, SP, Brasil.
| | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil.
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Guedes RA, Grilo JH, Carvalho AN, Fernandes PMP, Ressurreição AS, Brito V, Santos AO, Silvestre S, Gallerani E, Gama MJ, Gavioli R, Salvador JAR, Guedes RC. New Scaffolds of Proteasome Inhibitors: Boosting Anticancer Potential by Exploiting the Synergy of In Silico and In Vitro Methodologies. Pharmaceuticals (Basel) 2023; 16:1096. [PMID: 37631011 PMCID: PMC10458307 DOI: 10.3390/ph16081096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is a complex multifactorial disease whose pathophysiology involves multiple metabolic pathways, including the ubiquitin-proteasome system, for which several proteasome inhibitors have already been approved for clinical use. However, the resistance to existing therapies and the occurrence of severe adverse effects is still a concern. The purpose of this study was the discovery of novel scaffolds of proteasome inhibitors with anticancer activity, aiming to overcome the limitations of the existing proteasome inhibitors. Thus, a structure-based virtual screening protocol was developed using the structure of the human 20S proteasome, and 246 compounds from virtual databases were selected for in vitro evaluation, namely proteasome inhibition assays and cell viability assays. Compound 4 (JHG58) was shortlisted as the best hit compound based on its potential in terms of proteasome inhibitory activity and its ability to induce cell death (both with IC50 values in the low micromolar range). Molecular docking studies revealed that compound 4 interacts with key residues, namely with the catalytic Thr1, Ala20, Thr21, Lys33, and Asp125 at the chymotrypsin-like catalytic active site. The hit compound is a good candidate for additional optimization through a hit-to-lead campaign.
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Affiliation(s)
- Romina A. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Jorge H. Grilo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Andreia N. Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Pedro M. P. Fernandes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana S. Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Vanessa Brito
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Adriana O. Santos
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Samuel Silvestre
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Eleonora Gallerani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Maria João Gama
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Riccardo Gavioli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Jorge A. R. Salvador
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
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6
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Bhattacharjee A, Sarma S, Sen T, Devi MV, Deka B, Singh AK. Genome mining to identify valuable secondary metabolites and their regulation in Actinobacteria from different niches. Arch Microbiol 2023; 205:127. [PMID: 36944761 DOI: 10.1007/s00203-023-03482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/11/2023] [Indexed: 03/23/2023]
Abstract
Actinobacteria are the largest bacteria group with 18 significant lineages, which are ubiquitously distributed in all the possible terrains. They are known to produce more than 10,000 medically relevant compounds. Despite their ability to make critical secondary metabolites and genome sequences' availability, these two have not been linked with certainty. With this intent, our study aims at understanding the biosynthetic capacity in terms of secondary metabolite production in 528 Actinobacteria species from five different habitats, viz., soil, water, plants, animals, and humans. In our analysis of 9,646 clusters of 59 different classes, we have documented 64,000 SMs, of which more than 74% were of unique type, while 19% were partially conserved and 7% were conserved compounds. In the case of conserved compounds, we found the highest distribution in soil, 79.12%. We found alternate sources of antibiotics, such as viomycin, vancomycin, teicoplanin, fosfomycin, ficellomycin and patulin, and antitumour compounds, such as doxorubicin and tacrolimus in the soil. Also our study reported alternate sources for the toxin cyanobactin in water and plant isolates. We further analysed the clusters to determine their regulatory pathways and reported the prominent presence of the two component system of TetR/AcrR family, as well as other partial domains like CitB superfamily and HTH superfamily, and discussed their role in secondary metabolite production. This information will be helpful in exploring Actinobacteria from other environments and in discovering new chemical moieties of clinical significance.
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Affiliation(s)
- Abhilash Bhattacharjee
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
- Department of Botany, Dibrugarh Hanumanbax Surajmall Kanoi College, Dibrugarh, 786001, Assam, India
| | - Sangita Sarma
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
| | - Tejosmita Sen
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
| | - Moirangthem Veigyabati Devi
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
| | - Banani Deka
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
| | - Anil Kumar Singh
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, 785006, Assam, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India.
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7
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Aguilar C, Verdel-Aranda K, Ramos-Aboites HE, Licona-Cassani C, Barona-Gómez F. Streptomyces lividans 66 produces a protease inhibitor via a tRNA-utilizing enzyme interacting with a C-minus NRPS. J Ind Microbiol Biotechnol 2023; 50:kuad021. [PMID: 37669898 PMCID: PMC10548850 DOI: 10.1093/jimb/kuad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023]
Abstract
Small peptide aldehydes (SPAs) with protease inhibitory activity are naturally occurring compounds shown to be synthesized by non-ribosomal peptide synthetases (NRPS). SPAs are widely used in biotechnology and have been utilized as therapeutic agents. They are also physiologically relevant and have been postulated to regulate the development of their producing microorganisms. Previously, we identified an NRPS-like biosynthetic gene cluster (BGC) in Streptomyces lividans 66 that lacked a condensation (C) domain but included a tRNA-utilizing enzyme (tRUE) belonging to the leucyl/phenylalanyl (L/F) transferase family. This system was predicted to direct the synthesis of a novel SPA, which we named livipeptin. Using evolutionary genome mining approaches, here, we confirm the presence of L/F transferase tRUEs within the genomes of diverse Streptomyces and related organisms, including fusions with the anticipated C-minus NRPS-like protein. We then demonstrate genetic functional cooperation between the identified L/F-transferase divergent tRUE homolog with the C-minus NRPS, leading to the synthesis of a metabolic fraction with protease inhibitory activity. Semisynthetic assays in the presence of RNAse revealed that the productive interaction between the tRUE and the C-minus NRPS enzymes is indeed tRNA dependent. We expect our findings to boost the discovery of SPAs, as well as the development of protease-mediated biotechnologies, by exploiting the uncovered genetic basis for synthesizing putative acetyl-leu/phe-arginine protease inhibitors. Furthermore, these results will facilitate the purification and structural elucidation of livipeptin, which has proven difficult to chemically characterize. SIGNIFICANCE The discovery of natural products biosynthetic genes marks a significant advancement in our understanding of these metabolites, for example of their evolution, activity, and biosynthesis, but also opens biotechnological opportunities and knowledge to advance genome mining approaches. We made this possible by uncovering a new biosynthetic pathway in Streptomyces lividans 66 shown to direct the synthesis of a strong protease inhibitor, termed livipeptin, following unprecedented biosynthetic rules and genes. Thus, by shedding light on the genetic mechanisms predicted to govern the production of acetyl-leu/phe-arginine protease inhibitors, including the elusive livipeptin, this study enables novel protease-mediated biotechnologies as well as approaches for discovering protease inhibitors from genome data.
