1
|
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.
Collapse
Affiliation(s)
- Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
2
|
Zhang G, Li S, Wang F, Jones AC, Goldberg AFG, Lin B, Virgil S, Stoltz BM, Deshaies RJ, Chou TF. A covalent p97/VCP ATPase inhibitor can overcome resistance to CB-5083 and NMS-873 in colorectal cancer cells. Eur J Med Chem 2021; 213:113148. [PMID: 33476933 DOI: 10.1016/j.ejmech.2020.113148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
Small-molecule inhibitors of p97 are useful tools to study p97 function. Human p97 is an important AAA ATPase due to its diverse cellular functions and implication in mediating the turnover of proteins involved in tumorigenesis and virus infections. Multiple p97 inhibitors identified from previous high-throughput screening studies are thiol-reactive compounds targeting Cys522 in the D2 ATP-binding domain. Thus, these findings suggest a potential strategy to develop covalent p97 inhibitors. We first used purified p97 to assay several known covalent kinase inhibitors to determine if they can inhibit ATPase activity. We evaluated their selectivity using our dual reporter cells that can distinguish p97 dependent and independent degradation. We selected a β-nitrostyrene scaffold to further study the structure-activity relationship. In addition, we used p97 structures to design and synthesize analogues of pyrazolo[3,4-d]pyrimidine (PP). We incorporated electrophiles into a PP-like compound 17 (4-amino-1-tert-butyl-3-phenyl pyrazolo[3,4-d]pyrimidine) to generate eight compounds. A selective compound 18 (N-(1-(tert-butyl)-3-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)acrylamide, PPA) exhibited excellent selectivity in an in vitro ATPase activity assay: IC50 of 0.6 μM, 300 μM, and 100 μM for wild type p97, yeast Cdc48, and N-ethylmaleimide sensitive factor (NSF), respectively. To further examine the importance of Cys522 on the active site pocket during PPA inhibition, C522A and C522T mutants of p97 were purified and shown to increase IC50 values by 100-fold, whereas replacement of Thr532 of yeast Cdc48 with Cysteine decreased the IC50 by 10-fold. The molecular modeling suggested the hydrogen bonds and hydrophobic interactions in addition to the covalent bonding at Cys522 between WT-p97 and PPA. Furthermore, tandem mass spectrometry confirmed formation of a covalent bond between Cys522 and PPA. An anti-proliferation assay indicated that the proliferation of HCT116, HeLa, and RPMI8226 was inhibited by PPA with IC50 of 2.7 μM, 6.1 μM, and 3.4 μM, respectively. In addition, PPA is able to inhibit proliferation of two HCT116 cell lines that are resistant to CB-5083 and NMS-873, respectively. Proteomic analysis of PPA-treated HCT116 revealed Gene Ontology enrichment of known p97 functional pathways such as the protein ubiquitination and the ER to Golgi transport vesicle membrane. In conclusion, we have identified and characterized PPA as a selective covalent p97 inhibitor, which will allow future exploration to improve the potency of p97 inhibitors with different mechanisms of action.
Collapse
Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Amanda C Jones
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Alexander F G Goldberg
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Benjamin Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Scott Virgil
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Brian M Stoltz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, United States.
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, United States.
| |
Collapse
|
3
|
Hubbell GE, Tepe JJ. Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors. RSC Chem Biol 2020; 1:305-332. [PMID: 33791679 PMCID: PMC8009326 DOI: 10.1039/d0cb00111b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
The 20S proteasome is a valuable target for the treatment of a number of diseases including cancer, neurodegenerative disease, and parasitic infection. In an effort to discover novel inhibitors of the 20S proteasome, many reseaarchers have looked to natural products as potential leads for drug discovery. The following review discusses the efforts made in the field to isolate and identify natural products as inhibitors of the proteasome. In addition, we describe some of the modifications made to natural products in order to discover more potent and selective inhibitors for potential disease treatment.
Collapse
Affiliation(s)
- Grace E. Hubbell
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
| | - Jetze J. Tepe
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
| |
Collapse
|
4
|
Maurits E, Degeling CG, Kisselev AF, Florea BI, Overkleeft HS. Structure-Based Design of Fluorogenic Substrates Selective for Human Proteasome Subunits. Chembiochem 2020; 21:3220-3224. [PMID: 32598532 PMCID: PMC7754458 DOI: 10.1002/cbic.202000375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Proteasomes are established therapeutic targets for hematological cancers and promising targets for autoimmune diseases. In the past, we have designed and synthesized mechanism-based proteasome inhibitors that are selective for the individual catalytic activities of human constitutive proteasomes and immunoproteasomes: β1c, β1i, β2c, β2i, β5c and β5i. We show here that by taking the oligopeptide recognition element and substituting the electrophile for a fluorogenic leaving group, fluorogenic substrates are obtained that report on the proteasome catalytic activity also targeted by the parent inhibitor. Though not generally applicable (β5c and β2i substrates showing low activity), effective fluorogenic substrates reporting on the individual activity of β1c, β1i, β2c and β5i subunits in Raji (human B cell) lysates and purified 20S proteasome were identified in this manner. Our work thus adds to the expanding proteasome research toolbox through the identification of new and/or more effective subunit-selective fluorogenic substrates.
Collapse
Affiliation(s)
- Elmer Maurits
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christian G. Degeling
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Alexei F. Kisselev
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAL 36849USA
| | - Bogdan I. Florea
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| |
Collapse
|
5
|
Abstract
The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune responses, protein homeostasis, inflammation, apoptosis, and the response to proteotoxic stress. Acting as a major molecular machine for protein degradation, proteasome first identifies damaged or obsolete regulatory proteins by attaching ubiquitin chains and subsequently utilizes conserved pore loops of the heterohexameric ring of AAA+ (ATPases associated with diverse cellular activities) to pull and mechanically unfold and translocate the misfolded protein to the active site for proteolysis. A detailed knowledge of the reaction mechanism for this proteasomal proteolysis is of central importance, both for fundamental understanding and for drug discovery. The present study investigates the mechanism of the proteolysis by the proteasome with full consideration of the protein's flexibility and its impact on the reaction free energy. Major attention is paid to the role of the protein electrostatics in determining the activation barriers. The reaction mechanism is studied by considering a small artificial fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation barriers and reaction free energies for the acylation and deacylation steps, by using the empirical valence bond method. Our results shed light on the proteolysis mechanism and thus should be important for further studies of the proteasome action.
Collapse
Affiliation(s)
- Arjun Saha
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Gabriel Oanca
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Dibyendu Mondal
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| |
Collapse
|
6
|
Abstract
Covering: up to April 2020 Proteases are involved in the regulation of many physiological processes. Their overexpression and dysregulated activity are linked to diseases such as hypertension, diabetes, viral infections, blood clotting disorders, respiratory diseases, and cancer. Therefore, they represent an important class of therapeutic targets. Several protease inhibitors have reached the market and >60% of them are directly related to natural products, even when excluding synthetic natural product mimics. Historically, natural products have been a valuable and validated source of therapeutic agents, as over half of the marketed drugs across targets and diseases are inspired by natural product structures. In the past two decades the number of new protease inhibitors discovered from nature has sharply increased. Additionally, the availability of 3D structural information for proteases has permitted structure-based design and accelerated the synthesis of optimized lead structures with improved potency and selectivity profiles, resulting in some of the most-potent-in-class inhibitors. These discoveries were oftentimes maximized by in-depth biological assessments of lead inhibitors, linking them to a relevant disease state. This review will discuss some of the current and emerging drug targets and their involvement in various disease processes, highlighting selected success stories behind several FDA-approved protease inhibitors that have natural products scaffolds as well as recent selected pharmacologically well-characterized inhibitors derived from marine or terrestrial sources.
Collapse
Affiliation(s)
- Fatma H Al-Awadhi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait.
