1
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Zhou J, Sang X, Wu M, Qian T, Ciechanover A, An J, Xu Y, Huang Z. Discovery of Novel Nonpeptidic Proteasome Inhibitors Using Covalent Virtual Screening and Biological Evaluation. ACS Med Chem Lett 2024; 15:1741-1748. [PMID: 39411540 PMCID: PMC11472392 DOI: 10.1021/acsmedchemlett.4c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/19/2024] [Accepted: 09/05/2024] [Indexed: 10/19/2024] Open
Abstract
Many reported proteasome inhibitors, including the three clinically approved inhibitors, bortezomib, carfilzomib, and ixazomib, have peptidic structures. In this study, using a hybrid and versatile strategy for covalent virtual screening by combining warhead screening and preprocessing with GOLD and CovDock software that were applied to the ZINC virtual library, we identified multiple proteasome inhibitors with new nonpeptidic structural scaffolds. Proteasome inhibition assays confirmed the inhibitory activities of these new compounds. These results demonstrate the effectiveness of our computational strategy for large-scale covalent virtual screening. Furthermore, these identified proteasome inhibitors may serve as starting points for the development of a new class of nonpeptidic therapeutic agents.
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Affiliation(s)
- Jiao Zhou
- Ciechanover
Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xiaohong Sang
- Ciechanover
Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Meixian Wu
- Department
of Medicine, Division of Infectious Diseases and Global Public Health,
School of Medicine, University of California
at San Diego, La Jolla, California 92037, United States
| | - Tingli Qian
- Ciechanover
Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Aaron Ciechanover
- Ciechanover
Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Technion
Rappaport Integrated Cancer Center, The Rappaport Faculty of Medicine
and Research Institute, Technion-Israel
Institute of Technology, Haifa 3109601, Israel
| | - Jing An
- Department
of Medicine, Division of Infectious Diseases and Global Public Health,
School of Medicine, University of California
at San Diego, La Jolla, California 92037, United States
| | - Yan Xu
- Department
of Medicine, Division of Infectious Diseases and Global Public Health,
School of Medicine, University of California
at San Diego, La Jolla, California 92037, United States
| | - Ziwei Huang
- Ciechanover
Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Department
of Medicine, Division of Infectious Diseases and Global Public Health,
School of Medicine, University of California
at San Diego, La Jolla, California 92037, United States
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2
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Mishto M, Takala I, Bonfanti P, Liepe J. Proteasome isoforms in human thymi and mouse models. Immunol Lett 2024; 269:106899. [PMID: 39019403 DOI: 10.1016/j.imlet.2024.106899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
The thymus is the organ where functional and self-tolerant T cells are selected through processes of positive and negative selection before migrating to the periphery. The antigenic peptides presented on MHC class I molecules of thymic epithelial cells (TECs) in the cortex and medulla of the thymus are key players in these processes. It has been theorized that these cells express different proteasome isoforms, which generate MHC class I immunopeptidomes with features that differentiate cortex and medulla, and hence positive and negative CD8+ T cell selection. This theory is largely based on mouse models and does not consider the large variety of noncanonical antigenic peptides that could be produced by proteasomes and presented on MHC class I molecules. Here, we review the multi-omics, biochemical and cellular studies carried out on mouse models and human thymi to investigate their content of proteasome isoforms, briefly summarize the implication that noncanonical antigenic peptide presentation in the thymus could have on CD8+ T cell repertoire and put these aspects in the larger framework of anatomical and immunological differences between these two species.
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Affiliation(s)
- Michele Mishto
- Molecular Immunology laboratory, the Francis Crick Institute, NW1 1AT London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, United Kingdom.
| | - Iina Takala
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, London NW3 2PP, United Kingdom
| | - Juliane Liepe
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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3
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Lawong A, Gahalawat S, Ray S, Ho N, Han Y, Ward KE, Deng X, Chen Z, Kumar A, Xing C, Hosangadi V, Fairhurst KJ, Tashiro K, Liszczak G, Shackleford DM, Katneni K, Chen G, Saunders J, Crighton E, Casas A, Robinson JJ, Imlay LS, Zhang X, Lemoff A, Zhao Z, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Campbell SF, Fidock DA, Laleu B, Charman SA, Ready JM, Phillips MA. Identification of potent and reversible piperidine carboxamides that are species-selective orally active proteasome inhibitors to treat malaria. Cell Chem Biol 2024; 31:1503-1517.e19. [PMID: 39084225 DOI: 10.1016/j.chembiol.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
Malaria remains a global health concern as drug resistance threatens treatment programs. We identified a piperidine carboxamide (SW042) with anti-malarial activity by phenotypic screening. Selection of SW042-resistant Plasmodium falciparum (Pf) parasites revealed point mutations in the Pf_proteasome β5 active-site (Pfβ5). A potent analog (SW584) showed efficacy in a mouse model of human malaria after oral dosing. SW584 had a low propensity to generate resistance (minimum inoculum for resistance [MIR] >109) and was synergistic with dihydroartemisinin. Pf_proteasome purification was facilitated by His8-tag introduction onto β7. Inhibition of Pfβ5 correlated with parasite killing, without inhibiting human proteasome isoforms or showing cytotoxicity. The Pf_proteasome_SW584 cryoelectron microscopy (cryo-EM) structure showed that SW584 bound non-covalently distal from the catalytic threonine, in an unexplored pocket at the β5/β6/β3 subunit interface that has species differences between Pf and human proteasomes. Identification of a reversible, species selective, orally active series with low resistance propensity provides a path for drugging this essential target.
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Affiliation(s)
- Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Suraksha Gahalawat
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Sneha Ray
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Nhi Ho
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Kurt E Ward
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Ashwani Kumar
- Department of Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Chao Xing
- Department of Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Varun Hosangadi
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kate J Fairhurst
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kyuto Tashiro
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Glen Liszczak
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jessica Saunders
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Arturo Casas
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Joshua J Robinson
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Leah S Imlay
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Xiaoyu Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Zhiyu Zhao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iñigo Angulo-Barturen
- The Art of Discovery, Biscay Science and Technology Park, Astrondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- The Art of Discovery, Biscay Science and Technology Park, Astrondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland; University of Basel Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | | | - David A Fidock
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
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4
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Larsson P, De Rosa MC, Righino B, Olsson M, Florea BI, Forssell-Aronsson E, Kovács A, Karlsson P, Helou K, Parris TZ. Integrated transcriptomics- and structure-based drug repositioning identifies drugs with proteasome inhibitor properties. Sci Rep 2024; 14:18772. [PMID: 39138277 PMCID: PMC11322189 DOI: 10.1038/s41598-024-69465-6] [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: 12/23/2022] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Computational pharmacogenomics can potentially identify new indications for already approved drugs and pinpoint compounds with similar mechanism-of-action. Here, we used an integrated drug repositioning approach based on transcriptomics data and structure-based virtual screening to identify compounds with gene signatures similar to three known proteasome inhibitors (PIs; bortezomib, MG-132, and MLN-2238). In vitro validation of candidate compounds was then performed to assess proteasomal proteolytic activity, accumulation of ubiquitinated proteins, cell viability, and drug-induced expression in A375 melanoma and MCF7 breast cancer cells. Using this approach, we identified six compounds with PI properties ((-)-kinetin-riboside, manumycin-A, puromycin dihydrochloride, resistomycin, tegaserod maleate, and thapsigargin). Although the docking scores pinpointed their ability to bind to the β5 subunit, our in vitro study revealed that these compounds inhibited the β1, β2, and β5 catalytic sites to some extent. As shown with bortezomib, only manumycin-A, puromycin dihydrochloride, and tegaserod maleate resulted in excessive accumulation of ubiquitinated proteins and elevated HMOX1 expression. Taken together, our integrated drug repositioning approach and subsequent in vitro validation studies identified six compounds demonstrating properties similar to proteasome inhibitors.
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Affiliation(s)
- Peter Larsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Maria Cristina De Rosa
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC)-CNR, Rome, Italy
| | - Benedetta Righino
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC)-CNR, Rome, Italy
| | - Maxim Olsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bogdan Iulius Florea
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Center, Leiden, The Netherlands
| | - Eva Forssell-Aronsson
- Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Medical Radiation Sciences, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Medical Physics and Biomedical Engineering, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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5
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Pan YF, Zhong L, Wang M, Jiang TY, Lin YK, Chen YB, Li X, Hu HP, Zhou HB, Yan HZ, Dong LW. PTEN status determines therapeutic vulnerability to celastrol in cholangiocarcinoma. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 131:155790. [PMID: 38851099 DOI: 10.1016/j.phymed.2024.155790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/15/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND A balanced protein homeostasis network helps cholangiocarcinoma (CCA) maintain their oncogenic growth, and disrupting proteostasis therapeutically will induce proteotoxic stress. Phosphatase and tensin homolog (PTEN) have been reported to be involved in proteostasis, and PTEN-associated pathways are commonly altered in CCA. Celastrol, a triterpene from plants, exhibits cytotoxic effects in various types of cancer. However, the underlying mechanisms remain unclear. PURPOSE We investigated the therapeutic effect of celastrol in CCA and identified the molecular characteristics of tumors that were sensitive to celastrol. The target of celastrol was explored. We then evaluated the candidate combination therapeutic strategy to increase the effectiveness of celastrol in celastrol-insensitive CCA tumors. METHODS Various CCA cells were categorized as either celastrol-sensitive or celastrol-insensitive based on their response to celastrol. The molecular characteristics of cells from different groups were determined by RNA-seq. PTEN status and its role in proteasome activity in CCA cells were investigated. The CMAP analysis, molecular docking, and functional assay were performed to explore the effect of celastrol on proteasome activities. The correlation between PTEN status and clinical outcomes, as well as proteasomal activity, were measured in CCA patients. The synergistic therapeutic effect of autophagy inhibitors on celastrol-insensitive CCA cells were measured. RESULTS Diverse responses to celastrol were observed in CCA cells. PTEN expression varied among different CCA cells, and its status could impact cell sensitivity to celastrol: PTENhigh tumor cells were resistant to celastrol, while PTENlow cells were more sensitive. Celastrol induced proteasomal dysregulation in CCA cells by directly targeting PSMB5. Cells with low PTEN status transcriptionally promoted proteasome subunit expression in an AKT-dependent manner, making these cells more reliant on proteasomal activities to maintain proteostasis. This caused the PTENlow CCA cells sensitive to celastrol. A negative correlation was found between PTEN levels and the proteasome signature in CCA patients. Moreover, celastrol treatment could induce autophagy in PTENhigh CCA cells. Disrupting the autophagic pathway in PTENhigh CCA cells enhanced the cytotoxic effect of celastrol. CONCLUSION PTEN status in CCA cells determines their sensitivity to celastrol, and autophagy inhibitors could enhance the anti-tumor effect in PTENhigh CCA.