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Affiliation(s)
- César Aguilar
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Karina Verdel-Aranda
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Hilda E Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Cuauhtémoc Licona-Cassani
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
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8
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Krishna-K K, Behnisch T, Sajikumar S. Modulation of the Ubiquitin-Proteasome System Restores Plasticity in Hippocampal Pyramidal Neurons of the APP/PS1 Alzheimer’s Disease-Like Mice. J Alzheimers Dis 2022; 86:1611-1616. [DOI: 10.3233/jad-215718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer’s disease (AD) is characterized by memory and cognitive deficits that in part are related to a diminished ability to activity-dependent synaptic plasticity. In AD, an attenuated long-term potentiation has been correlated with a deficit of synaptic plasticity-relevant proteins and protein turnover. The ubiquitin-proteasome system (UPS) critically regulates the protein turnover and contributes to dynamic changes of the protein milieu within synapses. In AD, UPS aberration has been implicated in inadequate proteostasis and synaptic malfunction. However, here we show that the inhibition of proteasome-mediated protein degradation by MG132 or lactacystin restored an impaired activity-dependent synaptic plasticity in an AD-like mouse model. In this whole-cell voltage-clamp study, we provided evidence that an amelioration of long-term plasticity by modulating UPS activity in pyramidal neurons.
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Affiliation(s)
- Kumar Krishna-K
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Thomas Behnisch
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sreedharan Sajikumar
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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9
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Secondary Metabolites from Marine-Derived Fungi and Actinobacteria as Potential Sources of Novel Colorectal Cancer Drugs. Mar Drugs 2022; 20:md20010067. [PMID: 35049922 PMCID: PMC8777761 DOI: 10.3390/md20010067] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
Colorectal cancer is one of the most common cancers diagnosed in the world. Chemotheraphy is one of the most common methods used for the pharmacological treatment of this cancer patients. Nevertheless, the adverse effect of chemotherapy is not optimized for improving the quality of life of people who are older, who are the most vulnerable subpopulation. This review presents recent updates regarding secondary metabolites derived from marine fungi and actinobacteria as novel alternatives for cytotoxic agents against colorectal cancer cell lines HCT116, HT29, HCT15, RKO, Caco-2, and SW480. The observed marine-derived fungi were from the species Aspergillus sp., Penicillium sp., Neosartorya sp., Dichotomomyces sp., Paradendryphiella sp., and Westerdykella sp. Additionally, Streptomyces sp. and Nocardiopsis sp. are actinobacteria discussed in this study. Seventy one compounds reviewed in this study were grouped on the basis of their chemical structures. Indole alkaloids and diketopiperazines made up most compounds with higher potencies when compared with other groups. The potency of indole alkaloids and diketopiperazines was most probably due to halogen-based functional groups and sulfide groups, respectively.
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10
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Fungal Secondary Metabolites as Inhibitors of the Ubiquitin-Proteasome System. Int J Mol Sci 2021; 22:ijms222413309. [PMID: 34948102 PMCID: PMC8707610 DOI: 10.3390/ijms222413309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 12/19/2022] Open
Abstract
The ubiquitin–proteasome system (UPS) is the major non-lysosomal pathway responsible for regulated degradation of intracellular proteins in eukaryotes. As the principal proteolytic pathway in the cytosol and the nucleus, the UPS serves two main functions: the quality control function (i.e., removal of damaged, misfolded, and functionally incompetent proteins) and a major regulatory function (i.e., targeted degradation of a variety of short-lived regulatory proteins involved in cell cycle control, signal transduction cascades, and regulation of gene expression and metabolic pathways). Aberrations in the UPS are implicated in numerous human pathologies such as cancer, neurodegenerative disorders, autoimmunity, inflammation, or infectious diseases. Therefore, the UPS has become an attractive target for drug discovery and development. For the past two decades, much research has been focused on identifying and developing compounds that target specific components of the UPS. Considerable effort has been devoted to the development of both second-generation proteasome inhibitors and inhibitors of ubiquitinating/deubiquitinating enzymes. With the feature of unique structure and bioactivity, secondary metabolites (natural products) serve as the lead compounds in the development of new therapeutic drugs. This review, for the first time, summarizes fungal secondary metabolites found to act as inhibitors of the UPS components.
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Fidor A, Cekała K, Wieczerzak E, Cegłowska M, Kasprzykowski F, Edwards C, Mazur-Marzec H. Nostocyclopeptides as New Inhibitors of 20S Proteasome. Biomolecules 2021; 11:biom11101483. [PMID: 34680116 PMCID: PMC8533403 DOI: 10.3390/biom11101483] [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: 09/01/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Nostocyclopeptides (Ncps) are a small class of bioactive nonribosomal peptides produced solely by cyanobacteria of the genus Nostoc. In the current work, six Ncps were isolated from Nostoc edaphicum strain CCNP1411. The bioactivity of these compounds was tested in vitro against 20S proteasome, a proteolytic complex that plays an important role in maintaining cellular proteostasis. Dysfunction of the complex leads to many pathological disorders. The assays indicated selective activity of specific Ncp variants. For two linear peptide aldehydes, Ncp-A2-L and Ncp-E2-L, the inhibitory effects on chymotrypsin-like activity were revealed, while the cyclic variant, Ncp-A2, inactivated the trypsin-like site of this enzymatic complex. The aldehyde group was confirmed to be an important element of the chymotrypsin-like activity inhibitors. The nostocyclopeptides, as novel inhibitors of 20S proteasome, increased the number of natural products that can be considered potential regulators of cellular processes.
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Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Marszałka Józefa Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Katarzyna Cekała
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland; (K.C.); (E.W.); (F.K.)
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland; (K.C.); (E.W.); (F.K.)
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81712 Sopot, Poland;
| | - Franciszek Kasprzykowski
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland; (K.C.); (E.W.); (F.K.)
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK;
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Marszałka Józefa Piłsudskiego 46, PL-81378 Gdynia, Poland;
- Correspondence:
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12
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Upadhyay A. Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases. Acta Pharm Sin B 2021; 11:2995-3014. [PMID: 34729300 PMCID: PMC8546668 DOI: 10.1016/j.apsb.2021.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 11/03/2020] [Indexed: 01/13/2023] Open
Abstract
Cells have different sets of molecules for performing an array of physiological functions. Nucleic acids have stored and carried the information throughout evolution, whereas proteins have been attributed to performing most of the cellular functions. To perform these functions, proteins need to have a unique conformation and a definite lifespan. These attributes are achieved by a highly coordinated protein quality control (PQC) system comprising chaperones to fold the proteins in a proper three-dimensional structure, ubiquitin-proteasome system for selective degradation of proteins, and autophagy for bulk clearance of cell debris. Many kinds of stresses and perturbations may lead to the weakening of these protective cellular machinery, leading to the unfolding and aggregation of cellular proteins and the occurrence of numerous pathological conditions. However, modulating the expression and functional efficiency of molecular chaperones, E3 ubiquitin ligases, and autophagic proteins may diminish cellular proteotoxic load and mitigate various pathological effects. Natural medicine and small molecule-based therapies have been well-documented for their effectiveness in modulating these pathways and reestablishing the lost proteostasis inside the cells to combat disease conditions. The present article summarizes various similar reports and highlights the importance of the molecules obtained from natural sources in disease therapeutics.