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, USA.
| |
Collapse
|
7
|
Zhang X, Linder S, Bazzaro M. Drug Development Targeting the Ubiquitin-Proteasome System (UPS) for the Treatment of Human Cancers. Cancers (Basel) 2020; 12:cancers12040902. [PMID: 32272746 PMCID: PMC7226376 DOI: 10.3390/cancers12040902] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer cells are characterized by a higher rate of protein turnover and greater demand for protein homeostasis compared to normal cells. In this scenario, the ubiquitin-proteasome system (UPS), which is responsible for the degradation of over 80% of cellular proteins within mammalian cells, becomes vital to cancer cells, making the UPS a critical target for the discovery of novel cancer therapeutics. This review systematically categorizes all current reported small molecule inhibitors of the various essential components of the UPS, including ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), ubiquitin ligases (E3s), the 20S proteasome catalytic core particle (20S CP) and the 19S proteasome regulatory particles (19S RP), as well as their mechanism/s of action and limitations. We also discuss the immunoproteasome which is considered as a prospective therapeutic target of the next generation of proteasome inhibitors in cancer therapies.
Collapse
Affiliation(s)
- Xiaonan Zhang
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Oncology-Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;
- Department of Immunology, Genetics, and Pathology, Uppsala University, 751 05 Uppsala, Sweden
| | - Stig Linder
- Department of Oncology-Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden;
- Department of Medical and Health Sciences, Linköping University, SE-58183 Linköping, Sweden
| | - Martina Bazzaro
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence:
| |
Collapse
|
8
|
Mihalas BP, Bromfield EG, Sutherland JM, De Iuliis GN, McLaughlin EA, Aitken RJ, Nixon B. Oxidative damage in naturally aged mouse oocytes is exacerbated by dysregulation of proteasomal activity. J Biol Chem 2018; 293:18944-18964. [PMID: 30305393 DOI: 10.1074/jbc.ra118.005751] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
An increase in oxidative protein damage is a leading contributor to the age-associated decline in oocyte quality. By removing such damaged proteins, the proteasome plays an essential role in maintaining the fidelity of oocyte meiosis. In this study, we established that decreased proteasome activity in naturally aged, germinal vesicle (GV) mouse oocytes positively correlates with increased protein modification by the lipid aldehyde 4-hydroxynonenal (4-HNE). Furthermore, attenuation of proteasome activity in GV oocytes of young animals was accompanied by an increase in 4-HNE-modified proteins, including α-tubulin, thereby contributing to a reduction in tubulin polymerization, microtubule stability, and integrity of oocyte meiosis. A decrease in proteasome activity was also recapitulated in the GV oocytes of young animals following exposure to oxidative insults in the form of either hydrogen peroxide (H2O2) or 4-HNE. We also observed that upon oxidative insult, 4-HNE exhibits elevated adduction to multiple proteasomal subunits. Notably, the inclusion of the antioxidant penicillamine, to limit propagation of oxidative stress cascades, led to a complete recovery of proteasome activity and enhanced clearance of 4-HNE-adducted α-tubulin during a 6-h post-treatment recovery period. This strategy also proved effective in reducing the incidence of oxidative stress-induced aneuploidy following in vitro oocyte maturation, but was ineffective for naturally aged oocytes. Taken together, our results implicate proteasome dysfunction as an important factor in the accumulation of oxidatively induced protein damage in the female germline. This discovery holds promise for the design of therapeutic interventions to address the age-dependent decline in oocyte quality.
Collapse
Affiliation(s)
- Bettina P Mihalas
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and
| | - Elizabeth G Bromfield
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and
| | - Jessie M Sutherland
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and
| | - Geoffry N De Iuliis
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and
| | - Eileen A McLaughlin
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and.,the School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - R John Aitken
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and
| | - Brett Nixon
- From the Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia and
| |
Collapse
|
9
|
Park JE, Miller Z, Jun Y, Lee W, Kim KB. Next-generation proteasome inhibitors for cancer therapy. Transl Res 2018; 198:1-16. [PMID: 29654740 PMCID: PMC6151281 DOI: 10.1016/j.trsl.2018.03.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 02/06/2023]
Abstract
Over 2 decades ago, the proteasome was considered a risky or even untenable therapeutic target. Today, proteasome inhibitors are a mainstay in the treatment of multiple myeloma (MM) and have sales in excess of 3 billion US dollars annually. More importantly, the availability of proteasome inhibitors has greatly improved the survival and quality of life for patients with MM. Despite the remarkable success of proteasome inhibitor therapies to date, the potential for improvement remains, and the development and optimal use of proteasome inhibitors as anticancer agents continues to be an active area of research. In this review, we briefly discuss the features and limitations of the 3 proteasome inhibitor drugs currently used in the clinic and provide an update on current efforts to develop next-generation proteasome inhibitors with the potential to overcome the limitations of existing proteasome inhibitor drugs.
Collapse
Affiliation(s)
- Ji Eun Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Zachary Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky
| | - Yearin Jun
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Wooin Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Kyung Bo Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky.
| |
Collapse
|
10
|
Abstract
The ubiquitin-proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein-protein interactions (PPI) are involved in each step of the pathway. For many of the steps small-molecule inhibitors have been identified and often they directly or indirectly target PPI. The inhibitors may destabilize intracellular proteostasis and trigger apoptosis. So far this is the most explored option used as an anticancer strategy. Alternatively, substrate-specific polyubiquitination may be regulated for a precise intervention aimed at a particular metabolic pathway. This very attractive opportunity is moving close to clinical application. The best known drug target in UPP is the proteasome: the end point of the journey of a protein destined for degradation. The proteasome alone is a perfect object to study the mechanisms and roles of PPI on many levels. This giant protease is built from multisubunit modules and additionally utilizes a service from transient protein ligands, for example, delivering substrates. An elaborate set of PPI within the highest-order proteasome assembly is involved in substrate recognition and processing. Below we will outline PPI involved in the UPP and discuss the growing prospects for their utilization in pharmacological interventions.
Collapse
Affiliation(s)
- Maria Gaczynska
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.
| | - Pawel A Osmulski
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| |
Collapse
|
11
|
Rut W, Drag M. Human 20S proteasome activity towards fluorogenic peptides of various chain lengths. Biol Chem 2017; 397:921-6. [PMID: 27176742 DOI: 10.1515/hsz-2016-0176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 11/15/2022]
Abstract
The proteasome is a multicatalytic protease responsible for the degradation of misfolded proteins. We have synthesized fluorogenic substrates in which the peptide chain was systematically elongated from two to six amino acids and evaluated the effect of peptide length on all three catalytic activities of human 20S proteasome. In the cases of five- and six-membered peptides, we have also synthesized libraries of fluorogenic substrates. Kinetic analysis revealed that six-amino-acid substrates are significantly better for chymotrypsin-like and caspase-like activity than shorter peptidic substrates. In the case of trypsin-like activity, a five-amino-acid substrate was optimal.
Collapse
|
12
|
Paiva SL, da Silva SR, de Araujo ED, Gunning PT. Regulating the Master Regulator: Controlling Ubiquitination by Thinking Outside the Active Site. J Med Chem 2017; 61:405-421. [DOI: 10.1021/acs.jmedchem.6b01346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Stacey-Lynn Paiva
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Sara R. da Silva
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Elvin D. de Araujo
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Patrick T. Gunning
- Department
of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| |
Collapse
|
13
|
|
14
|
Abstract
Natural products have made significant contribution to cancer chemotherapy over the past decades and remain an indispensable source of molecular and mechanistic diversity for anticancer drug discovery. More often than not, natural products may serve as leads for further drug development rather than as effective anticancer drugs by themselves. Generally, optimization of natural leads into anticancer drugs or drug candidates should not only address drug efficacy, but also improve absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles and chemical accessibility associated with the natural leads. Optimization strategies involve direct chemical manipulation of functional groups, structure-activity relationship directed optimization and pharmacophore-oriented molecular design based on the natural templates. Both fundamental medicinal chemistry principles (e.g., bioisosterism) and state-of-the-art computer-aided drug design techniques (e.g., structure-based design) can be applied to facilitate optimization efforts. In this review, the strategies to optimize natural leads to anticancer drugs or drug candidates are illustrated with examples and described according to their purposes. Furthermore, successful case studies on lead optimization of bioactive compounds performed in the Natural Products Research Laboratories at UNC are highlighted.