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Affiliation(s)
- Yu-Fei Pan
- National Center for Liver Cancer, Naval Medical University, 366 Qianju Road, Shanghai, 201805, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education. 225 Changhai Road, Shanghai 200438, China
| | - Lin Zhong
- Department of Pathology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine (TCM), 358 Datong Road, Shanghai, 200137, China
| | - Min Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 700 Moyu Road, Shanghai, 201805, China
| | - Tian-Yi Jiang
- National Center for Liver Cancer, Naval Medical University, 366 Qianju Road, Shanghai, 201805, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education. 225 Changhai Road, Shanghai 200438, China
| | - Yun-Kai Lin
- National Center for Liver Cancer, Naval Medical University, 366 Qianju Road, Shanghai, 201805, China
| | - Yi-Bin Chen
- National Center for Liver Cancer, Naval Medical University, 366 Qianju Road, Shanghai, 201805, China
| | - Xin Li
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education. 225 Changhai Road, Shanghai 200438, China
| | - He-Ping Hu
- Department of Hepatobiliary Medicine, Eastern Hepatobiliary Surgery Hospital, 700 Moyu Road, Shanghai, 201805, China
| | - Hua-Bang Zhou
- Department of Hepatobiliary Medicine, Eastern Hepatobiliary Surgery Hospital, 700 Moyu Road, Shanghai, 201805, China.
| | - Hong-Zhu Yan
- Department of Pathology, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine (TCM), 358 Datong Road, Shanghai, 200137, China.
| | - Li-Wei Dong
- National Center for Liver Cancer, Naval Medical University, 366 Qianju Road, Shanghai, 201805, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education. 225 Changhai Road, Shanghai 200438, China.
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6
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Withers-Martinez C, Lidumniece E, Hackett F, Collins CR, Taha Z, Blackman MJ, Jirgensons A. Peptidic Boronic Acid Plasmodium falciparum SUB1 Inhibitors with Improved Selectivity over Human Proteasome. J Med Chem 2024. [PMID: 39051854 DOI: 10.1021/acs.jmedchem.4c01005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Plasmodium falciparum subtilisin-like serine protease 1 (PfSUB1) is essential for egress of invasive merozoite forms of the parasite, rendering PfSUB1 an attractive antimalarial target. Here, we report studies aimed to improve drug-like properties of peptidic boronic acid PfSUB1 inhibitors including increased lipophilicity and selectivity over human proteasome (H20S). Structure-activity relationship investigations revealed that lipophilic P3 amino acid side chains as well as N-capping groups were well tolerated in retaining PfSUB1 inhibitory potency. At the P1 position, replacing the methyl group with a carboxyethyl substituent led to boralactone PfSUB1 inhibitors with remarkably improved selectivity over H20S. Combining lipophilic end-capping groups with the boralactone reduced the selectivity over H20S. However, compound 4c still showed >60-fold selectivity versus H20S and low nanomolar PfSUB1 inhibitory potency. Importantly, this compound inhibited the growth of a genetically modified P. falciparum line expressing reduced levels of PfSUB1 13-fold more efficiently compared to a wild-type parasite line.
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Affiliation(s)
| | | | - Fiona Hackett
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Christine R Collins
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Zahie Taha
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, U.K
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7
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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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8
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Jagtap YA, Kumar P, Dubey AR, Kinger S, Choudhary A, Karmakar S, Lal G, Kumar A, Kumar A, Prasad A, Mishra A. Acetaminophen induces mitochondrial apoptosis through proteasome dysfunctions. Life Sci 2024; 349:122732. [PMID: 38768775 DOI: 10.1016/j.lfs.2024.122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/12/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Acetaminophen is a known antipyretic and non-opioid analgesic for mild pain and fever. Numerous studies uncover their hidden chemotherapeutics applications, including chronic cancer pain management. Acetaminophen also represents an anti-proliferative effect in some cancer cells. Few studies also suggest that the use of Acetaminophen can trigger apoptosis and impede cellular growth. However, Acetaminophen's molecular potential and precise mechanism against improper cellular proliferation and use as an effective anti-proliferative agent still need to be better understood. Here, our current findings show that Acetaminophen induces proteasomal dysfunctions, resulting in aberrant protein accumulation and mitochondrial abnormalities, and consequently induces cell apoptosis. We observed that the Acetaminophen treatment leads to improper aggregation of ubiquitylated expanded polyglutamine proteins, which may be due to the dysfunctions of proteasome activities. Our in-silico analysis suggests the interaction of Acetaminophen and proteasome. Furthermore, we demonstrated the accumulation of proteasome substrates and the depletion of proteasome activities after treating Acetaminophen in cells. Acetaminophen induces proteasome dysfunctions and mitochondrial abnormalities, leading to pro-apoptotic morphological changes and apoptosis successively. These results suggest that Acetaminophen can induce cell death and may retain a promising anti-proliferative effect. These observations can open new possible molecular strategies in the near future for developing and designing specific and effective proteasome inhibitors, which can be helpful in conjugation with other anti-tumor drugs for their better efficiency.
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Affiliation(s)
- Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Surojit Karmakar
- National Centre for Cell Science (NCCS), Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Girdhari Lal
- National Centre for Cell Science (NCCS), Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, 492010, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India.
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9
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Kumar P, Kinger S, Dubey AR, Jagtap YA, Choudhary A, Prasad A, Jha HC, Dhiman R, Gutti RK, Mishra A. Trehalose Promotes Clearance of Proteotoxic Aggregation of Neurodegenerative Disease-Associated Aberrant Proteins. Mol Neurobiol 2024; 61:4055-4073. [PMID: 38057642 DOI: 10.1007/s12035-023-03824-8] [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: 05/23/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Accumulation of misfolded proteins compromises overall cellular health and fitness. The failure to remove misfolded proteins is a critical reason for their unwanted aggregation in dense cellular protein pools. The accumulation of various inclusions serves as a clinical feature for neurodegenerative diseases. Previous findings suggest that different cellular compartments can store these abnormal inclusions. Studies of transgenic mice and cellular models of neurodegenerative diseases indicate that depleted chaperone capacity contributes to the aggregation of damaged or aberrant proteins, which consequently disturb proteostasis and cell viability. However, improving these abnormal proteins' selective elimination is yet to be well understood. Still, molecular strategies that can promote the effective degradation of abnormal proteins without compromising cellular viability are unclear. Here, we reported that the trehalose treatment elevates endogenous proteasome levels and enhances the activities of the proteasome. Trehalose-mediated proteasomal activation elevates the removal of both bona fide misfolded and various neurodegenerative disease-associated proteins. Our current study suggests that trehalose may retain a proteasome activation potential, which seems helpful in the solubilization of different mutant misfolded proteins, improving cell viability. These results reveal a possible molecular approach to reduce the overload of intracellular misfolded proteins, and such cytoprotective functions may play a critical role against protein conformational diseases.
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Affiliation(s)
- Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India.
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10
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Götz MG, Godwin K, Price R, Dorn R, Merrill-Steskal G, Klemmer W, Hansen H, Produturi G, Rocha M, Palmer M, Molacek L, Strater Z, Groll M. Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome. ACS Med Chem Lett 2024; 15:533-539. [PMID: 38628795 PMCID: PMC11017298 DOI: 10.1021/acsmedchemlett.4c00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/22/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Peptide macrocycles have recently gained attention as protease inhibitors due to their metabolic stability and specificity. However, the development of peptide macrocycles with improved binding potency has so far been challenging. Here we present macrocyclic peptides derived from the clinically applied proteasome inhibitor carfilzomib with an oxindole group that mimics the natural product TMC-95A. Fluorescence kinetic activity assays reveal a high potency of the oxindole group (IC50 = 0.19 μM) compared with agents lacking this motif. X-ray structures of the ligands with the β5-subunit of the yeast 20S proteasome illustrate that the installed macrocycle forces strong hydrogen bonding of the oxindole group with β5-Gly23NH. Thus, the binding of our designed oxindole epoxyketones is entropically and enthalpically favored in contrast to more flexible proteasome inhibitors such as carfilzomib.
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Affiliation(s)
- Marion G. Götz
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Kacey Godwin
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Rachel Price
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Robert Dorn
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | | | - William Klemmer
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Hunter Hansen
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Gautam Produturi
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Megan Rocha
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Mathias Palmer
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Lea Molacek
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Zack Strater
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Michael Groll
- Technical
University of Munich, TUM School of Natural
Sciences, Department of Bioscience, Center for Protein Assemblies
(CPA), Ernst-Otto-Fischer
Strasse 8, 85748 Garching, Germany
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11
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Grams RJ, Santos WL, Scorei IR, Abad-García A, Rosenblum CA, Bita A, Cerecetto H, Viñas C, Soriano-Ursúa MA. The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology. Chem Rev 2024; 124:2441-2511. [PMID: 38382032 DOI: 10.1021/acs.chemrev.3c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.
