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Peeples ES, Mirnics K, Korade Z. Chemical Inhibition of Sterol Biosynthesis. Biomolecules 2024; 14:410. [PMID: 38672427 PMCID: PMC11048061 DOI: 10.3390/biom14040410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Cholesterol is an essential molecule of life, and its synthesis can be inhibited by both genetic and nongenetic mechanisms. Hundreds of chemicals that we are exposed to in our daily lives can alter sterol biosynthesis. These also encompass various classes of FDA-approved medications, including (but not limited to) commonly used antipsychotic, antidepressant, antifungal, and cardiovascular medications. These medications can interfere with various enzymes of the post-lanosterol biosynthetic pathway, giving rise to complex biochemical changes throughout the body. The consequences of these short- and long-term homeostatic disruptions are mostly unknown. We performed a comprehensive review of the literature and built a catalogue of chemical agents capable of inhibiting post-lanosterol biosynthesis. This process identified significant gaps in existing knowledge, which fall into two main areas: mechanisms by which sterol biosynthesis is altered and consequences that arise from the inhibitions of the different steps in the sterol biosynthesis pathway. The outcome of our review also reinforced that sterol inhibition is an often-overlooked mechanism that can result in adverse consequences and that there is a need to develop new safety guidelines for the use of (novel and already approved) medications with sterol biosynthesis inhibiting side effects, especially during pregnancy.
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Affiliation(s)
- Eric S. Peeples
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Child Health Research Institute, Omaha, NE 68198, USA;
- Division of Neonatology, Children’s Nebraska, Omaha, NE 68114, USA
| | - Karoly Mirnics
- Child Health Research Institute, Omaha, NE 68198, USA;
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zeljka Korade
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Child Health Research Institute, Omaha, NE 68198, USA;
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Dorel R, Sun D, Carruthers N, Castanedo GM, Ung PMU, Factor DC, Li T, Baumann H, Janota D, Pang J, Salphati L, Meklemburg R, Korman AJ, Harper HE, Stubblefield S, Payandeh J, McHugh D, Lang BT, Tesar PJ, Dere E, Masureel M, Adams DJ, Volgraf M, Braun MG. Discovery and Optimization of Selective Brain-Penetrant EBP Inhibitors that Enhance Oligodendrocyte Formation. J Med Chem 2024. [PMID: 38470227 DOI: 10.1021/acs.jmedchem.3c02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The inhibition of emopamil binding protein (EBP), a sterol isomerase within the cholesterol biosynthesis pathway, promotes oligodendrocyte formation, which has been proposed as a potential therapeutic approach for treating multiple sclerosis. Herein, we describe the discovery and optimization of brain-penetrant, orally bioavailable inhibitors of EBP. A structure-based drug design approach from literature compound 1 led to the discovery of a hydantoin-based scaffold, which provided balanced physicochemical properties and potency and an improved in vitro safety profile. The long half-lives of early hydantoin-based EBP inhibitors in rodents prompted an unconventional optimization strategy, focused on increasing metabolic turnover while maintaining potency and a brain-penetrant profile. The resulting EBP inhibitor 11 demonstrated strong in vivo target engagement in the brain, as illustrated by the accumulation of EBP substrate zymostenol after repeated dosing. Furthermore, compound 11 enhanced the formation of oligodendrocytes in human cortical organoids, providing additional support for our therapeutic hypothesis.
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Affiliation(s)
- Ruth Dorel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Dawei Sun
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Carruthers
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Peter M-U Ung
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel C Factor
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Tianbo Li
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hannah Baumann
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Danielle Janota
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laurent Salphati
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Meklemburg
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Allison J Korman
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Halie E Harper
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel McHugh
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Bradley T Lang
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Paul J Tesar
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Edward Dere
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthieu Masureel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Drew J Adams
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Matthew Volgraf
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Tumenbayar BI, Tutino VM, Brazzo JA, Yao P, Bae Y. FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575789. [PMID: 38293187 PMCID: PMC10827115 DOI: 10.1101/2024.01.15.575789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Cellular metabolism is influenced by the stiffness of the extracellular matrix. Focal adhesion kinase (FAK) and its binding partner, p130Cas, transmit biomechanical signals about substrate stiffness to the cell to regulate a variety of cellular responses, but their roles in early transcriptional and metabolic responses remain largely unexplored. We cultured mouse embryonic fibroblasts with or without siRNA-mediated FAK or p130Cas knockdown and assessed the early transcriptional responses of these cells to placement on soft and stiff substrates by RNA sequencing and bioinformatics analyses. Exposure to the stiff ECM altered the expression of genes important for metabolic and biosynthetic processes, and these responses were influenced by knockdown of FAK and p130Cas. Our findings reveal that FAK-p130Cas signaling mechanotransduces ECM stiffness to early transcriptional changes that alter cellular metabolism and biosynthesis.