Collapse
Affiliation(s)
- Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Susan L. Morris-Natschke
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
- Chinese Medicine Research and Development Center, China Medical University and Hospital, Taichung, Taiwan
| |
Collapse
|
15
|
Momose I, Kawada M. The therapeutic potential of microbial proteasome inhibitors. Int Immunopharmacol 2015; 37:23-30. [PMID: 26589840 DOI: 10.1016/j.intimp.2015.11.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/05/2015] [Accepted: 11/08/2015] [Indexed: 11/16/2022]
Abstract
The proteasome influences cellular homeostasis through the degradation of regulatory proteins, many of which are also involved in disease pathogenesis. In particular, numerous regulatory proteins associated with tumor growth, such as cyclins, cyclin-dependent kinase inhibitors, tumor suppressors, and NF-κB inhibitors are degraded by the proteasome. Proteasome inhibitors can stabilize these regulatory proteins, resulting in the suppression of tumor development and the regulation of immune responses. Thus, proteasome inhibitors are promising candidate antitumor agents and immune-regulatory agents. Bortezomib is the first-in-class proteasome inhibitor approved for the treatment of multiple myeloma. Despite its high efficiency, however, a large proportion of patients do not attain sufficient clinical response due to toxicity and drug resistance. Therefore, the development of new proteasome inhibitors with improved pharmacological properties is needed. Natural products produced by microorganisms are a promising source of such compounds. This review provides an overview of proteasome inhibitors produced by microorganisms, with special focus on inhibitors isolated from actinomycetes.
Collapse
Affiliation(s)
- Isao Momose
- Institute of Microbial Chemistry (BIKAKEN), Numazu, 18-24 Miyamoto, Numazu-shi, Shizuoka 410-0301, Japan.
| | - Manabu Kawada
- Institute of Microbial Chemistry (BIKAKEN), Numazu, 18-24 Miyamoto, Numazu-shi, Shizuoka 410-0301, Japan; Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| |
Collapse
|
16
|
Abstract
Environmental microbes produce biologically active small molecules that have been mined extensively as antibiotics and a smaller number of drugs that act on eukaryotic cells. It is known that there are additional bioactives to be discovered from this source. While the discovery of new antibiotics is challenged by the frequent discovery of known compounds, we contend that the eukaryote-active compounds may be less saturated. Indeed, despite there being far fewer eukaryotic-active natural products these molecules interact with a far richer diversity of molecular and cellular targets.
Collapse
Affiliation(s)
- Louis K Ho
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
17
|
Totaro KA, Barthelme D, Simpson PT, Sauer RT, Sello JK. Substrate-guided optimization of the syringolins yields potent proteasome inhibitors with activity against leukemia cell lines. Bioorg Med Chem 2015; 23:6218-22. [PMID: 26296913 PMCID: PMC4562813 DOI: 10.1016/j.bmc.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/09/2015] [Accepted: 07/19/2015] [Indexed: 12/14/2022]
Abstract
Natural products that inhibit the proteasome have been fruitful starting points for the development of drug candidates. Those of the syringolin family have been underexploited in this context. Using the published model for substrate mimicry by the syringolins and knowledge about the substrate preferences of the proteolytic subunits of the human proteasome, we have designed, synthesized, and evaluated syringolin analogs. As some of our analogs inhibit the activity of the proteasome with second-order rate constants 5-fold greater than that of the methyl ester of syringolin B, we conclude that the substrate mimicry model for the syringolins is valid. The improvements in in vitro potency and the activities of particular analogs against leukemia cell lines are strong bases for further development of the syringolins as anti-cancer drugs.
Collapse
Affiliation(s)
- Kyle A Totaro
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912, United States
| | - Dominik Barthelme
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Peter T Simpson
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912, United States
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Jason K Sello
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912, United States.
| |
Collapse
|
18
|
Paniagua Soriano G, De Bruin G, Overkleeft HS, Florea BI. Toward understanding induction of oxidative stress and apoptosis by proteasome inhibitors. Antioxid Redox Signal 2014; 21:2419-43. [PMID: 24437477 DOI: 10.1089/ars.2013.5794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Proteasome inhibitors (PIs) are used in the clinic for the treatment of hematopoietic malignancies. PI inhibitors induce endoplasmatic reticulum (ER) stress and oxidative stress, disruption of signaling pathways, mitochondrial dysfunction, and, eventually, cell death by apoptosis. PIs designated as clinical candidates include natural product derivatives and compounds developed by rational design and feature a wide diversity of structural elements. The vast amount of literature on this topic underscores PIs significance in driving basic research alongside therapeutic benefit. RECENT ADVANCES Research in recent years has brought an in-depth insight into the molecular mechanisms of PI-induced apoptosis. However, there are some paradoxes and controversies in the literature. In this review, the advances and uncertainties, in particular on the time course events that make cells commit to apoptosis, are discussed. In addition, some mechanisms of evolved PI resistance are presented, and speculations on the difference in sensitivity between cell or tumor types are brought forward. The review concludes by giving an outlook of recent methods that may be employed to describe the system biology of how PIs impact cell survival decisions. CRITICAL ISSUES The biology of ER stress, reactive oxygen species (ROS) production, and apoptosis as induced by PIs is not well understood. Absorbed by the strong focus on PIs, one might overlook the importance of proteasome activity activators or modulators and the study of enzymatic pathways that lie up- or downstream from the proteasome function. FUTURE DIRECTIONS An increased understanding of the systems biology at mRNA and protein levels and the kinetics behind the interaction between PIs and cells is imperative. The design and synthesis of subunit specific inhibitors for each of the seven known proteasome activities and for the enzymes associated to proteasomes will aid in unraveling biology of the ubiquitin-proteasome system in relation to ER stress, ROS production, and apoptosis and will generate leads for therapeutic intervention.
Collapse
Affiliation(s)
- Guillem Paniagua Soriano
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre , Leiden, The Netherlands
| | | | | | | |
Collapse
|
19
|
Chari A, Hajje D. Case series discussion of cardiac and vascular events following carfilzomib treatment: possible mechanism, screening, and monitoring. BMC Cancer 2014; 14:915. [PMID: 25471129 PMCID: PMC4289164 DOI: 10.1186/1471-2407-14-915] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Carfilzomib is a selective proteasome inhibitor approved in the United States in 2012 for the treatment of relapsed and refractory multiple myeloma. Although cardiopulmonary and vascular events have been reported infrequently, they can be potentially serious complications, and their incidence and pathophysiology following carfilzomib treatment remain poorly characterized in a real-world patient population. METHODS We retrospectively reviewed the records of 67 patients with relapsed and/or refractory multiple myeloma treated at our institution. RESULTS We describe 12 patients who experienced cardiac or vascular-related adverse events subsequent to carfilzomib-based treatment (median age, 59 years [range, 49-77]). Nine patients had prior autologous stem cell transplant, and three had prior anthracycline exposure. Detailed case reports are provided for five representative patients: (1) systemic hypertension in a 65-year-old Caucasian female with a history of hypertension, hypothyroidism, and stage III chronic kidney disease; (2) pulmonary hypertension in a 72-year-old Caucasian male with a history of recurrent respiratory infections and chronic right lower extremity deep venous thrombosis; (3) acute renal insufficiency with increased blood pressure in a 50-year-old Caucasian male with a history of hypertension and stage IV chronic kidney disease; (4) heart failure in a 64-year-old African American female with a history of hypertension; and (5) dyspnea and lung disease in a 58-year-old Asian American male with a history significant for hepatitis B virus infection. CONCLUSIONS While cardiac and vascular-related adverse events were reported in patients with relapsed and/or refractory multiple myeloma who were treated with carfilzomib, most patients had a history of the specific cardiac or vascular adverse event they exhibited and demonstrated an improvement or resolution in symptoms after the discontinuation of therapy. Appropriate screening and monitoring could potentially allow at-risk patients to benefit fully from treatment with carfilzomib.