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Affiliation(s)
- R Justin Grams
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | | | - Antonio Abad-García
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
| | - Carol Ann Rosenblum
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Andrei Bita
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Hugo Cerecetto
- Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Marvin A Soriano-Ursúa
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
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12
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Zhang L, Du Y, Qu Q, Zheng Q. Structure basis for recognition of plant Rpn10 by phytoplasma SAP05 in ubiquitin-independent protein degradation. iScience 2024; 27:108892. [PMID: 38322988 PMCID: PMC10844826 DOI: 10.1016/j.isci.2024.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/26/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Besides traditional ubiquitin-dependent proteasome degradation, thousands of eukaryotic proteins more than previously appreciated could undergo ubiquitin-independent proteasomal degradation (UbInPD). A pathogen-encoded effector protein SAP05 secreted by phytoplasma, could hijack hostage Rpn10 subunit of proteasome derived from Arabidopsis thaliana and target the degradation of GATA BINDING FACTOR (GATA) or SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors (TFs) without ubiquitin or additional proteasome shuttle factors. To explain how could SAP05 target the degradation bypassing the ubiquitin-dependent pathway, we have determined the crystal structure of the complex between Arabidopsis thaliana Rpn10 and Aster Yellows witches'-broom phytoplasma SAP05 or onion yellow phytoplasma SAP05, which showed a previously unknown recognition interface. Sequence alignment and structural biological evidence showed that this interaction is highly conserved in various SAP05 homologs, suggesting a general mode in plant infection. After docking the complex structure to the plant proteasome, SAP05 was near to the adenosine triphosphatase (ATPase) central pore and enough to submit substrate to degradation process, which suggested a molecular glue-like role to bridge TFs close to the ATPase central pore of proteasomes for the direct degradation.
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Affiliation(s)
- Liying Zhang
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yunxiang Du
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qian Qu
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingyun Zheng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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13
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Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J, Mishto M. Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nat Commun 2024; 15:1147. [PMID: 38326304 PMCID: PMC10850103 DOI: 10.1038/s41467-024-45339-3] [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: 01/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
If and how proteasomes catalyze not only peptide hydrolysis but also peptide splicing is an open question that has divided the scientific community. The debate has so far been based on immunopeptidomics, in vitro digestions of synthetic polypeptides as well as ex vivo and in vivo experiments, which could only indirectly describe proteasome-catalyzed peptide splicing of full-length proteins. Here we develop a workflow-and cognate software - to analyze proteasome-generated non-spliced and spliced peptides produced from entire proteins and apply it to in vitro digestions of 15 proteins, including well-known intrinsically disordered proteins such as human tau and α-Synuclein. The results confirm that 20S proteasomes produce a sizeable variety of cis-spliced peptides, whereas trans-spliced peptides are a minority. Both peptide hydrolysis and splicing produce peptides with well-defined characteristics, which hint toward an intricate regulation of both catalytic activities. At protein level, both non-spliced and spliced peptides are not randomly localized within protein sequences, but rather concentrated in hotspots of peptide products, in part driven by protein sequence motifs and proteasomal preferences. At sequence level, the different peptide sequence preference of peptide hydrolysis and peptide splicing suggests a competition between the two catalytic activities of 20S proteasomes during protein degradation.
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Affiliation(s)
- Wai Tuck Soh
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Hanna P Roetschke
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Bei Fang Teo
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Nyet Cheng Chiam
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Monika Raabe
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ralf Pflanz
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ashwin Chari
- Research Group of Structural Biochemistry and Mechanisms, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Juliane Liepe
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK.
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK.
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14
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Cavalloro V, Marchesi N, Linciano P, Rossi D, Campagnoli LIM, Fossati A, Ahmed KM, Malacrida A, Miloso M, Mazzeo G, Abbate S, Longhi G, Ambrosio FA, Costa G, Alcaro S, Pascale A, Martino E, Collina S. Neurodegeneration: can metabolites from Eremurus persicus help? Front Pharmacol 2024; 15:1309766. [PMID: 38370479 PMCID: PMC10873958 DOI: 10.3389/fphar.2024.1309766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/19/2024] [Indexed: 02/20/2024] Open
Abstract
The number of patients affected by neurodegenerative diseases is increasing worldwide, and no effective treatments have been developed yet. Although precision medicine could represent a powerful tool, it remains a challenge due to the high variability among patients. To identify molecules acting with innovative mechanisms of action, we performed a computational investigation using SAFAN technology, focusing specifically on HuD. This target belongs to the human embryonic lethal abnormal visual-like (ELAV) proteins and plays a key role in neuronal plasticity and differentiation. The results highlighted that the molecule able to bind the selected target was (R)-aloesaponol-III-8-methyl ether [(R)-ASME], a metabolite extracted from Eremurus persicus. Notably, this molecule is a TNF-α inhibitor, a cytokine involved in neuroinflammation. To obtain a suitable amount of (R)-ASME to confirm its activity on HuD, we optimized the extraction procedure. Together with ASME, another related metabolite, germichrysone, was isolated. Both ASME and germichrysone underwent biological investigation, but only ASME confirmed its ability to bind HuD. Given the multifactorial nature of neurodegenerative diseases, we decided to investigate ASME as a proteasome activator, being molecules endowed with this kind of activity potentially able to counteract aggregations of dysregulated proteins. ASME was able to activate the considered target both in enzymatic and cellular assays. Therefore, ASME may be considered a promising hit in the fight against neurodegenerative diseases.
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Affiliation(s)
- Valeria Cavalloro
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | | | | | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | | | - Alice Fossati
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Karzan Mahmood Ahmed
- Department of Chemistry, College of Education, University of Garmian, Kalar, Iraq
| | - Alessio Malacrida
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy
| | - Mariarosaria Miloso
- School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Experimental Neurology Unit, University of Milano-Bicocca, Monza, Italy
| | - Giuseppe Mazzeo
- Department of Molecular and Translational Medicine, Università di Brescia, Brescia, Italy
| | - Sergio Abbate
- Department of Molecular and Translational Medicine, Università di Brescia, Brescia, Italy
| | - Giovanna Longhi
- Department of Molecular and Translational Medicine, Università di Brescia, Brescia, Italy
| | - Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Catanzaro, Italy
| | - Giosuè Costa
- Department of Health Sciences, Campus “S. Venuta”, “Magna Græcia” University of Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, Campus “S. Venuta”, “Magna Græcia” University of Catanzaro, Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Catanzaro, Italy
- Associazione CRISEA–Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, Italy
| | - Alessia Pascale
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Emanuela Martino
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Pavia, Italy
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15
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Kinger S, Jagtap YA, Dubey AR, Kumar P, Choudhary A, Dhiman R, Prajapati VK, Chitkara D, Poluri KM, Mishra A. Lanosterol elevates cytoprotective response through induced-proteasomal degradation of aberrant proteins. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119631. [PMID: 37967794 DOI: 10.1016/j.bbamcr.2023.119631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
Efficient protein synthesis is a basic requirement of our cells to replace the old or defective proteins from the intrinsic crowded biomolecular environment. The interconnection among synthesis, folding, and degradation of proteins represents central paradigm to proteostasis. Failure of protein quality control (PQC) mechanisms results in the disturbance and inadequate functions of proteome. The consequent misfolded protein accumulation can form the basis of neurodegeneration onset and largely represents imperfect aging. Understanding how cells improve the function of deregulated PQC mechanisms to establish and maintain proteostasis against the unwanted sequestration of normal proteins with misfolded proteinaceous inclusions is a major challenge. Here we show that treatment of Lanosterol, a cholesterol synthesis pathway intermediate, induces Proteasome proteolytic activities and, therefore, supports the PQC mechanism for the elimination of intracellular aberrant proteins. The exposure of Lanosterol not only promotes Proteasome catalytic functions but also elevates the removal of both bona fide and neurodegenerative diseases associated toxic proteins. Our current study suggests that increasing Proteasome functions with the help of small molecules such as Lanosterol could serve as a cytoprotective therapeutic approach against abnormal protein accumulation. Cumulatively, based on findings in this study, we can understand the critical importance of small molecules and their potential therapeutic influence in re-establishing disturbed proteostasis linked with neurodegeneration.
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Affiliation(s)
- Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342037, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342037, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342037, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Deepak Chitkara
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani (BITS-Pilani), Vidya Vihar Campus, Pilani 333031, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342037, India.
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16
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Fernandes PMP, Guedes RA, Victor BL, Salvador JAR, Guedes RC. Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome. Front Chem 2024; 11:1322628. [PMID: 38260042 PMCID: PMC10801056 DOI: 10.3389/fchem.2023.1322628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Acquired resistance to drugs that modulate specific protein functions, such as the human proteasome, presents a significant challenge in targeted therapies. This underscores the importance of devising new methodologies to predict drug binding and potential resistance due to specific protein mutations. In this work, we conducted an extensive computational analysis to ascertain the effects of selected mutations (Ala49Thr, Ala50Val, and Cys52Phe) within the active site of the human proteasome. Specifically, we sought to understand how these mutations might disrupt protein function either by altering protein stability or by impeding interactions with a clinical administered drug. Leveraging molecular dynamics simulations and molecular docking calculations, we assessed the effect of these mutations on protein stability and ligand affinity. Notably, our results indicate that the Cys52Phe mutation critically impacts protein-ligand binding, providing valuable insights into potential proteasome inhibitor resistance.