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Key Words
- 17-AAG, 17-allylamino-geldanamycin
- APC, anaphase-promoting complex
- Ageing
- Autophagy
- BAG, BCL2-associated athanogene
- CAP, chaperone-assisted proteasomal degradation
- CASA, chaperone-assisted selective autophagy
- CHIP, carboxy-terminus of HSC70 interacting protein
- CMA, chaperone-mediated autophagy
- Cancer
- Chaperones
- DUBs, deubiquitinases
- Drug discovery
- EGCG, epigallocatechin-3-gallate
- ESCRT, endosomal sorting complexes required for transport
- HECT, homologous to the E6-AP carboxyl terminus
- HSC70, heat shock cognate 70
- HSF1, heat shock factor 1
- HSP, heat shock protein
- KFERQ, lysine-phenylalanine-glutamate-arginine-glutamine
- LAMP2a, lysosome-associated membrane protein 2a
- LC3, light chain 3
- NBR1, next to BRCA1 gene 1
- Natural molecules
- Neurodegeneration
- PQC, protein quality control
- Proteinopathies
- Proteostasis
- RING, really interesting new gene
- UPS, ubiquitin–proteasome system
- Ub, ubiquitin
- Ubiquitin proteasome system
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Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Bandar Sindari, Kishangarh, Ajmer, Rajasthan 305817, India
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Iacovelli R, Bovenberg RAL, Driessen AJM. Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens. J Ind Microbiol Biotechnol 2021; 48:6324005. [PMID: 34279620 PMCID: PMC8788816 DOI: 10.1093/jimb/kuab045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPS) are large multimodular enzymes that synthesize a diverse variety of peptides. Many of these are currently used as pharmaceuticals, thanks to their activity as antimicrobials (penicillin, vancomycin, daptomycin, echinocandin), immunosuppressant (cyclosporin) and anticancer compounds (bleomycin). Because of their biotechnological potential, NRPSs have been extensively studied in the past decades. In this review, we provide an overview of the main structural and functional features of these enzymes, and we consider the challenges and prospects of engineering NRPSs for the synthesis of novel compounds. Furthermore, we discuss secondary metabolism and NRP synthesis in the filamentous fungus Penicillium rubens and examine its potential for the production of novel and modified β-lactam antibiotics.
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Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.,DSM Biotechnology Centre, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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14
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Hughes CC. Chemical labeling strategies for small molecule natural product detection and isolation. Nat Prod Rep 2021; 38:1684-1705. [PMID: 33629087 DOI: 10.1039/d0np00034e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: Up to 2020.It is widely accepted that small molecule natural products (NPs) evolved to carry out a particular ecological function and that these finely-tuned molecules can sometimes be appropriated for the treatment of disease in humans. Unfortunately, for the natural products chemist, NPs did not evolve to possess favorable physicochemical properties needed for HPLC-MS analysis. The process known as derivatization, whereby an NP in a complex mixture is decorated with a nonnatural moiety using a derivatizing agent (DA), arose from this sad state of affairs. Here, NPs are freed from the limitations of natural functionality and endowed, usually with some degree of chemoselectivity, with additional structural features that make HPLC-MS analysis more informative. DAs that selectively label amines, carboxylic acids, alcohols, phenols, thiols, ketones, and aldehydes, terminal alkynes, electrophiles, conjugated alkenes, and isocyanides have been developed and will be discussed here in detail. Although usually employed for targeted metabolomics, chemical labeling strategies have been effectively applied to uncharacterized NP extracts and may play an increasing role in the detection and isolation of certain classes of NPs in the future.
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Affiliation(s)
- Chambers C Hughes
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany 72076.
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15
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Hubbell GE, Tepe JJ. Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors. RSC Chem Biol 2020; 1:305-332. [PMID: 33791679 PMCID: PMC8009326 DOI: 10.1039/d0cb00111b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
The 20S proteasome is a valuable target for the treatment of a number of diseases including cancer, neurodegenerative disease, and parasitic infection. In an effort to discover novel inhibitors of the 20S proteasome, many reseaarchers have looked to natural products as potential leads for drug discovery. The following review discusses the efforts made in the field to isolate and identify natural products as inhibitors of the proteasome. In addition, we describe some of the modifications made to natural products in order to discover more potent and selective inhibitors for potential disease treatment.
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Affiliation(s)
- Grace E. Hubbell
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
| | - Jetze J. Tepe
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
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Maiolini M, Gause S, Taylor J, Steakin T, Shipp G, Lamichhane P, Deshmukh B, Shinde V, Bishayee A, Deshmukh RR. The War against Tuberculosis: A Review of Natural Compounds and Their Derivatives. Molecules 2020; 25:molecules25133011. [PMID: 32630150 PMCID: PMC7412169 DOI: 10.3390/molecules25133011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB), caused by the bacterial organism Mycobacterium tuberculosis, pose a major threat to public health, especially in middle and low-income countries. Worldwide in 2018, approximately 10 million new cases of TB were reported to the World Health Organization (WHO). There are a limited number of medications available to treat TB; additionally, multi-drug resistant TB and extensively-drug resistant TB strains are becoming more prevalent. As a result of various factors, such as increased costs of developing new medications and adverse side effects from current medications, researchers continue to evaluate natural compounds for additional treatment options. These substances have the potential to target bacterial cell structures and may contribute to successful treatment. For example, a study reported that green and black tea, which contains epigallocatechin gallate (a phenolic antioxidant), may decrease the risk of contracting TB in experimental subjects; cumin (a seed from the parsley plant) has been demonstrated to improve the bioavailability of rifampicin, an important anti-TB medication, and propolis (a natural substance produced by honeybees) has been shown to improve the binding affinity of anti-TB medications to bacterial cell structures. In this article, we review the opportunistic pathogen M. tuberculosis, various potential therapeutic targets, available therapies, and natural compounds that may have anti-TB properties. In conclusion, different natural compounds alone as well as in combination with already approved medication regimens should continue to be investigated as treatment options for TB.
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Affiliation(s)
- Morgan Maiolini
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Stacey Gause
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Jerika Taylor
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Tara Steakin
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Ginger Shipp
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
| | - Purushottam Lamichhane
- School of Dental Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
| | - Bhushan Deshmukh
- Department of Chemistry, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425 001, Maharashtra, India;
| | - Vaibhav Shinde
- Department of Pharmacognosy, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune-411 038, Maharashtra, India;
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
- Correspondence: or (A.B.); (R.R.D.); Tel.: +1-941-782-5950 (A.B.); +1-941-782-5646 (R.R.D.)
| | - Rahul R. Deshmukh
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
- Correspondence: or (A.B.); (R.R.D.); Tel.: +1-941-782-5950 (A.B.); +1-941-782-5646 (R.R.D.)
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17
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Dallery JF, Zimmer M, Halder V, Suliman M, Pigné S, Le Goff G, Gianniou DD, Trougakos IP, Ouazzani J, Gasperini D, O’Connell RJ. Inhibition of jasmonate-mediated plant defences by the fungal metabolite higginsianin B. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2910-2921. [PMID: 32006004 PMCID: PMC7260715 DOI: 10.1093/jxb/eraa061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/29/2020] [Indexed: 05/22/2023]
Abstract
Infection of Arabidopsis thaliana by the ascomycete fungus Colletotrichum higginsianum is characterized by an early symptomless biotrophic phase followed by a destructive necrotrophic phase. The fungal genome contains 77 secondary metabolism-related biosynthetic gene clusters, whose expression during the infection process is tightly regulated. Deleting CclA, a chromatin regulator involved in the repression of some biosynthetic gene clusters through H3K4 trimethylation, allowed overproduction of three families of terpenoids and isolation of 12 different molecules. These natural products were tested in combination with methyl jasmonate, an elicitor of jasmonate responses, for their capacity to alter defence gene induction in Arabidopsis. Higginsianin B inhibited methyl jasmonate-triggered expression of the defence reporter VSP1p:GUS, suggesting it may block bioactive jasmonoyl isoleucine (JA-Ile) synthesis or signalling in planta. Using the JA-Ile sensor Jas9-VENUS, we found that higginsianin B, but not three other structurally related molecules, suppressed JA-Ile signalling by preventing the degradation of JAZ proteins, the repressors of jasmonate responses. Higginsianin B likely blocks the 26S proteasome-dependent degradation of JAZ proteins because it inhibited chymotrypsin- and caspase-like protease activities. The inhibition of target degradation by higginsianin B also extended to auxin signalling, as higginsianin B treatment reduced auxin-dependent expression of DR5p:GUS. Overall, our data indicate that specific fungal secondary metabolites can act similarly to protein effectors to subvert plant immune and developmental responses.