Collapse
Affiliation(s)
- Ajai Chari
- Mt Sinai School of Medicine, 1 Gustave Levy Place, Box 1185, New York, NY, USA.
| | | |
Collapse
|
20
|
Marastoni M, Scotti A, Trapella C, Ferretti V, Sforza F, Gavioli R. Synthesis and activity of isoxazoline vinyl ester pseudopeptides as proteasome inhibitors. J Pept Sci 2014; 20:258-65. [PMID: 24677765 DOI: 10.1002/psc.2612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 11/07/2022]
Abstract
The ubiquitin–proteasome pathway (UPP) influences essential cellular functions including cell growth, differentiation, apoptosis, signal transduction, antigen processing and inflammatory responses. The main proteolytic component of the UPP is the 26S proteasome, which is responsible for the turnover of many cellular proteins and represents an attractive target for the treatment of pathologies such as cancer, as well as inflammatory, immune and neurodegenerative diseases. Natural and synthetic proteasome inhibitors having different chemical structures and potency have been discovered. We report herein the synthesis, proteasome inhibition and modelling studies of novel C-terminal isoxazoline vinyl ester pseudopeptides. Some new compounds that contain a C-terminal extended conjugation inhibit β1 and especially β5 proteasomal catalytic subunits with IC50 values ranging from 10 to 100 µm. These results will permit further optimization based on these structural moieties to develop more active and selective molecules.
Collapse
|
21
|
Kisselev AF, Groettrup M. Subunit specific inhibitors of proteasomes and their potential for immunomodulation. Curr Opin Chem Biol 2014; 23:16-22. [PMID: 25217863 DOI: 10.1016/j.cbpa.2014.08.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 11/20/2022]
Abstract
Specialized variants of the constitutive 20S proteasome in the immune system like the immunoproteasomes and the thymoproteasome contain active site-bearing subunits which differ in their cleavage priorities and substrate binding pockets. The immunoproteasome plays a crucial role in antigen processing and for the differentiation of pro-inflammatory T helper cells which are involved in the pathogenesis of autoimmunity. Selective inhibitors of the immunoproteasome and constitutive proteasome have recently been generated which interfere with the development and progression of autoimmune diseases. Here we describe these inhibitors and their therapeutic potential as predicted from preclinical models.
Collapse
Affiliation(s)
- Alexei F Kisselev
- Department of Pharmacology & Toxicology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH 03756, USA.
| | - Marcus Groettrup
- Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany; Biotechnology Institute Thurgau (BITg) at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland.
| |
Collapse
|
22
|
Li H, van der Linden WA, Verdoes M, Florea BI, McAllister FE, Govindaswamy K, Elias JE, Bhanot P, Overkleeft HS, Bogyo M. Assessing subunit dependency of the Plasmodium proteasome using small molecule inhibitors and active site probes. ACS Chem Biol 2014; 9:1869-76. [PMID: 24918547 PMCID: PMC4136710 DOI: 10.1021/cb5001263] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The ubiquitin-proteasome system (UPS)
is a potential pathway for
therapeutic intervention for pathogens such as Plasmodium, the causative agent of malaria. However, due to the essential nature
of this proteolytic pathway, proteasome inhibitors must avoid inhibition
of the host enzyme complex to prevent toxic side effects. The Plasmodium proteasome is poorly characterized, making rational
design of inhibitors that induce selective parasite killing difficult.
In this study, we developed a chemical probe that labels all catalytic
sites of the Plasmodium proteasome. Using this probe,
we identified several subunit selective small molecule inhibitors
of the parasite enzyme complex. Treatment with an inhibitor that is
specific for the β5 subunit during blood stage schizogony led
to a dramatic decrease in parasite replication while short-term inhibition
of the β2 subunit did not affect viability. Interestingly, coinhibition
of both the β2 and β5 catalytic subunits resulted in enhanced
parasite killing at all stages of the blood stage life cycle and reduced
parasite levels in vivo to barely detectable levels.
Parasite killing was achieved with overall low host toxicity, something
that has not been possible with existing proteasome inhibitors. Our
results highlight differences in the subunit dependency of the parasite
and human proteasome, thus providing a strategy for development of
potent antimalarial drugs with overall low host toxicity.
Collapse
Affiliation(s)
| | | | | | - Bogdan I. Florea
- Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Kavitha Govindaswamy
- Microbiology
and Molecular Genetics, Rutgers—New Jersey Medical School, 225 Warren Street E340B, Newark, New Jersey 07103, United States
| | | | - Purnima Bhanot
- Microbiology
and Molecular Genetics, Rutgers—New Jersey Medical School, 225 Warren Street E340B, Newark, New Jersey 07103, United States
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | |
Collapse
|
23
|
de Bruin G, Huber EM, Xin BT, van Rooden EJ, Al-Ayed K, Kim KB, Kisselev AF, Driessen C, van der Stelt M, van der Marel GA, Groll M, Overkleeft HS. Structure-Based Design of β1i or β5i Specific Inhibitors of Human Immunoproteasomes. J Med Chem 2014; 57:6197-209. [DOI: 10.1021/jm500716s] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Gerjan de Bruin
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Eva M. Huber
- Center
for Integrated Protein Science at the Department Chemie, Lehrstuhl
für Biochemie, Technische Unversität München, 85748 Garching, Germany
| | - Bo-Tao Xin
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Eva J. van Rooden
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Karol Al-Ayed
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kyung-Bo Kim
- Department
of Pharmaceutical Science, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Alexei F. Kisselev
- Department
of Pharmacology and Toxicology and Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, 1 Medical Centre Drive HB7936, Lebanon, New Hampshire 03756, United States
| | - Christoph Driessen
- Department
of Hematology and Oncology, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Mario van der Stelt
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gijsbert A. van der Marel
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Michael Groll
- Center
for Integrated Protein Science at the Department Chemie, Lehrstuhl
für Biochemie, Technische Unversität München, 85748 Garching, Germany
| | - Herman S. Overkleeft
- Gorlaeus
Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
24
|
Kawamura S, Unno Y, Asai A, Arisawa M, Shuto S. Development of a new class of proteasome inhibitors with an epoxyketone warhead: Rational hybridization of non-peptidic belactosin derivatives and peptide epoxyketones. Bioorg Med Chem 2014; 22:3091-5. [PMID: 24814885 DOI: 10.1016/j.bmc.2014.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/15/2014] [Accepted: 04/15/2014] [Indexed: 01/18/2023]
Abstract
Proteasome inhibitors are currently a focus of increased attention as anticancer drug candidates. We recently performed systematic structure-activity relationship studies of the peptidic natural product belactosin A and identified non-peptidic derivative 2 as a highly potent proteasome inhibitor. However, the cell growth inhibitory effect of 2 is only moderate, probably due to the biologically unstable β-lactone warhead. Peptide epoxyketones are an important class of proteasome inhibitors exhibit high potency in cellular systems based on the efficient α,β-epoxyketone warhead. Importantly, belactosin derivatives bind primarily to the primed binding site, while peptide epoxyketones bind only to the non-primed binding site of proteasome, suggesting that hybridization of them might lead to the development of a new class of proteasome inhibitors. Thus, we successfully identified a novel chemotype of proteasome inhibitors 3 and 4 by rational structure-based design, which are expected to bind to both the primed and non-primed binding sites of proteasome.