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Affiliation(s)
- Pedro M. P. Fernandes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Romina A. Guedes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Bruno L. Victor
- BioISI─Biosystems & Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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17
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Zhu Y, Shigeyoshi K, Hayakawa Y, Fujiwara S, Kishida M, Ohki H, Horibe T, Shionyu M, Mizukami T, Hasegawa M. Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution. Int J Mol Sci 2023; 24:17486. [PMID: 38139315 PMCID: PMC10743564 DOI: 10.3390/ijms242417486] [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: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Although the 20S core particle (CP) of the proteasome is an important component of the 26S holoenzyme, the stand-alone 20S CP acts directly on intrinsically disordered and oxidized/damaged proteins to degrade them in a ubiquitin-independent manner. It has been postulated that some structural features of substrate proteins are recognized by the 20S CP to promote substrate uptake, but the mechanism of substrate recognition has not been fully elucidated. In this study, we screened peptides that bind to the 20S CP from a random eight-residue pool of amino acid sequences using complementary DNA display an in vitro molecular evolution technique. The identified 20S CP-binding amino acid sequence was chemically synthesized and its effects on the 20S CP were investigated. The 20S CP-binding peptide stimulated the proteolytic activity of the inactive form of 20S CP. The peptide bound directly to one of the α-subunits, opening a gate for substrate entry on the α-ring. Furthermore, the attachment of this peptide sequence to α-synuclein enhanced its degradation by the 20S CP in vitro. In addition to these results, docking simulations indicated that this peptide binds to the top surface of the α-ring. These peptides could function as a key to control the opening of the α-ring gate.
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Affiliation(s)
- Yunhao Zhu
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Kaishin Shigeyoshi
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Yumiko Hayakawa
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Sae Fujiwara
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Masamichi Kishida
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Hitoshi Ohki
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Tomohisa Horibe
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Masafumi Shionyu
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Tamio Mizukami
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
- Frontier Pharma Inc., 1281-8 Tamura, Nagahama 526-0829, Japan
| | - Makoto Hasegawa
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
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18
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Hsu HC, Li D, Zhan W, Ye J, Liu YJ, Leung A, Qin J, Crespo B, Gamo FJ, Zhang H, Cui L, Roth A, Kirkman LA, Li H, Lin G. Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors. Nat Commun 2023; 14:8302. [PMID: 38097652 PMCID: PMC10721928 DOI: 10.1038/s41467-023-44077-2] [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: 05/30/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
The proteasome of the malaria parasite Plasmodium falciparum (Pf20S) is an advantageous drug target because its inhibition kills P. falciparum in multiple stages of its life cycle and synergizes with artemisinins. We recently developed a macrocyclic peptide, TDI-8304, that is highly selective for Pf20S over human proteasomes and is potent in vitro and in vivo against P. falciparum. A mutation in the Pf20S β6 subunit, A117D, confers resistance to TDI-8304, yet enhances both enzyme inhibition and anti-parasite activity of a tripeptide vinyl sulfone β2 inhibitor, WLW-vs. Here we present the high-resolution cryo-EM structures of Pf20S with TDI-8304, of human constitutive proteasome with TDI-8304, and of Pf20Sβ6A117D with WLW-vs that give insights into the species selectivity of TDI-8304, resistance to it, and the collateral sensitivity associated with resistance, including that TDI-8304 binds β2 and β5 in wild type Pf20S as well as WLW-vs binds β2 and β5 in Pf20Sβ6A117D. We further show that TDI-8304 kills P. falciparum as quickly as chloroquine and artemisinin and is active against P. cynomolgi at the liver stage. This increases interest in using these structures to facilitate the development of Pf20S inhibitors that target multiple proteasome subunits and limit the emergence of resistance.
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Affiliation(s)
- Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA
| | - Daqiang Li
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jianxiang Ye
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Yi Jing Liu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Annie Leung
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Junling Qin
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Benigno Crespo
- Global Health Medicines R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Francisco-Javier Gamo
- Global Health Medicines R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Hao Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Alison Roth
- Department of Drug Discovery, Experimental Therapeutics Branch, The Walter Reed Army Institute of Research, 503 Robert Grant Ave., Silver Spring, 20910, MD, USA
| | - Laura A Kirkman
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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19
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Marchese E, Gallo Cantafio ME, Ambrosio FA, Torcasio R, Valentino I, Trapasso F, Viglietto G, Alcaro S, Costa G, Amodio N. New Insights for Polyphenolic Compounds as Naturally Inspired Proteasome Inhibitors. Pharmaceuticals (Basel) 2023; 16:1712. [PMID: 38139838 PMCID: PMC10747119 DOI: 10.3390/ph16121712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Polyphenols, an important class of natural products, are widely distributed in plant-based foods. These compounds are endowed with several biological activities and exert protective effects in various physiopathological contexts, including cancer. We herein investigated novel potential mechanisms of action of polyphenols, focusing on the proteasome, which has emerged as an attractive therapeutic target in cancers such as multiple myeloma. We carried out a structure-based virtual screening study using the DrugBank database as a repository of FDA-approved polyphenolic molecules. Starting from 86 polyphenolic compounds, based on the theoretical binding affinity and the interactions established with key residues of the chymotrypsin binding site, we selected 2 promising candidates, namely Hesperidin and Diosmin. The further assessment of the biologic activity highlighted, for the first time, the capability of these two molecules to inhibit the β5-proteasome activity and to exert anti-tumor activity against proteasome inhibitor-sensitive or resistant multiple myeloma cell lines.
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Affiliation(s)
- Emanuela Marchese
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (E.M.); (S.A.); (G.C.)
| | - Maria Eugenia Gallo Cantafio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
| | - Roberta Torcasio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
| | - Ilenia Valentino
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
| | - Francesco Trapasso
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
| | - Giuseppe Viglietto
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (E.M.); (S.A.); (G.C.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy
- Associazione CRISEA—Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, Loc. Condoleo, 88055 Belcastro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (E.M.); (S.A.); (G.C.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy
| | - Nicola Amodio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (M.E.G.C.); (R.T.); (I.V.); (F.T.); (G.V.)
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20
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Appasamy SD, Berrisford J, Gaborova R, Nair S, Anyango S, Grudinin S, Deshpande M, Armstrong D, Pidruchna I, Ellaway JIJ, Leines GD, Gupta D, Harrus D, Varadi M, Velankar S. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Sci Data 2023; 10:853. [PMID: 38040737 PMCID: PMC10692154 DOI: 10.1038/s41597-023-02778-9] [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: 05/15/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023] Open
Abstract
Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names to over 90% of unique assemblies in the PDB and provided persistent identifiers for each assembly. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of macromolecular complexes. Furthermore, the data standardisation improves the PDB's FAIR attributes, fostering more effective basic and translational research and scientific education.
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Affiliation(s)
- Sri Devan Appasamy
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - John Berrisford
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Romana Gaborova
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sreenath Nair
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sergei Grudinin
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000, Grenoble, France
| | - Mandar Deshpande
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - David Armstrong
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ivanna Pidruchna
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Joseph I J Ellaway
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Grisell Díaz Leines
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Deepti Gupta
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Deborah Harrus
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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21
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Tian Y, Wan N, Zhang H, Shao C, Ding M, Bao Q, Hu H, Sun H, Liu C, Zhou K, Chen S, Wang G, Ye H, Hao H. Chemoproteomic mapping of the glycolytic targetome in cancer cells. Nat Chem Biol 2023; 19:1480-1491. [PMID: 37322158 DOI: 10.1038/s41589-023-01355-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely elusive. Here, we introduce a target-responsive accessibility profiling (TRAP) approach that measures changes in ligand binding-induced accessibility for target identification by globally labeling reactive proteinaceous lysines. With TRAP, we mapped 913 responsive target candidates and 2,487 interactions for 10 major glycolytic metabolites in a model cancer cell line. The wide targetome depicted by TRAP unveils diverse regulatory modalities of glycolytic metabolites, and these modalities involve direct perturbation of enzymes in carbohydrate metabolism, intervention of an orphan transcriptional protein's activity and modulation of targetome-level acetylation. These results further our knowledge of how glycolysis orchestrates signaling pathways in cancer cells to support their survival, and inspire exploitation of the glycolytic targetome for cancer therapy.
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Affiliation(s)
- Yang Tian
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ming Ding
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Haiyang Hu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Huiyong Sun
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chenguang Liu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Kun Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shuai Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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22
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Gazzaroli G, Angeli A, Giacomini A, Ronca R. Proteasome inhibitors as anticancer agents. Expert Opin Ther Pat 2023; 33:775-796. [PMID: 37847492 DOI: 10.1080/13543776.2023.2272648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/16/2023] [Indexed: 10/18/2023]
Abstract
INTRODUCTION The therapeutic targeting of the ubiquitin-proteasome pathway (UPP) through inhibitors of the 20S proteasome core proteolytic activities has revolutionized the treatment of hematological malignancies and is paving the way for its extension to solid tumors. AREAS COVERED This review covers the progress made in the field of proteasome inhibitors, ranging from the first-generation bortezomib to the latest second-generation inhibitors such as carfilzomib and ixazomib as well as the proteasome inhibitors in clinical phase such as oprozomib and marizomib. The development of selective and potent proteasome inhibitors with improved pharmacological properties is described from the synthesis to their basic biological, and clinical validation. EXPERT OPINION Proteasome inhibitors have transformed the treatment landscape for hematological malignancies and hold great promise for cancer therapy. Combination therapies targeting multiple pathways, the development of novel inhibitors or 'hybrid-inhibitors,' and the optimization of treatment protocols are key areas for future exploration. The extension of proteasome inhibitors for the treatment of solid tumors, and their ability to pass the blood-brain barrier open new possibilities for treating central nervous system cancers. However, managing adverse effects, particularly those affecting the central nervous system, remains a critical consideration and a strategic 'working on' aspect for the near future.