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Affiliation(s)
- Jean-Félix Dallery
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, Gif-sur-Yvette, France
| | - Marlene Zimmer
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Vivek Halder
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Current address: Rijk Zwaan, De Lier, 2678 ZG, Netherlands
| | - Mohamed Suliman
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Current address: Desert Research Center, Cairo, Egypt
| | - Sandrine Pigné
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
| | - Géraldine Le Goff
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, Gif-sur-Yvette, France
| | - Despoina D Gianniou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Jamal Ouazzani
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, Gif-sur-Yvette, France
| | - Debora Gasperini
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Correspondence: or
| | - Richard J O’Connell
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
- Correspondence: or
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18
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Romsdahl J, Wang CCC. Recent advances in the genome mining of Aspergillus secondary metabolites (covering 2012-2018). MEDCHEMCOMM 2019; 10:840-866. [PMID: 31303983 PMCID: PMC6590338 DOI: 10.1039/c9md00054b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/11/2019] [Indexed: 02/01/2023]
Abstract
Secondary metabolites (SMs) produced by filamentous fungi possess diverse bioactivities that make them excellent drug candidates. Whole genome sequencing has revealed that fungi have the capacity to produce a far greater number of SMs than have been isolated, since many of the genes involved in SM biosynthesis are either silent or expressed at very low levels in standard laboratory conditions. There has been significant effort to activate SM biosynthetic genes and link them to their downstream products, as the SMs produced by these "cryptic" pathways offer a promising source for new drug discovery. Further, an understanding of the genes involved in SM biosynthesis facilitates product yield optimization of first-generation molecules and genetic engineering of second-generation analogs. This review covers advances made in genome mining SMs produced by Aspergillus nidulans, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus in the past six years (2012-2018). Genetic identification and molecular characterization of SM biosynthetic gene clusters, along with proposed biosynthetic pathways, will be discussed in depth.
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Affiliation(s)
- Jillian Romsdahl
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Avenue , Los Angeles , CA 90089 , USA . ; Tel: (323) 442 1670
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Avenue , Los Angeles , CA 90089 , USA . ; Tel: (323) 442 1670
- Department of Chemistry , Dornsife College of Letters, Arts, and Sciences , University of Southern California , 3551 Trousdale Pkwy , Los Angeles , CA 90089 , USA
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20
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Brain ageing and neurodegenerative disease: The role of cellular waste management. Biochem Pharmacol 2018; 158:207-216. [DOI: 10.1016/j.bcp.2018.10.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022]
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Della Sala G, Agriesti F, Mazzoccoli C, Tataranni T, Costantino V, Piccoli C. Clogging the Ubiquitin-Proteasome Machinery with Marine Natural Products: Last Decade Update. Mar Drugs 2018; 16:E467. [PMID: 30486251 PMCID: PMC6316072 DOI: 10.3390/md16120467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/11/2018] [Accepted: 11/22/2018] [Indexed: 01/08/2023] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the central protein degradation system in eukaryotic cells, playing a key role in homeostasis maintenance, through proteolysis of regulatory and misfolded (potentially harmful) proteins. As cancer cells produce proteins inducing cell proliferation and inhibiting cell death pathways, UPP inhibition has been exploited as an anticancer strategy to shift the balance between protein synthesis and degradation towards cell death. Over the last few years, marine invertebrates and microorganisms have shown to be an unexhaustive factory of secondary metabolites targeting the UPP. These chemically intriguing compounds can inspire clinical development of novel antitumor drugs to cope with the incessant outbreak of side effects and resistance mechanisms induced by currently approved proteasome inhibitors (e.g., bortezomib). In this review, we report about (a) the role of the UPP in anticancer therapy, (b) chemical and biological properties of UPP inhibitors from marine sources discovered in the last decade, (c) high-throughput screening techniques for mining natural UPP inhibitors in organic extracts. Moreover, we will tell about the fascinating story of salinosporamide A, the first marine natural product to access clinical trials as a proteasome inhibitor for cancer treatment.
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Affiliation(s)
- Gerardo Della Sala
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Francesca Agriesti
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Carmela Mazzoccoli
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Tiziana Tataranni
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
| | - Valeria Costantino
- The NeaNat Group, Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy.
| | - Claudia Piccoli
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy.
- Department of Clinical and Experimental Medicine, University of Foggia, via L. Pinto c/o OO.RR., 71100 Foggia, Italy.
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22
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Lubos M, Dębowski D, Barcińska E, Meid A, Inkielewicz‐Stepniak I, Burster T, Rolka K. Inhibition of human constitutive 20S proteasome and 20S immunoproteasome with novel
N
‐terminally modified peptide aldehydes and their antitumor activity. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marta Lubos
- Department of Molecular Biochemistry, Faculty of ChemistryUniversity of Gdansk Gdansk Poland
| | - Dawid Dębowski
- Department of Molecular Biochemistry, Faculty of ChemistryUniversity of Gdansk Gdansk Poland
| | - Ewelina Barcińska
- Department of Medical ChemistryMedical University of Gdansk Gdansk Poland
| | - Annika Meid
- Department of Neurosurgery, Surgery CenterUlm University Medical Center Ulm Germany
| | | | - Timo Burster
- Department of BiologySchool of Science and Technology, Nazarbayev University Astana Kazakhstan Republic
| | - Krzysztof Rolka
- Department of Molecular Biochemistry, Faculty of ChemistryUniversity of Gdansk Gdansk Poland
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Reddy RG, Dachavaram SS, Reddy BR, Kalyankar KB, Rajan WD, Kootar S, Kumar A, Das S, Chakravarty S. Fellutamide B Synthetic Path Intermediates with in Vitro Neuroactive Function Shows Mood-Elevating Effect in Stress-Induced Zebrafish Model. ACS OMEGA 2018; 3:10534-10544. [PMID: 30320245 PMCID: PMC6173481 DOI: 10.1021/acsomega.8b00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Fellutamide B is reported to have cytotoxic and proteasome inhibitory activity. Interestingly, fellutamide B and its simplified analogues have also been observed for the neurotrophic activity by stimulating the synthesis and secretion of neurotrophins. Owing to the interesting structural and potent neurotrophic role of fellutamide B (a lipopeptide aldehyde), we have assessed the synthetic path intermediates (compounds A-D) of fellutamide B for their neuroactive potential (in vitro and in vivo). We have observed few compounds (comp #A-D) to have potential neurite outgrowth activity in Neuro2a cells with no observable negative effect on the cell viability. In addition, most compounds (comp #A, C, and D) have shown neurogenic activity ex vivo in hippocampal neurosphere culture, with increased acetyl H3 and acetyl H4 induction ability (comp #C). Furthermore, the intermediate product comp #C has shown anxiolytic and antidepressant-like activity in novel tank test and social interaction test, in the chronic unpredictable stress model of zebrafish mood disorder, inducing BDNF gene expression in the telencephalon region of the fish brain. Our results thus demonstrate that the fellutamide B synthetic path intermediates have potential neurotrophic, neurogenic, and mood-elevating effects and thus good prospect to be developed as potential therapeutics to treat psychiatric disorders.
