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Hoock JGF, Rossetti C, Bilgin M, Depta L, Enemark-Rasmussen K, Christianson JC, Laraia L. Identification of non-conventional small molecule degraders and stabilizers of squalene synthase. Chem Sci 2023; 14:12973-12983. [PMID: 38023519 PMCID: PMC10664564 DOI: 10.1039/d3sc04064j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/15/2023] [Indexed: 12/01/2023] Open
Abstract
Squalene synthase (SQS) is an essential enzyme in the mevalonate pathway, which controls cholesterol biosynthesis and homeostasis. Although catalytic inhibitors of SQS have been developed, none have been approved for therapeutic use so far. Herein we sought to develop SQS degraders using targeted protein degradation (TPD) to lower overall cellular cholesterol content. We found that KY02111, a small molecule ligand of SQS, selectively causes SQS to degrade in a proteasome-dependent manner. Unexpectedly, compounds based on the same scaffold linked to E3 ligase recruiting ligands led to SQS stabilization. Proteomic analysis found KY02111 to reduce only the levels of SQS, while lipidomic analysis determined that KY02111-induced degradation lowered cellular cholesteryl ester content. Stabilizers shielded SQS from its natural turnover without recruiting their matching E3 ligase or affecting enzymatic target activity. Our work shows that degradation of SQS is possible despite a challenging biological setting and provides the first chemical tools to degrade and stabilize SQS.
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Affiliation(s)
- Joseph G F Hoock
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - Cecilia Rossetti
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute Strandboulevarden 49 Copenhagen 2100 Denmark
| | - Laura Depta
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - Kasper Enemark-Rasmussen
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
| | - John C Christianson
- Nuffield Department of Rheumatology, Orthopaedics, and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford Headington Oxford OX3 7LD UK
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark Kemitorvet 207 Kongens Lyngby 2800 Denmark
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Ebetino FH, Sun S, Cherian P, Roshandel S, Neighbors JD, Hu E, Dunford JE, Sedghizadeh PP, McKenna CE, Srinivasan V, Boeckman RK, Russell RGG. Bisphosphonates: The role of chemistry in understanding their biological actions and structure-activity relationships, and new directions for their therapeutic use. Bone 2022; 156:116289. [PMID: 34896359 PMCID: PMC11023620 DOI: 10.1016/j.bone.2021.116289] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/16/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022]
Abstract
The bisphosphonates ((HO)2P(O)CR1R2P(O)(OH)2, BPs) were first shown to inhibit bone resorption in the 1960s, but it was not until 30 years later that a detailed molecular understanding of the relationship between their varied chemical structures and biological activity was elucidated. In the 1990s and 2000s, several potent bisphosphonates containing nitrogen in their R2 side chains (N-BPs) were approved for clinical use including alendronate, risedronate, ibandronate, and zoledronate. These are now mostly generic drugs and remain the leading therapies for several major bone-related diseases, including osteoporosis and skeletal-related events associated with bone metastases. The early development of chemistry in this area was largely empirical and only a few common structural features related to strong binding to calcium phosphate were clear. Attempts to further develop structure-activity relationships to explain more dramatic pharmacological differences in vivo at first appeared inconclusive, and evidence for mechanisms underlying cellular effects on osteoclasts and macrophages only emerged after many years of research. The breakthrough came when the intracellular actions on the osteoclast were first shown for the simpler bisphosphonates, via the in vivo formation of P-C-P derivatives of ATP. The synthesis and biological evaluation of a large number of nitrogen-containing bisphosphonates in the 1980s and 1990s led to the key discovery that the antiresorptive effects of these more complex analogs on osteoclasts result mostly from their potency as inhibitors of the enzyme farnesyl diphosphate synthase (FDPS/FPPS). This key branch-point enzyme in the mevalonate pathway of cholesterol biosynthesis is important for the generation of isoprenoid lipids that are utilized for the post-translational modification of small GTP-binding proteins essential for osteoclast function. Since then, it has become even more clear that the overall pharmacological effects of individual bisphosphonates on bone depend upon two key properties: the affinity for bone mineral and inhibitory effects on biochemical targets within bone cells, in particular FDPS. Detailed enzyme-ligand crystal structure analysis began in the early 2000s and advances in our understanding of the structure-activity relationships, based on interactions with this target within the mevalonate pathway and related enzymes in osteoclasts and other cells have continued to be the focus of research efforts to this day. In addition, while many members of the bisphosphonate drug class share common properties, now it is more clear that chemical modifications to create variations in these properties may allow customization of BPs for different uses. Thus, as the appreciation for new potential opportunities with this drug class grows, new chemistry to allow ready access to an ever-widening variety of bisphosphonates continues to be developed. Potential new uses of the calcium phosphate binding mechanism of bisphosphonates for the targeting of other drugs to the skeleton, and effects discovered on other cellular targets, even at non-skeletal sites, continue to intrigue scientists in this research field.