Collapse
Affiliation(s)
- Shuhei Kawamura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuka Unno
- Graduate School of Pharmaceutical Sciences, University of Shizuoka, Yada, Shizuoka 422-8526, Japan
| | - Akira Asai
- Graduate School of Pharmaceutical Sciences, University of Shizuoka, Yada, Shizuoka 422-8526, Japan
| | - Mitsuhiro Arisawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| |
Collapse
|
25
|
Ding HX, Leverett CA, Kyne RE, Liu KK, Sakya SM, Flick AC, O’donnell CJ. Synthetic approaches to the 2012 new drugs. Bioorg Med Chem 2014; 22:2005-32. [DOI: 10.1016/j.bmc.2014.02.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/11/2014] [Accepted: 02/13/2014] [Indexed: 12/19/2022]
|
26
|
Micale N, Scarbaci K, Troiano V, Ettari R, Grasso S, Zappalà M. Peptide-Based Proteasome Inhibitors in Anticancer Drug Design. Med Res Rev 2014; 34:1001-69. [DOI: 10.1002/med.21312] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicola Micale
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute; Università degli Studi di Messina; Viale Annunziata 98168 Messina Italy
| | - Kety Scarbaci
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute; Università degli Studi di Messina; Viale Annunziata 98168 Messina Italy
| | - Valeria Troiano
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute; Università degli Studi di Messina; Viale Annunziata 98168 Messina Italy
| | - Roberta Ettari
- Dipartimento di Scienze Farmaceutiche; Università degli Studi di Milano; Via Mangiagalli 25 20133 Milano Italy
| | - Silvana Grasso
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute; Università degli Studi di Messina; Viale Annunziata 98168 Messina Italy
| | - Maria Zappalà
- Dipartimento di Scienze del Farmaco e dei Prodotti per la Salute; Università degli Studi di Messina; Viale Annunziata 98168 Messina Italy
| |
Collapse
|
27
|
Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
Collapse
Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| |
Collapse
|
28
|
Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
29
|
Neklesa TK, Noblin DJ, Kuzin A, Lew S, Seetharaman J, Acton TB, Kornhaber G, Xiao R, Montelione GT, Tong L, Crews CM. A bidirectional system for the dynamic small molecule control of intracellular fusion proteins. ACS Chem Biol 2013; 8:2293-2300. [PMID: 23978068 DOI: 10.1021/cb400569k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small molecule control of intracellular protein levels allows temporal and dose-dependent regulation of protein function. Recently, we developed a method to degrade proteins fused to a mutant dehalogenase (HaloTag2) using small molecule hydrophobic tags (HyTs). Here, we introduce a complementary method to stabilize the same HaloTag2 fusion proteins, resulting in a unified system allowing bidirectional control of cellular protein levels in a temporal and dose-dependent manner. From a small molecule screen, we identified N-(3,5-dichloro-2-ethoxybenzyl)-2H-tetrazol-5-amine as a nanomolar HALoTag2 Stabilizer (HALTS1) that reduces the Hsp70:HaloTag2 interaction, thereby preventing HaloTag2 ubiquitination. Finally, we demonstrate the utility of the HyT/HALTS system in probing the physiological role of therapeutic targets by modulating HaloTag2-fused oncogenic H-Ras, which resulted in either the cessation (HyT) or acceleration (HALTS) of cellular transformation. In sum, we present a general platform to study protein function, whereby any protein of interest fused to HaloTag2 can be either degraded 10-fold or stabilized 5-fold using two corresponding compounds.
Collapse
Affiliation(s)
- Taavi K. Neklesa
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
| | - Devin J. Noblin
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
| | - Alexander Kuzin
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Scott Lew
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Jayaraman Seetharaman
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Thomas B. Acton
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gregory Kornhaber
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Rong Xiao
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gaetano T. Montelione
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Biochemistry and Molecular Biology, Robert Wood Johnson
Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Liang Tong
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, 333 Cedar Street, New Haven, Connecticut 06511, United States
| |
Collapse
|
30
|
Giddings LA, Newman DJ. Microbial natural products: molecular blueprints for antitumor drugs. J Ind Microbiol Biotechnol 2013; 40:1181-210. [PMID: 23999966 DOI: 10.1007/s10295-013-1331-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Microbes from two of the three domains of life, the Prokarya, and Eukarya, continue to serve as rich sources of structurally complex chemical scaffolds that have proven to be essential for the development of anticancer therapeutics. This review describes only a handful of exemplary natural products and their derivatives as well as those that have served as elegant blueprints for the development of novel synthetic structures that are either currently in use or in clinical or preclinical trials together with some of their earlier analogs in some cases whose failure to proceed aided in the derivation of later compounds. In every case, a microbe has been either identified as the producer of secondary metabolites or speculated to be involved in the production via symbiotic associations. Finally, rapidly evolving next-generation sequencing technologies have led to the increasing availability of microbial genomes. Relevant examples of genome mining and genetic manipulation are discussed, demonstrating that we have only barely scratched the surface with regards to harnessing the potential of microbes as sources of new pharmaceutical leads/agents or biological probes.
Collapse
|
31
|
Abstract
The initial enthusiasm following the discovery of a pharmacologically active natural product is often fleeting due to the poor prospects for its ultimate clinical application. Despite this, the ever-changing landscape of modern biology has a constant need for molecular probes that can aid in our understanding of biological processes. After its initial discovery by Bristol-Myers Squibb as a microbial anti-tumor natural product, epoxomicin was deemed unfit for development due to its peptide structure and potentially labile epoxyketone pharmacophore. Despite its drawbacks, epoxomicin's pharmacophore was found to provide unprecedented selectivity for the proteasome. Epoxomicin also served as a scaffold for the generation of a synthetic tetrapeptide epoxyketone with improved activity, YU-101, which became the parent lead compound of carfilzomib (Kyprolis™), the recently approved therapeutic agent for multiple myeloma. In this era of rational drug design and high-throughput screening, the prospects for turning an active natural product into an approved therapy are often slim. However, by understanding the journey that began with the discovery of epoxomicin and ended with the successful use of carfilzomib in the clinic, we may find new insights into the keys for success in natural product-based drug discovery.
Collapse
Affiliation(s)
- Kyung Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | | |
Collapse
|
32
|
Abstract
Proteasomal inhibition revolutionized myeloma therapies in this decade of novel agents. The only US Food and Drug Administration approved proteasome inhibitor so far, bortezomib effectively targets the constitutive proteasome subunit β5 of the 26S proteasome. Bortezomib induces high and quality response rates that are durable. However, myeloma cells acquire resistance to bortezomib through various mechanisms. Further, grade 3/4 peripheral neuropathy is seen in up to a quarter of patients treated with bortezomib. While the recent change in the mode of administration via the subcutaneous route is associated with a lower incidence of grade 3/4 peripheral neuropathy, it remains a major concern. The second generation proteasome inhibitors are promising, with increased preclinical efficacy and a better administration schedule. The current review spotlights the second generation proteasome inhibitors with special focus on the safety and efficacy of carfilzomib, an epoxyketone with lesser peripheral neuropathy, which exhibits irreversible proteasome inhibition. In this article, we review the pharmacology and preclinical and clinical efficacy and safety of carfilzomib alone and in combination with other chemotherapeutic agents in the various lymphoid neoplasms and multiple myeloma as well as ongoing clinical trials.