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Affiliation(s)
- Giorgia Gazzaroli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Andrea Angeli
- Neurofarba Department, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Arianna Giacomini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Roberto Ronca
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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23
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Clay KJ, Yang Y, Clark C, Petrascheck M. Proteostasis is differentially modulated by inhibition of translation initiation or elongation. eLife 2023; 12:e76465. [PMID: 37795690 PMCID: PMC10581687 DOI: 10.7554/elife.76465] [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: 12/17/2021] [Accepted: 08/29/2023] [Indexed: 10/06/2023] Open
Abstract
Recent work has revealed an increasingly important role for mRNA translation in maintaining proteostasis. Here, we use chemical inhibitors targeting discrete steps of translation to compare how lowering the concentration of all or only translation initiation-dependent proteins rescues Caenorhabditis elegans from proteotoxic stress. We systematically challenge proteostasis and show that pharmacologically inhibiting translation initiation or elongation elicits a distinct protective profile. Inhibiting elongation protects from heat and proteasome dysfunction independently from HSF-1 but does not protect from age-associated protein aggregation. Conversely, inhibition of initiation protects from heat and age-associated protein aggregation and increases lifespan, dependent on hsf-1, but does not protect from proteotoxicity caused by proteasome dysfunction. Surprisingly, we find that the ability of the translation initiation machinery to control the concentration of newly synthesized proteins depends on HSF-1. Inhibition of translation initiation in wild-type animals reduces the concentration of newly synthesized proteins but increases it in hsf-1 mutants. Our findings suggest that the HSF-1 pathway is not only a downstream target of translation but also directly cooperates with the translation initiation machinery to control the concentration of newly synthesized proteins to restore proteostasis.
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Affiliation(s)
- Khalyd J Clay
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Yongzhi Yang
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Christina Clark
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Michael Petrascheck
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
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24
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Du C, Cleary SP, Kostelic MM, Jones BJ, Kafader JO, Wysocki VH. Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes. Anal Chem 2023; 95:13889-13896. [PMID: 37672632 PMCID: PMC10874503 DOI: 10.1021/acs.analchem.3c02185] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc.) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogeneous assemblies that are not readily obtained by traditional MS measurements.
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Affiliation(s)
- Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sean P Cleary
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Marius M Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jared O Kafader
- Departments of Chemistry, Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Corless BC, Geißen R, Prescott NA, David Y, Scheinberg DA, Tan DS. Chemoenzymatic Synthesis of Novel Cytotoxic Epoxyketones Using the Eponemycin Biosynthetic Enzyme EpnF. ACS Chem Biol 2023; 18:1360-1367. [PMID: 37172287 PMCID: PMC10358350 DOI: 10.1021/acschembio.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Eponemycin is an α,β-epoxyketone natural product that inhibits the proteasome via covalent interaction of the epoxyketone warhead with catalytic N-terminal threonine residues. The epoxyketone warhead is biosynthesized from a β-ketoacid substrate by EpnF, a recently identified flavin-dependent acyl-CoA dehydrogenase-like enyzme. Herein, we report biochemical characterization of EpnF kinetics and substrate scope using a series of synthetic β-ketoacid substrates. These studies indicate that epoxide formation likely occurs prior to other tailoring reactions in the biosynthetic pathway, and have led to the identification of novel epoxyketone analogues with potent anticancer activity.
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Affiliation(s)
- Broderick C Corless
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Chemical Biology Program, Sloan Kettering Institute
| | - Raphael Geißen
- Doctoral Program, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
- Master of Biochemistry Program, Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
- Chemical Biology Program, Sloan Kettering Institute
| | - Nicholas A Prescott
- Chemical Biology Program, Sloan Kettering Institute
- Tri-Institutional PhD Program in Chemical Biology
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Chemical Biology Program, Sloan Kettering Institute
- Tri-Institutional PhD Program in Chemical Biology
| | - David A Scheinberg
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Tri-Institutional PhD Program in Chemical Biology
- Molecular Pharmacology Program, Sloan Kettering Institute
- Department of Medicine, Memorial Hospital
| | - Derek S Tan
- Pharmacology Graduate Program, Weill Cornell Graduate College of Medical Sciences
- Chemical Biology Program, Sloan Kettering Institute
- Tri-Institutional PhD Program in Chemical Biology
- Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
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26
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Chari A, Stark H. Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. Annu Rev Biophys 2023; 52:391-411. [PMID: 37159297 DOI: 10.1146/annurev-biophys-111622-091300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.
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Affiliation(s)
- Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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27
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Ng R, Zhang G, Li JJ. An update on the discovery and development of reversible covalent inhibitors. Med Chem Res 2023; 32:1039-1062. [PMID: 37305209 PMCID: PMC10148018 DOI: 10.1007/s00044-023-03065-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/18/2023] [Indexed: 06/13/2023]
Abstract
Small molecule drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety. Graphical Abstract
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Affiliation(s)
- Raymond Ng
- Olema Oncology, 512 2nd St., 4th Floor, San Francisco, 94107 CA USA
| | - Guiping Zhang
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
| | - Jie Jack Li
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
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28
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D’Urso A, Purrello R, Cunsolo A, Milardi D, Fattorusso C, Persico M, Gaczynska M, Osmulski PA, Santoro AM. Electronic Circular Dichroism Detects Conformational Changes Associated with Proteasome Gating Confirmed Using AFM Imaging. Biomolecules 2023; 13:704. [PMID: 37189451 PMCID: PMC10136135 DOI: 10.3390/biom13040704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Many chronic diseases, including cancer and neurodegeneration, are linked to proteasome dysregulation. Proteasome activity, essential for maintaining proteostasis in a cell, is controlled by the gating mechanism and its underlying conformational transitions. Thus, developing effective methods to detect gate-related specific proteasome conformations could be a significant contribution to rational drug design. Since the structural analysis suggests that gate opening is associated with a decrease in the content of α-helices and β-sheets and an increase in random coil structures, we decided to explore the application of electronic circular dichroism (ECD) in the UV region to monitor the proteasome gating. A comparison of ECD spectra of wild type yeast 20S proteasome (predominantly closed) and an open-gate mutant (α3ΔN) revealed an increased intensity in the ECD band at 220 nm, which suggests increased contents of random coil and β-turn structures. This observation was further supported by evaluating ECD spectra of human 20S treated with low concentration of SDS, known as a gate-opening reagent. Next, to evaluate the power of ECD to probe a ligand-induced gate status, we treated the proteasome with H2T4, a tetracationic porphyrin that we showed previously to induce large-scale protein conformational changes upon binding to h20S. H2T4 caused a significant increase in the ECD band at 220 nm, interpreted as an induced opening of the 20S gate. In parallel, we imaged the gate-harboring alpha ring of the 20S with AFM, a technique that we used previously to visualize the predominantly closed gate in latent human or yeast 20S and the open gate in α3ΔN mutant. The results were convergent with the ECD data and showed a marked decrease in the content of closed-gate conformation in the H2T4-treated h20S. Our findings provide compelling support for the use of ECD measurements to conveniently monitor proteasome conformational changes related to gating phenomena. We predict that the observed association of spectroscopic and structural results will help with efficient design and characterization of exogenous proteasome regulators.
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Affiliation(s)
- Alessandro D’Urso
- Dipartimento Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (R.P.); (A.C.)
| | - Roberto Purrello
- Dipartimento Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (R.P.); (A.C.)
| | - Alessandra Cunsolo
- Dipartimento Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (R.P.); (A.C.)
| | - Danilo Milardi
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy;
| | - Caterina Fattorusso
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (C.F.); (M.P.)
| | - Marco Persico
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (C.F.); (M.P.)
| | - Maria Gaczynska
- Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; (M.G.); (P.A.O.)
| | - Pawel A. Osmulski
- Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, TX 78229, USA; (M.G.); (P.A.O.)
| | - Anna Maria Santoro
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 18, 95126 Catania, Italy;
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Müller P, Meta M, Meidner JL, Schwickert M, Meyr J, Schwickert K, Kersten C, Zimmer C, Hammerschmidt SJ, Frey A, Lahu A, de la Hoz-Rodríguez S, Agost-Beltrán L, Rodríguez S, Diemer K, Neumann W, Gonzàlez FV, Engels B, Schirmeister T. Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors-A Comprehensive Reactivity and Selectivity Study. Int J Mol Sci 2023; 24:ijms24087226. [PMID: 37108388 PMCID: PMC10138721 DOI: 10.3390/ijms24087226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
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Affiliation(s)
- Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jan Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Stefan Josef Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Albin Lahu
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | | | - Laura Agost-Beltrán
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Kira Diemer
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Wilhelm Neumann
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Florenci V Gonzàlez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
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30
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Muli CS, Trader DJ. 20S proteasome hydrolysis of LLVY substrates to determine preferences for moieties in its primed substrate channel. Bioorg Med Chem Lett 2023; 85:129233. [PMID: 36905968 PMCID: PMC10165662 DOI: 10.1016/j.bmcl.2023.129233] [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: 01/20/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
The proteasome is an essential multi-catalytic enzyme in cells that is responsible for degrading proteins with a ubiquitin-dependent or -independent mechanism. Many activity-based probes, inhibitors, and stimulators have been developed to study or modulate the activity of the proteasome. The development of these proteasome probes or inhibitors have been based on their interaction with the amino acids of the β5 substrate channel proceeding the catalytically active threonine residue. There is potential for positive interactions with a substrate to increase selectivity or cleavage rate with the β5 substrate channel after the catalytic threonine as evidenced by the proteasome inhibitor belactosin. To study what moieties the proteasome could accept in its primed substrate channel, we developed a liquid chromatography- mass spectrometry (LC-MS) method to quantitate the cleavage of substrates by purified human proteasome. This method allowed us to rapidly evaluate proteasome substrates that contain a moiety that could interact with the S1' site of the β5 proteasome channel. We were able to determine a preference for a polar moiety at the S1' substrate position. We believe this information can be used in the design of future inhibitors or activity-based probes for the proteasome.
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Affiliation(s)
- Christine S Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN 47907, United States
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN 47907, United States.