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Affiliation(s)
- R. Gajendra Reddy
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Soma Shekar Dachavaram
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
| | - B. Raghunath Reddy
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Kondbarao Balasaheb Kalyankar
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Wenson D. Rajan
- CSIR-Centre
for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, India
| | - Scherazad Kootar
- CSIR-Centre
for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, India
| | - Arvind Kumar
- CSIR-Centre
for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Saibal Das
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Sumana Chakravarty
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
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Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ. Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 2018; 35:847-878. [PMID: 29916519 PMCID: PMC6146020 DOI: 10.1039/c8np00013a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
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Affiliation(s)
- Michael W Mullowney
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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25
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Mishra R, Upadhyay A, Prajapati VK, Mishra A. Proteasome-mediated proteostasis: Novel medicinal and pharmacological strategies for diseases. Med Res Rev 2018; 38:1916-1973. [DOI: 10.1002/med.21502] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/13/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Ribhav Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Vijay Kumar Prajapati
- Department of Biochemistry; School of Life Sciences; Central University of Rajasthan; Rajasthan India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
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26
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Total Synthesis and Stereochemical Assignment of Nostosin B. Mar Drugs 2017; 15:md15030058. [PMID: 28264450 PMCID: PMC5367015 DOI: 10.3390/md15030058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 02/04/2023] Open
Abstract
Nostosins A and B were isolated from a hydrophilic extract of Nostoc sp. strain from Iran, which exhibits excellent tryps inhibitory activity. Nostosin A was the most potent natural tripeptide aldehyde as trypsin inhibitor up to now. Both R- and S-2-hydroxy-4-(4-hydroxy-phenyl) butanoic acid (Hhpba) were prepared and incorporated into the total synthesis of nostosin B, respectively. Careful comparison of the NMR spectra and optical rotation data of synthetic nostosin B (1a and 1b) with the natural product led to the unambiguous identification of the R-configuration of the Hhpba fragment, which was further confirmed by co-injection with the authentic sample on HPLC using both reversed phase column and the chiral AD-RH column.
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27
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Yeh HH, Ahuja M, Chiang YM, Oakley CE, Moore S, Yoon O, Hajovsky H, Bok JW, Keller NP, Wang CCC, Oakley BR. Resistance Gene-Guided Genome Mining: Serial Promoter Exchanges in Aspergillus nidulans Reveal the Biosynthetic Pathway for Fellutamide B, a Proteasome Inhibitor. ACS Chem Biol 2016; 11:2275-84. [PMID: 27294372 DOI: 10.1021/acschembio.6b00213] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fungal genome projects are revealing thousands of cryptic secondary metabolism (SM) biosynthetic gene clusters that encode pathways that potentially produce valuable compounds. Heterologous expression systems should allow these clusters to be expressed and their products obtained, but approaches are needed to identify the most valuable target clusters. The inp cluster of Aspergillus nidulans contains a gene, inpE, that encodes a proteasome subunit, leading us to hypothesize that the inp cluster produces a proteasome inhibitor and inpE confers resistance to this compound. Previous efforts to express this cluster have failed, but by sequentially replacing the promoters of the genes of the cluster with a regulatable promotor, we have expressed them successfully. Expression reveals that the product of the inp cluster is the proteasome inhibitor fellutamide B, and our data allow us to propose a biosynthetic pathway for the compound. By deleting inpE and activating expression of the inp cluster, we demonstrate that inpE is required for resistance to internally produced fellutamide B. These data provide experimental validation for the hypothesis that some fungal SM clusters contain genes that encode resistant forms of the enzymes targeted by the compound produced by the cluster.
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Affiliation(s)
- Hsu-Hua Yeh
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Manmeet Ahuja
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Yi-Ming Chiang
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department
of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 71710, Taiwan
| | - C. Elizabeth Oakley
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Shauna Moore
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Olivia Yoon
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Heather Hajovsky
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Jin-Woo Bok
- Department
of Bacteriology and Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Nancy P. Keller
- Department
of Bacteriology and Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Clay C. C. Wang
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, Dornsife College of Letters, Arts, and Sciences, Los Angeles, California 90089, United States
| | - Berl R. Oakley
- Department
of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
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Pirrung MC, Zhang F, Ambadi S, Gangadhara Rao Y. Total synthesis of fellutamides, lipopeptide proteasome inhibitors. More sustainable peptide bond formation. Org Biomol Chem 2016; 14:8367-75. [PMID: 27533920 DOI: 10.1039/c6ob01233g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solution-phase syntheses of three bioactive natural products of mixed polypeptide-polyketide biogenesis, fellutamides A, B, and C, have been achieved. Three peptide bonds are generated without the use of coupling reagents in each synthesis of the fellutamides, which act against proteasomes.
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Affiliation(s)
- Michael C Pirrung
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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29
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Computational Approaches for the Discovery of Human Proteasome Inhibitors: An Overview. Molecules 2016; 21:molecules21070927. [PMID: 27438821 PMCID: PMC6274525 DOI: 10.3390/molecules21070927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 01/10/2023] Open
Abstract
Proteasome emerged as an important target in recent pharmacological research due to its pivotal role in degrading proteins in the cytoplasm and nucleus of eukaryotic cells, regulating a wide variety of cellular pathways, including cell growth and proliferation, apoptosis, DNA repair, transcription, immune response, and signaling processes. The last two decades witnessed intensive efforts to discover 20S proteasome inhibitors with significant chemical diversity and efficacy. To date, the US FDA approved to market three proteasome inhibitors: bortezomib, carfilzomib, and ixazomib. However new, safer and more efficient drugs are still required. Computer-aided drug discovery has long being used in drug discovery campaigns targeting the human proteasome. The aim of this review is to illustrate selected in silico methods like homology modeling, molecular docking, pharmacophore modeling, virtual screening, and combined methods that have been used in proteasome inhibitors discovery. Applications of these methods to proteasome inhibitors discovery will also be presented and discussed to raise improvements in this particular field.
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A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome. Nat Commun 2016; 7:10900. [PMID: 26964885 PMCID: PMC4792962 DOI: 10.1038/ncomms10900] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/31/2016] [Indexed: 11/28/2022] Open
Abstract
Biogenesis of the 20S proteasome is tightly regulated. The N-terminal propeptides protecting the active-site threonines are autocatalytically released only on completion of assembly. However, the trigger for the self-activation and the reason for the strict conservation of threonine as the active site nucleophile remain enigmatic. Here we use mutagenesis, X-ray crystallography and biochemical assays to suggest that Lys33 initiates nucleophilic attack of the propeptide by deprotonating the Thr1 hydroxyl group and that both residues together with Asp17 are part of a catalytic triad. Substitution of Thr1 by Cys disrupts the interaction with Lys33 and inactivates the proteasome. Although a Thr1Ser mutant is active, it is less efficient compared with wild type because of the unfavourable orientation of Ser1 towards incoming substrates. This work provides insights into the basic mechanism of proteolysis and propeptide autolysis, as well as the evolutionary pressures that drove the proteasome to become a threonine protease. The proteasome, an essential molecular machine, is a threonine protease, but the evolution and the components of its proteolytic centre are unclear. Here, the authors use structural biology and biochemistry to investigate the role of proteasome active site residues on maturation and activity.