Collapse
Affiliation(s)
- Ajay Nooka
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta GA, USA
| | | | | | | |
Collapse
|
33
|
Lichter DI, Danaee H, Pickard MD, Tayber O, Sintchak M, Shi H, Richardson PG, Cavenagh J, Bladé J, Façon T, Niesvizky R, Alsina M, Dalton W, Sonneveld P, Lonial S, van de Velde H, Ricci D, Esseltine DL, Trepicchio WL, Mulligan G, Anderson KC. Sequence analysis of β-subunit genes of the 20S proteasome in patients with relapsed multiple myeloma treated with bortezomib or dexamethasone. Blood 2012; 120:4513-6. [PMID: 23018640 DOI: 10.1182/blood-2012-05-426924] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Variations within proteasome β (PSMB) genes, which encode the β subunits of the 20S proteasome, may affect proteasome function, assembly, and/or binding of proteasome inhibitors. To investigate the potential association between PSMB gene variants and treatment-emergent resistance to bortezomib and/or long-term outcomes, in the present study, PSMB gene sequence variation was characterized in tumor DNA samples from patients who participated in the phase 3 Assessment of Proteasome Inhibition for Extending Remissions (APEX) study of bortezomib versus high-dose dexamethasone for treatment of relapsed multiple myeloma. Twelve new PSMB variants were identified. No associations were found between PSMB single nucleotide polymorphism genotype frequency and clinical response to bortezomib or dexamethasone treatment or between PSMB single nucleotide polymorphism allelic frequency and pooled overall survival or time to progression. Although specific PSMB5 variants have been identified previously in preclinical models of bortezomib resistance, these variants were not detected in patient tumor samples collected after clinical relapse from bortezomib, which suggests that alternative mechanisms underlie bortezomib insensitivity.
Collapse
|
34
|
Ao L, Wu Y, Kim D, Jang ER, Kim K, Lee DM, Kim KB, Lee W. Development of peptide-based reversing agents for p-glycoprotein-mediated resistance to carfilzomib. Mol Pharm 2012; 9:2197-205. [PMID: 22734651 DOI: 10.1021/mp300044b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Carfilzomib is a novel class of peptidyl epoxyketone proteasome inhibitor and has demonstrated promising activity in multiple clinical trials to treat patients with multiple myeloma and other types of cancers. Here, we investigated molecular mechanisms underlying acquired resistance to carfilzomib and a potential strategy to restore cellular sensitivity to carfilzomib. H23 and DLD-1 cells (human lung and colon adenocarcinoma cell lines) with acquired resistance to carfilzomib displayed marked cross-resistance to YU-101, a closely related proteasome inhibitor, and paclitaxel, a known substrate of Pgp. However, carfilzomib-resistant cells remained sensitive to bortezomib, a clinically used dipeptide with boronic acid pharmacophore. In accordance with these observations, carfilzomib-resistant H23 and DLD-1 cells showed marked upregulation of P-glycoprotein (Pgp) as compared to their parental controls, and coincubation with verapamil, a Pgp inhibitor, led to an almost complete restoration of cellular sensitivity to carfilzomib. These results indicate that Pgp upregulation plays a major role in the development of carfilzomib resistance in these cell lines. In developing a potential strategy to overcome carfilzomib resistance, we as a proof of concept prepared a small library of peptide analogues derived from the peptide backbone of carfilzomib and screened these molecules for their activity to restore carfilzomib sensitivity when cotreated with carfilzomib. We found that compounds as small as dipeptides are sufficient in restoring carfilzomib sensitivity. Taken together, we found that Pgp upregulation plays a major role in the development of resistance to carfilzomib in lung and colon adenocarcinoma cell lines and that small peptide analogues lacking the pharmacophore can be used as agents to reverse acquired carfilzomib resistance. Our findings may provide important information in developing a potential strategy to overcome drug resistance.
Collapse
Affiliation(s)
- Lin Ao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, United States
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Kisselev AF, van der Linden WA, Overkleeft HS. Proteasome inhibitors: an expanding army attacking a unique target. ACTA ACUST UNITED AC 2012; 19:99-115. [PMID: 22284358 DOI: 10.1016/j.chembiol.2012.01.003] [Citation(s) in RCA: 404] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 12/30/2022]
Abstract
Proteasomes are large, multisubunit proteolytic complexes presenting multiple targets for therapeutic intervention. The 26S proteasome consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of active sites. Many structurally diverse inhibitors of these active sites, both natural product and synthetic, have been discovered in the last two decades. One, bortezomib, is used clinically for treatment of multiple myeloma, mantle cell lymphoma, and acute allograft rejection. Five more recently developed proteasome inhibitors are in trials for treatment of myeloma and other cancers. Proteasome inhibitors also have activity in animal models of autoimmune and inflammatory diseases, reperfusion injury, promote bone and hair growth, and can potentially be used as anti-infectives. In addition, inhibitors of ATPases and deubiquitinases of 19S regulatory particles have been discovered in the last decade.
Collapse
Affiliation(s)
- Alexei F Kisselev
- Department of Pharmacology and Toxicology, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH 03756, USA.
| | | | | |
Collapse
|
36
|
Pereira AR, Kale AJ, Fenley AT, Byrum T, Debonsi HM, Gilson MK, Valeriote FA, Moore BS, Gerwick WH. The carmaphycins: new proteasome inhibitors exhibiting an α,β-epoxyketone warhead from a marine cyanobacterium. Chembiochem 2012; 13:810-7. [PMID: 22383253 PMCID: PMC3393770 DOI: 10.1002/cbic.201200007] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Indexed: 01/01/2023]
Abstract
Two new peptidic proteasome inhibitors were isolated as trace components from a Curaçao collection of the marine cyanobacterium Symploca sp. Carmaphycin A (1) and carmaphycin B (2) feature a leucine-derived α,β-epoxyketone warhead directly connected to either methionine sulfoxide or methionine sulfone. Their structures were elucidated on the basis of extensive NMR and MS analyses and confirmed by total synthesis, which in turn provided more material for further biological evaluations. Pure carmaphycins A and B were found to inhibit the β5 subunit (chymotrypsin-like activity) of the S. cerevisiae 20S proteasome in the low nanomolar range. Additionally, they exhibited strong cytotoxicity to lung and colon cancer cell lines, as well as exquisite antiproliferative effects in the NCI60 cell-line panel. These assay results as well as initial structural biology studies suggest a distinctive binding mode for these new inhibitors.
Collapse
Affiliation(s)
- Alban R. Pereira
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA 92093-0212 (USA), Fax: (+1)858-534-0576
| | - Andrew J. Kale
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA 92093-0212 (USA), Fax: (+1)858-534-0576
| | - Andrew T. Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736 (USA)
| | - Tara Byrum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA 92093-0212 (USA), Fax: (+1)858-534-0576
| | - Hosana M. Debonsi
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA 92093-0212 (USA), Fax: (+1)858-534-0576
- Departamento de Física e Química, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040903 (Brazil)
| | - Michael K. Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736 (USA)
| | - Frederick A. Valeriote
- Henry Ford Health System, Department of Internal Medicine, Josephine Ford Cancer Center, 440 Burroughs, Room 415, Detroit, MI 48202 (USA)
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA 92093-0212 (USA), Fax: (+1)858-534-0576
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736 (USA)
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, 9500 Gilman Drive, La Jolla, CA 92093-0212 (USA), Fax: (+1)858-534-0576
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0736 (USA)
| |
Collapse
|
37
|
Buckley DL, Van Molle I, Gareiss PC, Tae HS, Michel J, Noblin DJ, Jorgensen WL, Ciulli A, Crews CM. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction. J Am Chem Soc 2012; 134:4465-8. [PMID: 22369643 PMCID: PMC3448299 DOI: 10.1021/ja209924v] [Citation(s) in RCA: 319] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
E3 ubiquitin ligases, which bind protein targets, leading
to their
ubiquitination and subsequent degradation, are attractive drug targets
due to their exquisite substrate specificity. However, the development
of small-molecule inhibitors has proven extraordinarily challenging
as modulation of E3 ligase activities requires the targeting of protein–protein
interactions. Using rational design, we have generated the first small
molecule targeting the von Hippel–Lindau protein (VHL), the
substrate recognition subunit of an E3 ligase, and an important target
in cancer, chronic anemia, and ischemia. We have also obtained the
crystal structure of VHL bound to our most potent inhibitor, confirming
that the compound mimics the binding mode of the transcription factor
HIF-1α, a substrate of VHL. These results have the potential
to guide future development of improved lead compounds as therapeutics
for the treatment of chronic anemia and ischemia.