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31
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Allardyce D, Adu Mantey P, Szalecka M, Nkwo R, Loizidou EZ. Identification of a new class of proteasome inhibitors based on a naphthyl-azotricyclic-urea-phenyl scaffold. RSC Med Chem 2023; 14:573-582. [PMID: 36970145 PMCID: PMC10034219 DOI: 10.1039/d2md00404f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/06/2023] [Indexed: 02/09/2023] Open
Abstract
Proteasomes play an important role in protein degradation and regulation of many cellular pathways by maintaining protein balance. Inhibitors of proteasomes disrupt this balance affecting proteins that are key in malignancies and as such have found applications in the treatment of multiple myeloma and mantle cell lymphoma. However, resistance mechanisms have been reported for these proteasome inhibitors including mutations at the β5 site which necessitates the constant development of new inhibitors. In this work, we report the identification of a new class of proteasome inhibitors, polycyclic molecules bearing a naphthyl-azotricyclic-urea-phenyl scaffold, from screening of the ZINC library of natural products. The most potent of these compounds showed evidence of dose dependency through proteasome assays with IC50 values in the low micromolar range, and kinetic analysis revealed competitive binding at the β5c site with an estimated inhibition constant, K i, of 1.15 μM. Inhibition was also shown for the β5i site of the immunoproteasome at levels similar to those of the constitutive proteasome. Structure-activity relationship studies identified the naphthyl substituent to be crucial for activity and this was attributed to enhanced hydrophobic interactions within β5c. Further to this, halogen substitution within the naphthyl ring enhanced the activity and allowed for π-π interactions with Y169 in β5c and Y130 and F124 in β5i. The combined data highlight the importance of hydrophobic and halogen interactions in β5 binding and assist in the design of next generation inhibitors of proteasomes.
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Affiliation(s)
- Duncan Allardyce
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Priscilla Adu Mantey
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Monika Szalecka
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Robert Nkwo
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Eriketi Z Loizidou
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
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32
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Huang C, Zabala D, de los Santos ELC, Song L, Corre C, Alkhalaf L, Challis G. Parallelized gene cluster editing illuminates mechanisms of epoxyketone proteasome inhibitor biosynthesis. Nucleic Acids Res 2023; 51:1488-1499. [PMID: 36718812 PMCID: PMC9943649 DOI: 10.1093/nar/gkad009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
Advances in DNA sequencing technology and bioinformatics have revealed the enormous potential of microbes to produce structurally complex specialized metabolites with diverse uses in medicine and agriculture. However, these molecules typically require structural modification to optimize them for application, which can be difficult using synthetic chemistry. Bioengineering offers a complementary approach to structural modification but is often hampered by genetic intractability and requires a thorough understanding of biosynthetic gene function. Expression of specialized metabolite biosynthetic gene clusters (BGCs) in heterologous hosts can surmount these problems. However, current approaches to BGC cloning and manipulation are inefficient, lack fidelity, and can be prohibitively expensive. Here, we report a yeast-based platform that exploits transformation-associated recombination (TAR) for high efficiency capture and parallelized manipulation of BGCs. As a proof of concept, we clone, heterologously express and genetically analyze BGCs for the structurally related nonribosomal peptides eponemycin and TMC-86A, clarifying remaining ambiguities in the biosynthesis of these important proteasome inhibitors. Our results show that the eponemycin BGC also directs the production of TMC-86A and reveal contrasting mechanisms for initiating the assembly of these two metabolites. Moreover, our data shed light on the mechanisms for biosynthesis and incorporation of 4,5-dehydro-l-leucine (dhL), an unusual nonproteinogenic amino acid incorporated into both TMC-86A and eponemycin.
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Affiliation(s)
- Chuan Huang
- Correspondence may also be addressed to Chuan Huang. Tel: +61 03 9905 1750;
| | - Daniel Zabala
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Emmanuel L C de los Santos
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Christophe Corre
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Lona M Alkhalaf
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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Brulet JW, Ciancone AM, Yuan K, Hsu K. Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeffrey W. Brulet
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Anthony M. Ciancone
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Kun Yuan
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Ku‐Lung Hsu
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
- Department of Pharmacology University of Virginia School of Medicine Charlottesville Virginia 22908 United States
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia 22908 United States
- University of Virginia Cancer Center University of Virginia Charlottesville VA 22903 USA
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Ambrosio FA, Costa G, Gallo Cantafio ME, Torcasio R, Trapasso F, Alcaro S, Viglietto G, Amodio N. Natural Agents as Novel Potential Source of Proteasome Inhibitors with Anti-Tumor Activity: Focus on Multiple Myeloma. Molecules 2023; 28:molecules28031438. [PMID: 36771100 PMCID: PMC9919276 DOI: 10.3390/molecules28031438] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Multiple myeloma (MM) is an aggressive and incurable disease for most patients, characterized by periods of treatment, remission and relapse. The introduction of new classes of drugs, such as proteasome inhibitors (PIs), has improved survival outcomes in these patient populations. The proteasome is the core of the ubiquitin-proteasome system (UPS), a complex and conserved pathway involved in the control of multiple cellular processes, including cell cycle control, transcription, DNA damage repair, protein quality control and antigen presentation. To date, PIs represent the gold standard for the treatment of MM. Bortezomib was the first PI approved by the FDA, followed by next generation of PIs, namely carfilzomib and ixazomib. Natural agents play an important role in anti-tumor drug discovery, and many of them have recently been reported to inhibit the proteasome, thus representing a new potential source of anti-MM drugs. Based on the pivotal biological role of the proteasome and on PIs' significance in the management of MM, in this review we aim to briefly summarize recent evidence on natural compounds capable of inhibiting the proteasome, thus triggering anti-MM activity.
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Affiliation(s)
- Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: (G.C.); (N.A.)
| | - Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Roberta Torcasio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Department of Biology, Ecology and Earth Sciences (Di.B.E.S.T.), University of Calabria, 87036 Rende, Italy
| | - Francesco Trapasso
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Associazione CRISEA—Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, Loc. Condoleo, 88055 Belcastro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: (G.C.); (N.A.)
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Yadav R, Nath UK, Celik I, Handu S, Jain N, Dhamija P. Identification and in-vitro analysis of potential proteasome inhibitors targeting PSMβ5 for multiple myeloma. Biomed Pharmacother 2023; 157:113963. [PMID: 36399828 DOI: 10.1016/j.biopha.2022.113963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022] Open
Abstract
The proteasome subunit β5 (PSMβ5) is a chief target of proteasome inhibitors (PIs) for treatment of multiple myeloma (MM). The relevance of PSMβ5 mutations and their functional impact on the development of resistance to PIs have been demonstrated recently. Therefore, this present study deals with an in-depth E-pharmacophore based screening and repurposing of FDA-approved drugs that could target PSMβ5 for MM. Our molecular docking-based investigation revealed risedronate and zoledronate as potential alternative therapeutic molecules for targeting the PSMβ5 gene. Risedronate and zoledronate displayed high binding affinity (-9.51 and -8.56 kcal/mol respectively) to PSMβ5. Moreover, 100 ns molecular dynamics simulation analysis of docking complexes revealed risedronate and zoledronate with a superior binding free energies and stable interactions with PSMβ5. The RMSD plot shows that the risedronate-PSMβ5 (mean: 0.24 nm) and zoledronate-PSMβ5 (mean: 0.25 nm) complexes are identical and stays stable until 100 ns. We further validated the activity of zoledronate in MM cell lines RPMI8226 and U266 where zoledronate showed significant anti-proliferative and apoptotic activity. Importantly, zoledronate showed an enhanced anti-proliferative activity when combined with bortezomib in MM cell lines. Thus, this study demonstrates that combining bortezomib with zoledronate could have a significant impact on reducing MM cell growth and can be an alternative strategy for treating MM.
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh 249203, India.
| | - Uttam Kumar Nath
- Department of Medical Oncology/Haematology, All India Institute of Medical Sciences, Rishikesh 249203, India.
| | - Ismail Celik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey.
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh 249203, India.
| | - Neeraj Jain
- Division of Cancer Biology, Central Drug Research Institute, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh 249203, India.
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Wang S, Ren Y, Wang Z, Jiang X, Xu S, Zhang X, Zhao S, Zalloum WA, Liu X, Zhan P. The current progress in the use of boron as a platform for novel antiviral drug design. Expert Opin Drug Discov 2022; 17:1329-1340. [PMID: 36448326 DOI: 10.1080/17460441.2023.2153829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
INTRODUCTION Boron has attracted extensive interest due to several FDA-approved boron-containing drugs and other pharmacological agents in clinical trials. As a semimetal, it has peculiar biochemical characteristics which could be utilized in designing novel drugs against drug-resistant viruses. Emerging and reemerging viral pandemics are major threats to human health. Accordingly, we aim to comprehensively review the current status of antiviral boron-containing compounds. AREAS COVERED This review focuses on the utilization of boron to design molecules against viruses from two perspectives: (i) single boron atom-containing compounds acting on miscellaneous viral targets and (ii) boron clusters. The peculiar properties of antiviral boron-containing compounds and their diverse binding modes with viral targets are described in detail in this review. EXPERT OPINION Compounds bearing boronic acid can interact with viral targets by forming covalent or robust hydrogen bonds. This feature is valuable for combating resistant viruses. Furthermore, boron clusters can form dihydrogen bonds and bear features such as three-dimensional aromaticity, hydrophobicity, and biological stability. All these features demonstrated boron as a probable essential element with immense potential for drug design.