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31
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Wei D, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA). Org Biomol Chem 2016; 13:6857-65. [PMID: 26018983 DOI: 10.1039/c5ob00737b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
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Nicoletti R, Trincone A. Bioactive Compounds Produced by Strains of Penicillium and Talaromyces of Marine Origin. Mar Drugs 2016; 14:md14020037. [PMID: 26901206 PMCID: PMC4771990 DOI: 10.3390/md14020037] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/14/2022] Open
Abstract
In recent years, the search for novel natural compounds with bioactive properties has received a remarkable boost in view of their possible pharmaceutical exploitation. In this respect the sea is entitled to hold a prominent place, considering the potential of the manifold animals and plants interacting in this ecological context, which becomes even greater when their associated microbes are considered for bioprospecting. This is the case particularly of fungi, which have only recently started to be considered for their fundamental contribution to the biosynthetic potential of other more valued marine organisms. Also in this regard, strains of species which were previously considered typical terrestrial fungi, such as Penicillium and Talaromyces, disclose foreground relevance. This paper offers an overview of data published over the past 25 years concerning the production and biological activities of secondary metabolites of marine strains belonging to these genera, and their relevance as prospective drugs.
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Affiliation(s)
- Rosario Nicoletti
- Council for Agricultural Research and Agricultural Economy Analysis, Rome 00184, Italy.
| | - Antonio Trincone
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli 80078, Italy.
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33
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Grigoreva TA, Tribulovich VG, Garabadzhiu AV, Melino G, Barlev NA. The 26S proteasome is a multifaceted target for anti-cancer therapies. Oncotarget 2015; 6:24733-49. [PMID: 26295307 PMCID: PMC4694792 DOI: 10.18632/oncotarget.4619] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 07/10/2015] [Indexed: 12/30/2022] Open
Abstract
Proteasomes play a critical role in the fate of proteins that are involved in major cellular processes, including signal transduction, gene expression, cell cycle, replication, differentiation, immune response, cellular response to stress, etc. In contrast to non-specific degradation by lysosomes, proteasomes are highly selective and destroy only the proteins that are covalently labelled with small proteins, called ubiquitins. Importantly, many diseases, including neurodegenerative diseases and cancers, are intimately connected to the activity of proteasomes making them an important pharmacological target. Currently, the vast majority of inhibitors are aimed at blunting the proteolytic activities of proteasomes. However, recent achievements in solving structures of proteasomes at very high resolution provided opportunities to design new classes of small molecules that target other physiologically-important enzymatic activities of proteasomes, including the de-ubiquitinating one. This review attempts to catalog the information available to date about novel classes of proteasome inhibitors that may have important pharmacological ramifications.
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Affiliation(s)
- Tatyana A Grigoreva
- St. Petersburg State Technological Institute (Technical University), St. Petersburng, Russia
| | | | | | - Gerry Melino
- St. Petersburg State Technological Institute (Technical University), St. Petersburng, Russia
- University of Rome Tor Vergata, Roma, Italy
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Albright JC, Henke MT, Soukup AA, McClure RA, Thomson RJ, Keller NP, Kelleher NL. Large-scale metabolomics reveals a complex response of Aspergillus nidulans to epigenetic perturbation. ACS Chem Biol 2015; 10:1535-41. [PMID: 25815712 DOI: 10.1021/acschembio.5b00025] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The microbial world offers a rich source of bioactive compounds for those able to sift through it. Technologies capable of quantitatively detecting natural products while simultaneously identifying known compounds would expedite the search for new pharmaceutical leads. Prior efforts have targeted histone deacetylases in fungi to globally activate the production of new secondary metabolites, yet no study has directly assessed its effects with minimal bias at the metabolomic level. Using untargeted metabolomics, we monitored changes in >1000 small molecules secreted from the model fungus, Aspergillus nidulans, following genetic or chemical reductions in histone deacetylase activity (HDACi). Through quantitative, differential analyses, we found that nearly equal numbers of compounds were up- and down-regulated by >100 fold. We detected products from both known and unknown biosynthetic pathways and discovered that A. nidulans is capable of producing fellutamides, proteasome inhibitors whose expression was induced by ∼100 fold or greater upon HDACi. This work adds momentum to an "omics"-driven resurgence in natural products research, where direct detection replaces bioactivity as the primary screen for new pharmacophores.
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Affiliation(s)
- Jessica C. Albright
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Matthew T. Henke
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Alexandra A. Soukup
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ryan A. McClure
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Regan J. Thomson
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Nancy P. Keller
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Neil L. Kelleher
- Department of Chemistry, ‡Department of Molecular Biosciences, §Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Department of Genetics, ⊥Department of Bacteriology, #Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
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Ortíz-López FJ, Monteiro MC, González-Menéndez V, Tormo JR, Genilloud O, Bills GF, Vicente F, Zhang C, Roemer T, Singh SB, Reyes F. Cyclic colisporifungin and linear cavinafungins, antifungal lipopeptides isolated from Colispora cavincola. JOURNAL OF NATURAL PRODUCTS 2015; 78:468-475. [PMID: 25636062 DOI: 10.1021/np500854j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Colisporifungin (1), a cyclic depsilipopeptide structurally related to the aselacins, and cavinafungins A and B, two linear peptides, were isolated from liquid culture broths of the hitherto unstudied fungus Colispora cavincola using a Candida albicans whole-cell assay as well as a bioassay to detect compounds potentiating the antifungal activity of caspofungin. The structural elucidation, including the absolute configuration of the new molecules, was accomplished using a combination of spectroscopic and chemical techniques, including 1D and 2D NMR, HRMS, and Marfey's analysis. The cyclic peptide colisporifungin displayed a strong potentiation of the growth inhibitory effect of caspofungin against Aspergillus fumigatus and, to a lesser extent, against Candida albicans. The linear peptides displayed broad-spectrum antifungal activities inhibiting growth of Candida species (MIC values 0.5-4 μg/mL) as well as A. fumigatus with a prominent inhibition of 8 μg/mL.