Collapse
Affiliation(s)
- Dennis L Buckley
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
van der Linden WA, Willems LI, Shabaneh TB, Li N, Ruben M, Florea BI, van der Marel GA, Kaiser M, Kisselev AF, Overkleeft HS. Discovery of a potent and highly β1 specific proteasome inhibitor from a focused library of urea-containing peptide vinyl sulfones and peptide epoxyketones. Org Biomol Chem 2011; 10:181-94. [PMID: 22105930 DOI: 10.1039/c1ob06554h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Syringolins, a class of natural products, potently and selectively inhibit the proteasome and show promising antitumour activity. To gain insight in the mode of action of syringolins, the ureido structural element present in syringolins is incorporated in oligopeptide vinyl sulfones and peptide epoxyketones yielding a focused library of potent new proteasome inhibitors. The distance of the ureido linkage with respect to the electrophilic trap strongly influences subunit selectivity within the proteasome. Compounds 13 and 15 are β5 selective and their potency exceeds that of syringolin A. In contrast, 5 may well be the most potent β1 selective compound active in living cells reported to date.
Collapse
|
39
|
Abstract
Cancer is the No. 2 cause of death in the Western world and one of the most expensive diseases to treat. Thus, it is not surprising, that every major pharmaceutical and biotechnology company has a blockbuster oncology product. In 2003, Millennium Pharmaceuticals entered the race with Velcade®, a first-in-class proteasome inhibitor that has been approved by the FDA for treatment of multiple myeloma and its sales have passed the billion dollar mark. Velcade®'s extremely toxic boronic acid pharmacophore, however, contributes to a number of severe side effects. Nevertheless, the launching of this product has validated the proteasome as a target in fighting cancer and further proteasome inhibitors have entered the market as anti-cancer drugs. Additionally, proteasome inhibitors have found application as crop protection agents, anti-parasitics, immunosuppressives, as well as in new therapies for muscular dystrophies and inflammation. Many of these compounds are based on microbial metabolites. In this review, we emphasize the important role of the structural elucidation of the various unique binding mechanisms of these compounds that have been optimized throughout evolution to target the proteasome. Based on this knowledge, medicinal chemists have further optimized these natural products, resulting in potential drugs with reduced off-target activities.
Collapse
Affiliation(s)
- Melissa Ann Gräwert
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | | |
Collapse
|
40
|
Neklesa TK, Tae HS, Schneekloth AR, Stulberg MJ, Corson TW, Sundberg TB, Raina K, Holley SA, Crews CM. Small-molecule hydrophobic tagging-induced degradation of HaloTag fusion proteins. Nat Chem Biol 2011; 7:538-43. [PMID: 21725302 PMCID: PMC3139752 DOI: 10.1038/nchembio.597] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 04/13/2011] [Indexed: 01/29/2023]
Abstract
The ability to regulate any protein of interest in living systems with small molecules remains a challenge. We hypothesized that appending a hydrophobic moiety to the surface of a protein would mimic the partially denatured state of the protein, thus engaging the cellular quality control machinery to induce its proteasomal degradation. We designed and synthesized bifunctional small molecules that bind a bacterial dehalogenase (HaloTag protein) and present a hydrophobic group on its surface. Remarkably, hydrophobic tagging of the HaloTag protein with an adamantyl moiety induced the degradation of cytosolic, isoprenylated, and transmembrane fusion proteins in cell culture. We demonstrated the in vivo utility of hydrophobic tagging by degrading proteins expressed in zebrafish embryos and by inhibiting RasG12V-driven tumor progression in mice. Therefore, hydrophobic tagging of HaloTag fusion proteins affords small molecule control over any protein of interest, making it an ideal system for validating potential drug targets in disease models.
Collapse
Affiliation(s)
- Taavi K Neklesa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Milo LJ, Lai JH, Wu W, Liu Y, Maw H, Li Y, Jin Z, Shu Y, Poplawski SE, Wu Y. Chemical and biological evaluation of dipeptidyl boronic acid proteasome inhibitors for use in prodrugs and pro-soft drugs targeting solid tumors. J Med Chem. 2011;54:4365-4377. [PMID: 21634429 DOI: 10.1021/jm200460q] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bortezomib, a dipeptidyl boronic acid and potent inhibitor of the 26S proteasome, is remarkably effective against multiple myeloma (MM) but not against solid tumors. Dose-limiting adverse effects from "on target" inhibition of the proteasome in normal cells and tissues appear to be a key obstacle. Achieving efficacy against solid tumors therefore is likely to require making the inhibitor more selective for tumor tissue over normal tissues. The simplest strategy that might provide such tissue specificity would be to employ a tumor specific protease to release an inhibitor from a larger, noninhibitory structure. However, such release would necessarily generate an inhibitor with a free N-terminal amino group, raising a key question: Can short peptide boronic acids with N-terminal amino groups have the requisite properties to serve as warheads in prodrugs? Here we show that dipeptides of boroLeu, the smallest plausible candidates for the task, can indeed be sufficiently potent, cell-penetrating, cytotoxic, and stable to degradation by cellular peptidases to serve in this capacity.
Collapse
|
42
|
Chou TF, Deshaies RJ. Quantitative cell-based protein degradation assays to identify and classify drugs that target the ubiquitin-proteasome system. J Biol Chem 2011; 286:16546-54. [PMID: 21343295 PMCID: PMC3089497 DOI: 10.1074/jbc.m110.215319] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/14/2011] [Indexed: 01/09/2023] Open
Abstract
We have generated a set of dual-reporter human cell lines and devised a chase protocol to quantify proteasomal degradation of a ubiquitin fusion degradation (UFD) substrate, a ubiquitin ligase CRL2(VHL) substrate, and a ubiquitin-independent substrate. Well characterized inhibitors that target different aspects of the ubiquitin-proteasome system can be distinguished by their distinctive patterns of substrate stabilization, enabling assignment of test compounds as inhibitors of the proteasome, ubiquitin chain formation or perception, CRL activity, or the UFD-p97 pathway. We confirmed that degradation of the UFD but not the CRL2(VHL) or ubiquitin-independent substrates depends on p97 activity. We optimized our suite of assays to establish conditions suitable for high-throughput screening and then validated their performance by screening against 160 cell-permeable protein kinase inhibitors. This screen identified Syk inhibitor III as an irreversible p97/vasolin containing protein inhibitor (IC(50) = 1.7 μM) that acts through Cys-522 within the D2 ATPase domain. Our work establishes a high-throughput screening-compatible pipeline for identification and classification of small molecules, cDNAs, or siRNAs that target components of the ubiquitin-proteasome system.
Collapse
Affiliation(s)
| | - Raymond J. Deshaies
- From the Division of Biology and
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125
| |
Collapse
|
43
|
Buckley DL, Corson TW, Aberle N, Crews CM. HIV protease-mediated activation of sterically capped proteasome inhibitors and substrates. J Am Chem Soc 2011; 133:698-700. [PMID: 21186803 DOI: 10.1021/ja109377p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Strategies for selectively killing HIV-infected cells present an appealing alternative to traditional antiretroviral drugs. We show here the first example of an inactive “Trojan horse” molecule that releases a cytotoxic, small-molecule proteasome inhibitor upon cleavage by HIV-1 protease. As a proof-of-concept strategy, the protein avidin was used to block entry of the compound into the proteasome in the absence of HIV-1 protease. We demonstrate that this strategy is also feasible without requiring an exogenous protein; a polylysine dendrimer-containing molecule is unable to enter the proteasome until cleaved by HIV-1 protease. These results demonstrate that conditional proteasome inhibitors could prove useful in the development of new tools for chemical biology and future therapeutics.