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Affiliation(s)
- Shuo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Yujie Ren
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882 11821, Amman, Jordan
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, PR China
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Khan TK, You Y, Nelson TJ, Kundu S, Pramanik S, Das J. Modulation of proteasome activity by curcumin and didemethylcurcumin. J Biomol Struct Dyn 2022; 40:8332-8339. [PMID: 33876718 PMCID: PMC8827141 DOI: 10.1080/07391102.2021.1911853] [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: 12/13/2020] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
Modulation of proteasome function by pharmacological interventions and molecular biology tools is an active area of research in cancer biology and neurodegenerative diseases. Curcumin (diferuloylmethane) is a naturally occurring polyphenol that affects multiple signaling pathways. Curcumin shows anti-inflammatory, antioxidant, anti-angiogenic, or anti-apoptotic properties. Recent research suggests that the therapeutic efficacy of curcumin may be due to its activity as a potent inhibitor of the proteasome. Using in vitro cell culture and molecular docking methods, here we show that both curcumin and its synthetic polyphenolic derivative (didemethylcurcumin, CUIII) modulated proteasome activity in a biphasic manner. Curcumin and CUIII increased proteasome activity at nanomolar concentrations, but inhibited proteasome activity at micromolar concentrations. Curcumin was more effective than CUIII in increasing relative proteasome activity at nanomolar concentrations. Also, curcumin was more effective than CUIII in inhibiting relative proteasome activity at micromolar concentrations. Docking simulations of curcumin and didemethylcurcumin binding to the 20S proteasome catalytic subunit estimated Kd values of 0.0054 µM and 1.3167 µM, respectively. These values correlate well with the results of the effectiveness of modulation by curcumin compared to CUIII. The small size of CUIII allows it to dock to the narrow cavity of the active site, but the binding interaction is not strong compared to curcumin. These results indicate that curcumin and its didemethyl derivative can be used to modulate proteasome activity and suggest that curcumin and its didemethyl derivative may be useful in treating two different disease classes: neurodegeneration and cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tapan K. Khan
- Center for Neurodegenerative Diseases, Blanchette Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV 26506, USA
- Department of Veterans Affairs, Rocky Mountain Mental Illness, Research, Education and Clinical Care, Denver, Aurora, CO 80045
| | - Youngki You
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204
| | - Thomas J. Nelson
- Center for Neurodegenerative Diseases, Blanchette Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV 26506, USA
- Department of Neurology, Marshall University School of Medicine, Huntington WV 25704
| | - Subrata Kundu
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
| | - Saroj Pramanik
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Joydip Das
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204
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Listro R, Malacrida A, Ambrosio FA, Rossino G, Di Giacomo M, Cavalloro V, Garbagnoli M, Linciano P, Rossi D, Cavaletti G, Costa G, Alcaro S, Miloso M, Collina S. From Nature to Synthetic Compounds: Novel 1(N),2,3 Trisubstituted-5-oxopyrrolidines Targeting Multiple Myeloma Cells. Int J Mol Sci 2022; 23:13061. [PMID: 36361848 PMCID: PMC9658545 DOI: 10.3390/ijms232113061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 01/15/2024] Open
Abstract
The insurgence of drug resistance in treating Multiple Myeloma (MM) still represents a major hamper in finding effective treatments, although over the past decades new classes of drugs, such as proteasome inhibitors and immunomodulatory drugs, have been discovered. Recently, our research team, within a Nature-Aided Drug Discovery project, isolated from Hibiscus Sabdariffa L. calyces the secondary metabolite called Hib-ester which possesses antiproliferative properties against human multiple myeloma RPMI 8226 cells, reduces migration and cell invasion and inhibits proteasome without neurotoxic effects. In the present study, we explored the chemical spaces of the hit compound Hib-ester. We explored the structure-activity relationships (SAR), and we optimized the scaffold through sequentially modifying Hib-ester subunits. Compound screening was performed based on cytotoxicity against the RPMI 8226 cells to assess the potential efficacy toward human MM. The ability of the most effective molecules to inhibit the proteasome was evaluated and the binding mode of the most promising compounds in the proteasome chymotrypsin binding pocket was deciphered through molecular modeling simulations. Compounds 13 and 14 are more potent than Hib-ester, demonstrating that our strategy was suitable for the identification of a novel chemotype for developing possible drug candidates and hopefully widening the drug armamentarium against MM.
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Affiliation(s)
- Roberta Listro
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Alessio Malacrida
- School of Medicine and Surgery, Milan Center for Neuroscience, University of Milan Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Marcello Di Giacomo
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Valeria Cavalloro
- Department of Earth and Environmental Sciences, University of Pavia, Via Sant’Epifanio 14, 27100 Pavia, Italy
| | - Martina Garbagnoli
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Pasquale Linciano
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Guido Cavaletti
- School of Medicine and Surgery, Milan Center for Neuroscience, University of Milan Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Giosuè Costa
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Mariarosaria Miloso
- School of Medicine and Surgery, Milan Center for Neuroscience, University of Milan Bicocca, Via Cadore 48, 20900 Monza, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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Novel Class of Proteasome Inhibitors: In Silico and In Vitro Evaluation of Diverse Chloro(trifluoromethyl)aziridines. Int J Mol Sci 2022; 23:ijms232012363. [PMID: 36293216 PMCID: PMC9603864 DOI: 10.3390/ijms232012363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the major proteolytic system in the cytosol and nucleus of all eukaryotic cells. The role of proteasome inhibitors (PIs) as critical agents for regulating cancer cell death has been established. Aziridine derivatives are well-known alkylating agents employed against cancer. However, to the best of our knowledge, aziridine derivatives showing inhibitory activity towards proteasome have never been described before. Herein we report a new class of selective and nonPIs bearing an aziridine ring as a core structure. In vitro cell-based assays (two leukemia cell lines) also displayed anti-proliferative activity for some compounds. In silico studies indicated non-covalent binding mode and drug-likeness for these derivatives. Taken together, these results are promising for developing more potent PIs.
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Biran A, Myers N, Steinberger S, Adler J, Riutin M, Broennimann K, Reuven N, Shaul Y. The C-Terminus of the PSMA3 Proteasome Subunit Preferentially Traps Intrinsically Disordered Proteins for Degradation. Cells 2022; 11:cells11203231. [PMID: 36291102 PMCID: PMC9600399 DOI: 10.3390/cells11203231] [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: 08/09/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 12/29/2022] Open
Abstract
The degradation of intrinsically disordered proteins (IDPs) by a non-26S proteasome process does not require proteasomal targeting by polyubiquitin. However, whether and how IDPs are recognized by the non-26S proteasome, including the 20S complex, remains unknown. Analyses of protein interactome datasets revealed that the 20S proteasome subunit, PSMA3, preferentially interacts with many IDPs. In vivo and cell-free experiments revealed that the C-terminus of PSMA3, a 69-amino-acids-long fragment, is an IDP trapper. A recombinant trapper is sufficient to interact with many IDPs, and blocks IDP degradation in vitro by the 20S proteasome, possibly by competing with the native trapper. In addition, over a third of the PSMA3 trapper-binding proteins have previously been identified as 20S proteasome substrates and, based on published datasets, many of the trapper-binding proteins are associated with the intracellular proteasomes. The PSMA3-trapped IDPs that are proteasome substrates have the unique features previously recognized as characteristic 20S proteasome substrates in vitro. We propose a model whereby the PSMA3 C-terminal region traps a subset of IDPs to facilitate their proteasomal degradation.
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Deng L, Mo J, Zhang Y, Peng K, Li H, Ouyang S, Feng Z, Fang W, Wei J, Rong D, Zhang X, Wang Y. Boronic Acid: A Novel Pharmacophore Targeting Src Homology 2 (SH2) Domain of STAT3. J Med Chem 2022; 65:13094-13111. [PMID: 36170649 DOI: 10.1021/acs.jmedchem.2c00940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SH2 domains have been recognized as promising targets for various human diseases. However, targeting SH2 domains with phosphopeptides or small-molecule inhibitors derived from bioisosteres of the phosphate group is still challenging. Identifying novel bioisosteres of the phosphate group to achieve favorable in vivo potency is urgently needed. Here, we report the feasibility of targeting the STAT3-SH2 domain with a boronic acid group and the identification of a highly potent inhibitor compound 7 by replacing the carboxylic acid of compound 4 with a boronic acid. Compound 7 shows higher binding affinity, better cellular potency, more favorable PK profiles, and higher in vivo antitumor activity than 4. The stronger anticancer effect of 7 partially stems from its covalent binding mode with the SH2 domain, verified by the washout experiments. The relatively high level of sequence conservation among SH2 domains makes the results presented here of general significance.
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Affiliation(s)
- Lin Deng
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jianshan Mo
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yi Zhang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Keren Peng
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huaxuan Li
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shumin Ouyang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zongbo Feng
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Wei Fang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jianwei Wei
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiaolei Zhang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory (BBDDL), School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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Serrano-Aparicio N, Ferrer S, Świderek K. Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies. Pharmaceuticals (Basel) 2022; 15:ph15050531. [PMID: 35631358 PMCID: PMC9143130 DOI: 10.3390/ph15050531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
20S proteasome is a main player in the protein degradation pathway in the cytosol, thus intervening in multiple pivotal cellular processes. Over the years the proteasome has emerged as a crucial target for the treatment of many diseases such as neurodegenerative diseases, cancer, autoimmune diseases, developmental disorders, cystic fibrosis, diabetes, cardiac diseases, atherosclerosis, and aging. In this work, the mechanism of proteasome covalent inhibition with bisbenzyl-protected homobelactosin C (hBelC) was explored using quantum mechanics/molecular mechanics (QM/MM) methods. Molecular dynamic simulations were used to describe key interactions established between the hBelC and its unique binding mode in the primed site of the β5 subunit. The free energy surfaces were computed to characterize the kinetics and thermodynamics of the inhibition process. This study revealed that although the final inhibition product for hBelC is formed according to the same molecular mechanism as one described for hSalA, the free energy profile of the reaction pathway differs significantly from the one previously reported for γ-lactam-β-lactone containing inhibitors in terms of the height of the activation barrier as well as the stabilization of the final product. Moreover, it was proved that high stabilization of the covalent adduct formed between β5-subunit and hBelC, together with the presence of aminocarbonyl side chain in the structure of the inhibitor which prevents the hydrolysis of the ester bond from taking place, determines its irreversible character.