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Affiliation(s)
- Francisco Javier Ortíz-López
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Maria Cândida Monteiro
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Víctor González-Menéndez
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - José R Tormo
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Olga Genilloud
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Gerald F Bills
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Francisca Vicente
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Chaowei Zhang
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Terry Roemer
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Sheo B Singh
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Fernando Reyes
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
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Pautasso C, Troia R, Genuardi M, Palumbo A. Pharmacophore modeling technique applied for the discovery of proteasome inhibitors. Expert Opin Drug Discov 2014; 9:931-43. [PMID: 24877566 DOI: 10.1517/17460441.2014.923838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION The 26S proteasome has many important roles in the biological functions of the cells, and proteasome inhibitors have multiple and complex activities on cells. These compounds can be natural or synthesized. Most synthetic derivatives have been rationally designed, synthesized and optimized to obtain the best selectivity and increase the activity. The design of chemical entities with desired molecular identification, which plays an important role in biological systems, is provided by pharmacophore modeling. Indeed, pharmacophore models can be established either in a ligand-based manner or in a receptor-based manner. AREAS COVERED The authors discuss the application of pharmacophore modeling techniques to proteasome inhibitors development. Furthermore, the article reviews the classification of the currently discovered proteasome inhibitors where the principal mechanism of action and clinical application are represented. EXPERT OPINION In the era of new drug development, database of compounds should be thoroughly evaluated with a combination of methods that consider both pharmacophore- and ligand-based virtual screening. The concept of pharmacophore helps to discover new active compounds and to evaluate their activity. The nature of proteasome inhibitor pharmacophore affects the secondary active-site specificity; indeed, increasing specificity decreases the cytotoxicity of the proteasome inhibitors. It is hypothesized that the balanced simultaneous modulation of a few druggable targets may have superior efficacy and fewer side effects than single-target or combination therapies for the treatment of human cancers. The discovery of new compounds should aim to find more active compounds that improve the compliance of patients.
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Affiliation(s)
- Chiara Pautasso
- University of Torino, Myeloma Unit, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Division of Hematology , Torino , Italy ;
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Seven new and two known lipopeptides as well as five known polyketides: the activated production of silent metabolites in a marine-derived fungus by chemical mutagenesis strategy using diethyl sulphate. Mar Drugs 2014; 12:1815-38. [PMID: 24686557 PMCID: PMC4012460 DOI: 10.3390/md12041815] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 11/17/2022] Open
Abstract
AD-2-1 is an antitumor fungal mutant obtained by diethyl sulfate mutagenesis of a marine-derived Penicillium purpurogenum G59. The G59 strain originally did not produce any metabolites with antitumor activities in MTT assays using K562 cells. Tracing newly produced metabolites under guidance of MTT assay and TLC analysis by direct comparison with control G59 extract, seven new (1–7) and two known (8–9) lipopeptides were isolated together with five known polyketides 10–14 from the extract of mutant AD-2-1. Structures of the seven new compounds including their absolute configurations were determined by spectroscopic and chemical evidences and named as penicimutalides A–G (1–7). Seven known compounds were identified as fellutamide B (8), fellutamide C (9), 1′-O-methylaverantin (10), averantin (11), averufin (12), nidurufin (13), and sterigmatocystin (14). In the MTT assay, 1–14 inhibited several human cancer cell lines to varying extents. All the bioassays and HPLC-photodiode array detector (PDAD)-UV and HPLC-electron spray ionization (ESI)-MS analyses demonstrated that the production of 1–14 in the mutant AD-2-1 was caused by the activated production of silent metabolites in the original G59 fungal strain. Present results provided additional examples for effectiveness of the chemical mutagenesis strategy using diethyl sulphate mutagenesis to discover new compounds by activating silent metabolites in fungal isolates.
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Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Xu J, Lacoske MH, Theodorakis EA. Neurotrophic natural products: chemistry and biology. Angew Chem Int Ed Engl 2014; 53:956-87. [PMID: 24353244 PMCID: PMC3945720 DOI: 10.1002/anie.201302268] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases and spinal cord injury affect approximately 50 million people worldwide, bringing the total healthcare cost to over 600 billion dollars per year. Nervous system growth factors, that is, neurotrophins, are a potential solution to these disorders, since they could promote nerve regeneration. An average of 500 publications per year attests to the significance of neurotrophins in biomedical sciences and underlines their potential for therapeutic applications. Nonetheless, the poor pharmacokinetic profile of neurotrophins severely restricts their clinical use. On the other hand, small molecules that modulate neurotrophic activity offer a promising therapeutic approach against neurological disorders. Nature has provided an impressive array of natural products that have potent neurotrophic activities. This Review highlights the current synthetic strategies toward these compounds and summarizes their ability to induce neuronal growth and rehabilitation. It is anticipated that neurotrophic natural products could be used not only as starting points in drug design but also as tools to study the next frontier in biomedical sciences: the brain activity map project.
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Affiliation(s)
- Jing Xu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358 (USA), Homepage: http://theodorakisgroup.ucsd.edu
| | - Michelle H. Lacoske
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358 (USA), Homepage: http://theodorakisgroup.ucsd.edu
| | - Emmanuel A. Theodorakis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358 (USA), Homepage: http://theodorakisgroup.ucsd.edu
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Xu J, Lacoske MH, Theodorakis EA. Neurotrophe Naturstoffe - ihre Chemie und Biologie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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43
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Roberts DM, Personne Y, Ollinger J, Parish T. Proteases in Mycobacterium tuberculosis pathogenesis: potential as drug targets. Future Microbiol 2013; 8:621-31. [PMID: 23642117 DOI: 10.2217/fmb.13.25] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
TB is still a major global health problem causing over 1 million deaths per year. An increasing problem of drug resistance in the causative agent, Mycobacterium tuberculosis, as well as problems with the current lengthy and complex treatment regimens, lends urgency to the need to develop new antitubercular agents. Proteases have been targeted for therapy in other infections, most notably these have been successful as antiviral agents in the treatment of HIV infection. M. tuberculosis has a number of proteases with good potential as novel drug targets and developing drugs against these should result in agents that are effective against drug-resistant and drug-sensitive strains. In this review, the authors summarize the current status of proteases with potential as drug targets in this pathogen, particularly focusing on proteases involved in protein secretion (signal peptidases LepB and LspA), protein degradation and turnover (ClpP and the proteasome) and virulence (mycosins and HtrA).
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Affiliation(s)
- David M Roberts
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
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44
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Wei D, Fang L, Tang M, Zhan CG. Fundamental reaction pathway for peptide metabolism by proteasome: insights from first-principles quantum mechanical/molecular mechanical free energy calculations. J Phys Chem B 2013; 117:13418-34. [PMID: 24111489 DOI: 10.1021/jp405337v] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteasome is the major component of the crucial non-lysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-O(γ). The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-O(γ), followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-N(z). Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-N(z) to Thr1-O(γ). According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3(b)) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally derived activation free energy of ∼18.3-19.4 kcal/mol, suggesting that the computational results are reasonable.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University , 75 Daxue Road, Zhengzhou, Henan 450052, China
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Lee YM, Kim MJ, Li H, Zhang P, Bao B, Lee KJ, Jung JH. Marine-derived Aspergillus species as a source of bioactive secondary metabolites. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:499-519. [PMID: 23709045 DOI: 10.1007/s10126-013-9506-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 04/29/2013] [Indexed: 06/02/2023]
Abstract
This report reviews biologically active secondary metabolites from marine-derived members of the fungal genus Aspergillus. Pharmacological activities and biological roles of the secondary metabolites from marine-derived Aspergillus spp. were addressed in respect of pharmaceutical potential.