Collapse
Affiliation(s)
- Dennis L Buckley
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | | | | | | |
Collapse
|
44
|
Liu J, Zhang H, Xiao Z, Wang F, Wang X, Wang Y. Combined 3D-QSAR, molecular docking and molecular dynamics study on derivatives of peptide epoxyketone and tyropeptin-boronic acid as inhibitors against the β5 subunit of human 20S proteasome. Int J Mol Sci 2011; 12:1807-35. [PMID: 21673924 PMCID: PMC3111635 DOI: 10.3390/ijms12031807] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 02/14/2011] [Accepted: 02/28/2011] [Indexed: 12/13/2022] Open
Abstract
An abnormal ubiquitin-proteasome is found in many human diseases, especially in cancer, and has received extensive attention as a promising therapeutic target in recent years. In this work, several in silico models have been built with two classes of proteasome inhibitors (PIs) by using 3D-QSAR, homology modeling, molecular docking and molecular dynamics (MD) simulations. The study resulted in two types of satisfactory 3D-QSAR models, i.e., the CoMFA model (Q(2) = 0.462, R(2) (pred) = 0.820) for epoxyketone inhibitors (EPK) and the CoMSIA model (Q(2) = 0.622, R(2) (pred) = 0.821) for tyropeptin-boronic acid derivatives (TBA). From the contour maps, some key structural factors responsible for the activity of these two series of PIs are revealed. For EPK inhibitors, the N-cap part should have higher electropositivity; a large substituent such as a benzene ring is favored at the C6-position. In terms of TBA inhibitors, hydrophobic substituents with a larger size anisole group are preferential at the C8-position; higher electropositive substituents like a naphthalene group at the C3-position can enhance the activity of the drug by providing hydrogen bond interaction with the protein target. Molecular docking disclosed that residues Thr60, Thr80, Gly106 and Ser189 play a pivotal role in maintaining the drug-target interactions, which are consistent with the contour maps. MD simulations further indicated that the binding modes of each conformation derived from docking is stable and in accord with the corresponding structure extracted from MD simulation overall. These results can offer useful theoretical references for designing more potent PIs.
Collapse
Affiliation(s)
- Jianling Liu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
| | - Hong Zhang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
| | - Zhengtao Xiao
- Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China; E-Mail:
| | - Fangfang Wang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
| | - Xia Wang
- School of Chemical Engineering, Dalian University of Technology, Dalian 116012, China
| | - Yonghua Wang
- Center of Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China; E-Mail:
| |
Collapse
|
45
|
Chou TF, Brown SJ, Minond D, Nordin BE, Li K, Jones AC, Chase P, Porubsky PR, Stoltz BM, Schoenen FJ, Patricelli MP, Hodder P, Rosen H, Deshaies RJ. Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways. Proc Natl Acad Sci U S A 2011; 108:4834-9. [PMID: 21383145 DOI: 10.1073/pnas.1015312108] [Citation(s) in RCA: 260] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A specific small-molecule inhibitor of p97 would provide an important tool to investigate diverse functions of this essential ATPase associated with diverse cellular activities (AAA) ATPase and to evaluate its potential to be a therapeutic target in human disease. We carried out a high-throughput screen to identify inhibitors of p97 ATPase activity. Dual-reporter cell lines that simultaneously express p97-dependent and p97-independent proteasome substrates were used to stratify inhibitors that emerged from the screen. N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ) was identified as a selective, potent, reversible, and ATP-competitive p97 inhibitor. DBeQ blocks multiple processes that have been shown by RNAi to depend on p97, including degradation of ubiquitin fusion degradation and endoplasmic reticulum-associated degradation pathway reporters, as well as autophagosome maturation. DBeQ also potently inhibits cancer cell growth and is more rapid than a proteasome inhibitor at mobilizing the executioner caspases-3 and -7. Our results provide a rationale for targeting p97 in cancer therapy.
Collapse
|
46
|
Touchet S, Carreaux F, Carboni B, Bouillon A, Boucher JL. Aminoboronic acids and esters: from synthetic challenges to the discovery of unique classes of enzyme inhibitors. Chem Soc Rev 2011; 40:3895-914. [DOI: 10.1039/c0cs00154f] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
47
|
Screen M, Britton M, Downey SL, Verdoes M, Voges MJ, Blom AEM, Geurink PP, Risseeuw MDP, Florea BI, van der Linden WA, Pletnev AA, Overkleeft HS, Kisselev AF. Nature of pharmacophore influences active site specificity of proteasome inhibitors. J Biol Chem 2010; 285:40125-34. [PMID: 20937826 DOI: 10.1074/jbc.m110.160606] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteasomes degrade most proteins in mammalian cells and are established targets of anti-cancer drugs. The majority of proteasome inhibitors are composed of short peptides with an electrophilic functionality (pharmacophore) at the C terminus. All eukaryotic proteasomes have three types of active sites as follows: chymotrypsin-like, trypsin-like, and caspase-like. It is widely believed that active site specificity of inhibitors is determined primarily by the peptide sequence and not the pharmacophore. Here, we report that active site specificity of inhibitors can also be tuned by the chemical nature of the pharmacophore. Specifically, replacement of the epoxyketone by vinyl sulfone moieties further improves the selectivity of β5-specific inhibitors NC-005, YU-101, and PR-171 (carfilzomib). This increase in specificity is likely the basis of the decreased cytotoxicity of vinyl sulfone-based inhibitors to HeLa cells as compared with that of epoxyketone-based inhibitors.
Collapse
Affiliation(s)
- Michael Screen
- Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Risseeuw MD, Florea BI, van der Marel GA, Overkleeft HS, Overhand M. Sugar amino acid based peptide epoxyketones as potential proteasome inhibitors. Bioorg Chem 2010; 38:202-9. [DOI: 10.1016/j.bioorg.2010.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 04/20/2010] [Accepted: 04/22/2010] [Indexed: 01/30/2023]
|
49
|
Baldisserotto A, Ferretti V, Destro F, Franceschini C, Marastoni M, Gavioli R, Tomatis R. Alpha,beta-unsaturated N-acylpyrrole peptidyl derivatives: new proteasome inhibitors. J Med Chem 2010; 53:6511-5. [PMID: 20687609 DOI: 10.1021/jm100122e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Because of the encouraging results obtained using vinyl ester derivatives, we synthesized and tested a novel series of peptide-based proteasome inhibitors bearing a new pharmacophore unit at the C-terminal. N-Acylpyrrole moiety is a potential substrate for Michael addition by catalytic threonine. Several analogues have demonstrated a selective inhibition of the multicatalytic complex beta1 subunits, the capacity to permeate cellular membrane, and good pharmacokinetics properties.
Collapse
Affiliation(s)
- Anna Baldisserotto
- Department of Pharmaceutical Sciences and Biotechnology Center, University of Ferrara, I-44100 Ferrara, Italy
| | | | | | | | | | | | | |
Collapse
|
50
|
van der Linden WA, Geurink PP, Oskam C, van der Marel GA, Florea BI, Overkleeft HS. Proteasome selectivity towards Michael acceptor containing oligopeptide-based inhibitors. Org Biomol Chem 2010; 8:1885-93. [PMID: 20449494 DOI: 10.1039/b924134e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and biological evaluation of ten Michael acceptors containing potential proteasome inhibitors are described. Cellular targets of azide containing inhibitors and were assessed in HEK293T and RAW264.7 cells by a two step labeling strategy, followed by biotin-pulldown, affinity purification, on-bead tryptic digestion and LC-MS(2) identification. This strategy appears to be an attractive alternative to gel-based competition assays.
Collapse
Affiliation(s)
- Wouter A van der Linden
- Leiden Institute of Chemistry and Netherlands Proteomics Centre, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | | | | | | | | | | |
Collapse
|