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43
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Das BC, Nandwana NK, Das S, Nandwana V, Shareef MA, Das Y, Saito M, Weiss LM, Almaguel F, Hosmane NS, Evans T. Boron Chemicals in Drug Discovery and Development: Synthesis and Medicinal Perspective. Molecules 2022; 27:2615. [PMID: 35565972 PMCID: PMC9104566 DOI: 10.3390/molecules27092615] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
A standard goal of medicinal chemists has been to discover efficient and potent drug candidates with specific enzyme-inhibitor abilities. In this regard, boron-based bioactive compounds have provided amphiphilic properties to facilitate interaction with protein targets. Indeed, the spectrum of boron-based entities as drug candidates against many diseases has grown tremendously since the first clinically tested boron-based drug, Velcade. In this review, we collectively represent the current boron-containing drug candidates, boron-containing retinoids, benzoxaboroles, aminoboronic acid, carboranes, and BODIPY, for the treatment of different human diseases.In addition, we also describe the synthesis, key structure-activity relationship, and associated biological activities, such as antimicrobial, antituberculosis, antitumor, antiparasitic, antiprotozoal, anti-inflammatory, antifolate, antidepressant, antiallergic, anesthetic, and anti-Alzheimer's agents, as well as proteasome and lipogenic inhibitors. This compilation could be very useful in the exploration of novel boron-derived compounds against different diseases, with promising efficacy and lesser side effects.
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Affiliation(s)
- Bhaskar C. Das
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA;
| | - Nitesh K. Nandwana
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sasmita Das
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
| | - Varsha Nandwana
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
| | - Mohammed Adil Shareef
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY 11201, USA; (N.K.N.); (S.D.); (V.N.); (M.A.S.)
| | - Yogarupa Das
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA; (Y.D.); (M.S.)
| | - Mariko Saito
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA; (Y.D.); (M.S.)
| | - Louis M. Weiss
- Department of Pathology, Division of Parasitology and Tropical Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Frankis Almaguel
- School of Medicine, Loma Linda University Health, Loma Linda, CA 92350, USA;
| | - Narayan S. Hosmane
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA;
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA;
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Structural basis to repurpose boron-based proteasome inhibitors Bortezomib and Ixazomib as β-lactamase inhibitors. Sci Rep 2022; 12:5510. [PMID: 35365689 PMCID: PMC8976068 DOI: 10.1038/s41598-022-09392-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/21/2022] [Indexed: 12/23/2022] Open
Abstract
β-lactamases are a major cause of rapidly emerging and spreading antibiotic resistance. Currently β-lactamase inhibitors (BLIs) in clinical use act only on Ambler Class A, C and some class D lactamases. The urgent need to identify new BLIs recently lead to FDA approval of boron-based compounds BLIs, e.g. Vaborbactam. The boron-based proteasome inhibitors Bortezomib and Ixazomib are used in cancer therapy as multiple myeloma drugs but they also bind to Ser-/Thr- proteases. In this study we show the crystal structures of the β-lactamase CTX-M-14 with covalently bound Bortezomib and Ixazomib at high resolutions of 1.3 and 1.1 Å, respectively. Ixazomib is well defined in electron density whereas Bortezomib show some disorder which corresponds to weaker inhibition efficiency observed for Ixazomib. Both inhibitors mimic the deacylation transition state of β-lactam hydrolysis, because they replace the deacylating water molecule. We further investigate differences in binding of Bortezomib/Ixazomib to CTX-M-14 and its target proteases as well as known β-lactamase drugs. Our findings can help to use Bortezomib/Ixazomib as lead compounds for development of new BLIs.
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45
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Revisiting Proteasome Inhibitors: Molecular Underpinnings of Their Development, Mechanisms of Resistance and Strategies to Overcome Anti-Cancer Drug Resistance. Molecules 2022; 27:molecules27072201. [PMID: 35408601 PMCID: PMC9000344 DOI: 10.3390/molecules27072201] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Proteasome inhibitors have shown relevant clinical activity in several hematological malignancies, namely in multiple myeloma and mantle cell lymphoma, improving patient outcomes such as survival and quality of life, when compared with other therapies. However, initial response to the therapy is a challenge as most patients show an innate resistance to proteasome inhibitors, and those that respond to the therapy usually develop late relapses suggesting the development of acquired resistance. The mechanisms of resistance to proteasome inhibition are still controversial and scarce in the literature. In this review, we discuss the development of proteasome inhibitors and the mechanisms of innate and acquired resistance to their activity—a major challenge in preclinical and clinical therapeutics. An improved understanding of these mechanisms is crucial to guiding the design of new and more effective drugs to tackle these devastating diseases. In addition, we provide a comprehensive overview of proteasome inhibitors used in combination with other chemotherapeutic agents, as this is a key strategy to combat resistance.
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46
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Grams RJ, Hsu KL. Reactive chemistry for covalent probe and therapeutic development. Trends Pharmacol Sci 2022; 43:249-262. [PMID: 34998611 PMCID: PMC8840975 DOI: 10.1016/j.tips.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 02/06/2023]
Abstract
Bioactive small molecules that form covalent bonds with a target protein are important tools for basic research and can be highly effective drugs. This review highlights reactive groups found in a collection of thiophilic and oxophilic drugs that mediate pharmacological activity through a covalent mechanism of action (MOA). We describe the application of advanced proteomic and bioanalytical methodologies for assessing selectivity of these covalent agents to guide and inspire the search for additional electrophiles suitable for covalent probe and therapeutic development. While the emphasis is on chemistry for modifying catalytic serine, threonine or cysteine residues, we devote a substantial fraction of the review to a collection of exploratory reactive groups of understudied residues on proteins.
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Affiliation(s)
- R. Justin Grams
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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47
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Lü Z, Li X, Li K, Ripani P, Shi X, Xu F, Wang M, Zhang L, Brunner T, Xu P, Niu Y. Nitazoxanide and related thiazolides induce cell death in cancer cells by targeting the 20S proteasome with novel binding modes. Biochem Pharmacol 2022; 197:114913. [PMID: 35032461 DOI: 10.1016/j.bcp.2022.114913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/02/2022]
Abstract
Nitazoxanide and related thiazolides are a novel class of anti-infectious agents against protozoan parasites, bacteria and viruses. In recent years, it is demonstrated thatthiazolides also can induced cell cycle arrest and apoptotic cell death in cancer cells. Due to their fast proliferating nature, cancer cells highly depend on the proteasome system to remove aberrant proteins. Many of these aberrant proteins are regulators of cell cycle progression and apoptosis, such as the cyclins, BCL2 family members and nuclear factor of κB (NF-κB). Here, we demonstrate at both molecular and cellular levels that the 20S proteasome is a direct target of NTZ and other thiazolides. By concurrently inhibiting the multiple catalytic subunits of 20S proteasome, NTZ promotes cell cycle arrest and triggers cell death in colon cancer cells, either directly or a sensitizer to other anti-tumor agents, especially doxorubicin. We further show that the binding mode of NTZ in the β5 subunit of the 20S proteasome is different from that of bortezomib and other existing proteasome inhibitors. These findings provide new insights in the design of novel small molecular proteasome inhibitors as anti-tumor agents suitable for solid tumor treatment in an oral dosing form.
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Affiliation(s)
- Zirui Lü
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Xiaona Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Kebin Li
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Paola Ripani
- Biochemical Pharmacology, Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Xiaomeng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Fengrong Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Mopei Wang
- Department of Tumor Chemotherapy and Radiation Sickness, Peking University Third Hospital, Beijing, 100191, China
| | - Liangren Zhang
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China
| | - Thomas Brunner
- Biochemical Pharmacology, Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Ping Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China.
| | - Yan Niu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University Health Science Center, Xueyuan Road 38, Beijing, 100191, China.
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48
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Abstract
Fatty acid (FA) biosynthesis plays a central role in the metabolism of living cells as building blocks of biological membranes, energy reserves of the cell, and precursors to second messenger molecules. In keeping with its central metabolic role, FA biosynthesis impacts several cellular functions and its misfunction is linked to disease, such as cancer, obesity, and non-alcoholic fatty liver disease. Cellular FA biosynthesis is conducted by fatty acid synthases (FAS). All FAS enzymes catalyze similar biosynthetic reactions, but the functional architectures adopted by these cellular catalysts can differ substantially. This variability in FAS structure amongst various organisms and the essential role played by FA biosynthetic pathways makes this metabolic route a valuable target for the development of antibiotics. Beyond cellular FA biosynthesis, the quest for renewable energy sources has piqued interest in FA biosynthetic pathway engineering to generate biofuels and fatty acid derived chemicals. For these applications, based on FA biosynthetic pathways, to succeed, detailed metabolic, functional and structural insights into FAS are required, along with an intimate knowledge into the regulation of FAS. In this review, we summarize our present knowledge about the functional, structural, and regulatory aspects of FAS.
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Affiliation(s)
- Aybeg N Günenc
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Benjamin Graf
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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49
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Kisselev AF. Site-Specific Proteasome Inhibitors. Biomolecules 2021; 12:54. [PMID: 35053202 PMCID: PMC8773591 DOI: 10.3390/biom12010054] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/14/2022] Open
Abstract
Proteasome is a multi-subunit protein degradation machine, which plays a key role in the maintenance of protein homeostasis and, through degradation of regulatory proteins, in the regulation of numerous cell functions. Proteasome inhibitors are essential tools for biomedical research. Three proteasome inhibitors, bortezomib, carfilzomib, and ixazomib are approved by the FDA for the treatment of multiple myeloma; another inhibitor, marizomib, is undergoing clinical trials. The proteolytic core of the proteasome has three pairs of active sites, β5, β2, and β1. All clinical inhibitors and inhibitors that are widely used as research tools (e.g., epoxomicin, MG-132) inhibit multiple active sites and have been extensively reviewed in the past. In the past decade, highly specific inhibitors of individual active sites and the distinct active sites of the lymphoid tissue-specific immunoproteasome have been developed. Here, we provide a comprehensive review of these site-specific inhibitors of mammalian proteasomes and describe their utilization in the studies of the biology of the active sites and their roles as drug targets for the treatment of different diseases.
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Affiliation(s)
- Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA
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50
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Barbosa CRR, Barton J, Shepherd AJ, Mishto M. Mechanistic diversity in MHC class I antigen recognition. Biochem J 2021; 478:4187-4202. [PMID: 34940832 PMCID: PMC8786304 DOI: 10.1042/bcj20200910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.
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Affiliation(s)
- Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| | - Justin Barton
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Adrian J. Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
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