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Affiliation(s)
- Yoon Mi Lee
- College of Pharmacy, Pusan National University, Busan, 609-735, Republic of Korea
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46
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Chen Y, McClure RA, Zheng Y, Thomson RJ, Kelleher NL. Proteomics guided discovery of flavopeptins: anti-proliferative aldehydes synthesized by a reductase domain-containing non-ribosomal peptide synthetase. J Am Chem Soc 2013; 135:10449-56. [PMID: 23763305 DOI: 10.1021/ja4031193] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Due to the importance of proteases in regulating cellular processes, the development of protease inhibitors has garnered great attention. Peptide-based aldehydes are a class of compounds that exhibit inhibitory activities against various proteases and proteasomes in the context of anti-proliferative treatments for cancer and other diseases. More than a dozen peptide-based natural products containing aldehydes have been discovered such as chymostatin, leupeptin, and fellutamide; however, the biosynthetic origin of the aldehyde functionality has yet to be elucidated. Herein we describe the discovery of a new group of lipopeptide aldehydes, the flavopeptins, and the corresponding biosynthetic pathway arising from an orphan gene cluster in Streptomyces sp. NRRL-F6652, a close relative of Streptomyces flavogriseus ATCC 33331. This research was initiated using a proteomics approach that screens for expressed enzymes involved in secondary metabolism in microorganisms. Flavopeptins are synthesized through a non-ribosomal peptide synthetase containing a terminal NAD(P)H-dependent reductase domain likely for the reductive release of the peptide with a C-terminal aldehyde. Solid-phase peptide synthesis of several flavopeptin species and derivatives enabled structural verification and subsequent screening of biological activity. Flavopeptins exhibit sub-micromolar inhibition activities against cysteine proteases such as papain and calpain as well as the human 20S proteasome. They also show anti-proliferative activities against multiple myeloma and lymphoma cell lines.
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Affiliation(s)
- Yunqiu Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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47
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Posttranslational protein knockdown coupled to receptor tyrosine kinase activation with phosphoPROTACs. Proc Natl Acad Sci U S A 2013; 110:8942-7. [PMID: 23674677 DOI: 10.1073/pnas.1217206110] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Posttranslational knockdown of a specific protein is an attractive approach for examining its function within a system. Here we introduce phospho-dependent proteolysis targeting chimeras (phosphoPROTACs), a method to couple the conditional degradation of targeted proteins to the activation state of particular kinase-signaling pathways. We generated two phosphoPROTACs that couple the tyrosine phosphorylation sequences of either the nerve growth factor receptor, TrkA (tropomyosin receptor kinase A), or the neuregulin receptor, ErbB3 (erythroblastosis oncogene B3), with a peptide ligand for the E3 ubiquitin ligase von Hippel Lindau protein. These phosphoPROTACs recruit either the neurotrophic signaling effector fibroblast growth factor receptor substrate 2α or the survival-promoting phosphatidylinositol-3-kinase, respectively, to be ubiquitinated and degraded upon activation of specific receptor tyrosine kinases and phosphorylation of the phosphoPROTACs. We demonstrate the ability of these phosphoPROTACs to suppress the short- and long-term effects of their respective activating receptor tyrosine kinase pathways both in vitro and in vivo. In addition, we show that activation of phosphoPROTACs is entirely dependent on their kinase-mediated phosphorylation, as phenylalanine-containing null variants are inactive. Furthermore, stimulation of unrelated growth factor receptors does not induce target protein knockdown. Although comparable in efficiency to RNAi, this approach has the added advantage of providing a degree of temporal and dosing control as well as cell-type selectivity unavailable using nucleic acid-based strategies. By varying the autophosphorylation sequence of a phosphoPROTAC, it is conceivable that other receptor tyrosine kinase/effector pairings could be similarly exploited to achieve other biological effects.
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Kawamura S, Unno Y, List A, Mizuno A, Tanaka M, Sasaki T, Arisawa M, Asai A, Groll M, Shuto S. Potent Proteasome Inhibitors Derived from the Unnatural cis-Cyclopropane Isomer of Belactosin A: Synthesis, Biological Activity, and Mode of Action. J Med Chem 2013; 56:3689-700. [DOI: 10.1021/jm4002296] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Shuhei Kawamura
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Yuka Unno
- Graduate
School of Pharmaceutical
Sciences, University of Shizuoka, Yada,
Shizuoka 422-8526, Japan
| | - Anja List
- Center for Integrated Protein
Science at the Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse
4, 85747 Garching, Germany
| | - Akirai Mizuno
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Motohiro Tanaka
- School of Pharmacy, Aichi Gakuin
University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Takuma Sasaki
- School of Pharmacy, Aichi Gakuin
University, 1-100 Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Mitsuhiro Arisawa
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
| | - Akira Asai
- Graduate
School of Pharmaceutical
Sciences, University of Shizuoka, Yada,
Shizuoka 422-8526, Japan
| | - Michael Groll
- Center for Integrated Protein
Science at the Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse
4, 85747 Garching, Germany
| | - Satoshi Shuto
- Faculty of
Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo
060-0812, Japan
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49
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Desvergne A, Genin E, Maréchal X, Gallastegui N, Dufau L, Richy N, Groll M, Vidal J, Reboud-Ravaux M. Dimerized Linear Mimics of a Natural Cyclopeptide (TMC-95A) Are Potent Noncovalent Inhibitors of the Eukaryotic 20S Proteasome. J Med Chem 2013; 56:3367-78. [DOI: 10.1021/jm4002007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Audrey Desvergne
- Enzymologie
Moléculaire
et Fonctionnelle, UR4, University Paris 6, Pierre et Marie Curie, UPMC-Sorbonne Universités, Case 256, 7 Quai
Saint Bernard, 75252 Paris Cedex 05, France
| | - Emilie Genin
- Chimie et Photonique Moléculaires, Université de Rennes 1, CNRS-UMR 6510, Bâtiment
10A, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Xavier Maréchal
- Enzymologie
Moléculaire
et Fonctionnelle, UR4, University Paris 6, Pierre et Marie Curie, UPMC-Sorbonne Universités, Case 256, 7 Quai
Saint Bernard, 75252 Paris Cedex 05, France
| | - Nerea Gallastegui
- Center for Integrated Protein
Science, Department Chemie Lehrstuhl für Biochemie, Technische Universität München, Lichetenbergstrasse
4, 85747 Garching, Germany
| | - Laure Dufau
- Enzymologie
Moléculaire
et Fonctionnelle, UR4, University Paris 6, Pierre et Marie Curie, UPMC-Sorbonne Universités, Case 256, 7 Quai
Saint Bernard, 75252 Paris Cedex 05, France
| | - Nicolas Richy
- Chimie et Photonique Moléculaires, Université de Rennes 1, CNRS-UMR 6510, Bâtiment
10A, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Michael Groll
- Center for Integrated Protein
Science, Department Chemie Lehrstuhl für Biochemie, Technische Universität München, Lichetenbergstrasse
4, 85747 Garching, Germany
| | - Joëlle Vidal
- Chimie et Photonique Moléculaires, Université de Rennes 1, CNRS-UMR 6510, Bâtiment
10A, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Michèle Reboud-Ravaux
- Enzymologie
Moléculaire
et Fonctionnelle, UR4, University Paris 6, Pierre et Marie Curie, UPMC-Sorbonne Universités, Case 256, 7 Quai
Saint Bernard, 75252 Paris Cedex 05, France
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50
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Rentsch A, Landsberg D, Brodmann T, Bülow L, Girbig AK, Kalesse M. Synthese und Pharmakologie von Proteasom-Inhibitoren. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207900] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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