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Affiliation(s)
- Frank H Ebetino
- BioVinc LLC, 2265 E. Foothill Blvd, Pasadena, CA 91107, USA; Department of Chemistry, University of Rochester, Rochester, NY 14617, USA; Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK.
| | - Shuting Sun
- BioVinc LLC, 2265 E. Foothill Blvd, Pasadena, CA 91107, USA.
| | - Philip Cherian
- BioVinc LLC, 2265 E. Foothill Blvd, Pasadena, CA 91107, USA
| | | | | | - Eric Hu
- BioVinc LLC, 2265 E. Foothill Blvd, Pasadena, CA 91107, USA
| | - James E Dunford
- Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, The Oxford University Institute of Musculoskeletal Sciences, The Botnar Research Centre, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, UK
| | - Parish P Sedghizadeh
- Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Venkat Srinivasan
- Department of Chemistry, University of Rochester, Rochester, NY 14617, USA
| | - Robert K Boeckman
- Department of Chemistry, University of Rochester, Rochester, NY 14617, USA
| | - R Graham G Russell
- Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK; Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, The Oxford University Institute of Musculoskeletal Sciences, The Botnar Research Centre, Nuffield Orthopaedic Centre, Headington, Oxford OX3 7LD, UK; Mellanby Centre for Musculoskeletal Research, University of Sheffield, Sheffield, UK
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Caruso L, Nadur NF, Brandão M, Peixoto Ferreira LDA, Lacerda RB, Graebin CS, Kümmerle AE. The Design of Multi-target Drugs to Treat Cardiovascular Diseases: Two (or more) Birds on one Stone. Curr Top Med Chem 2022; 22:366-394. [PMID: 35105288 DOI: 10.2174/1568026622666220201151248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/25/2021] [Accepted: 12/27/2021] [Indexed: 11/22/2022]
Abstract
Cardiovascular diseases (CVDs) comprise a group of diseases and disorders of the heart and blood vessels, which together are the number one cause of death worldwide, being associated with multiple genetic and modifiable risk factors, and that may directly arise from different etiologies. For a long time, the search for cardiovascular drugs was based on the old paradigm "one compound - one target", which aims to obtain a highly potent and selective molecule with only one desired molecular target. Although historically successful in the last decades, this approach ignores the multiple causes and the multifactorial nature of CVD's. Thus, over time, treatment strategies for cardiovascular diseases have changed and, currently, pharmacological therapies for CVD are mainly based on the association of two or more drugs to control symptoms and reduce cardiovascular death. In this context, the development of multitarget drugs, i.e, compounds having the ability to act simultaneously at multiple sites, is an attractive and relevant strategy that can be even more advantageous to achieve predictable pharmacokinetic and pharmacodynamics correlations as well as better patient compliance. In this review, we aim to highlight the efforts and rational pharmacological bases for the design of some promising multitargeted compounds to treat important cardiovascular diseases like heart failure, atherosclerosis, acute myocardial infarction, pulmonary arterial hypertension and arrhythmia.
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Affiliation(s)
- Lucas Caruso
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Nathalia Fonseca Nadur
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Marina Brandão
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Larissa de Almeida Peixoto Ferreira
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Renata Barbosa Lacerda
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Cedric Stephan Graebin
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Arthur Eugen Kümmerle
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
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