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Affiliation(s)
- Bat-Ider Tumenbayar
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Vincent M. Tutino
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Joseph A. Brazzo
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Yongho Bae
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biomedical Engineering, School of Engineering and Applied Sciences, University at Buffalo, Buffalo, NY 14260, USA
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Qian L, Scott NA, Capell-Hattam IM, Draper EA, Fenton NM, Luu W, Sharpe LJ, Brown AJ. Cholesterol synthesis enzyme SC4MOL is fine-tuned by sterols and targeted for degradation by the E3 ligase MARCHF6. J Lipid Res 2023; 64:100362. [PMID: 36958722 PMCID: PMC10176258 DOI: 10.1016/j.jlr.2023.100362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/09/2023] [Accepted: 02/25/2023] [Indexed: 03/25/2023] Open
Abstract
Cholesterol biosynthesis is a highly regulated pathway, with over 20 enzymes controlled at the transcriptional and post-translational level. Whilst some enzymes remain stable, increased sterol levels can trigger degradation of several synthesis enzymes via the ubiquitin-proteasome system. Of note, we previously identified four cholesterol synthesis enzymes as substrates for one E3 ubiquitin ligase, membrane-associated RING-CH-type finger 6 (MARCHF6). Whether MARCHF6 targets the cholesterol synthesis pathway at other points is unknown. In addition, the post-translational regulation of many cholesterol synthesis enzymes, including the C4-demethylation complex (sterol-C4-methyl oxidase-like, SC4MOL; NAD(P) dependent steroid dehydrogenase-like, NSDHL; hydroxysteroid 17-beta dehydrogenase, HSD17B7) is largely uncharacterized. Using cultured mammalian cell-lines (human-derived and Chinese Hamster Ovary cells), we show SC4MOL, the first acting enzyme of C4-demethylation, is a MARCHF6 substrate, and is rapidly turned over and sensitive to sterols. Sterol depletion stabilizes SC4MOL protein levels, whilst sterol excess downregulates both transcript and protein levels. Furthermore, we found SC4MOL depletion by siRNA results in a significant decrease in total cell cholesterol. Thus, our work indicates SC4MOL is the most regulated enzyme in the C4-demethylation complex. Our results further implicate MARCHF6 as a crucial post-translational regulator of cholesterol synthesis, with this E3 ubiquitin ligase controlling levels of at least five enzymes of the pathway.
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Affiliation(s)
- Lydia Qian
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Nicola A Scott
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Isabelle M Capell-Hattam
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eliza A Draper
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Nicole M Fenton
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Winnie Luu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Laura J Sharpe
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia.
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The landscape of targets and lead molecules for remyelination. Nat Chem Biol 2022; 18:925-933. [PMID: 35995862 PMCID: PMC9773298 DOI: 10.1038/s41589-022-01115-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/18/2022] [Indexed: 12/24/2022]
Abstract
Remyelination, or the restoration of myelin sheaths around axons in the central nervous system, is a multi-stage repair process that remains a major need for millions of patients with multiple sclerosis and other diseases of myelin. Even into adulthood, rodents and humans can generate new myelin-producing oligodendrocytes, leading to the therapeutic hypothesis that enhancing remyelination could lessen disease burden in multiple sclerosis. Multiple labs have used phenotypic screening to identify dozens of drugs that enhance oligodendrocyte formation, and several hit molecules have now advanced to clinical evaluation. Target identification studies have revealed that a large majority of these hits share the ability to inhibit a narrow range of cholesterol pathway enzymes and thereby induce cellular accumulation of specific sterol precursors to cholesterol. This Perspective surveys the recent fruitful intersection of chemical biology and remyelination and suggests multiple approaches toward new targets and lead molecules to promote remyelination.
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Sax JL, Hershman SN, Hubler Z, Allimuthu D, Elitt MS, Bederman I, Adams DJ. Enhancers of Human and Rodent Oligodendrocyte Formation Predominantly Induce Cholesterol Precursor Accumulation. ACS Chem Biol 2022; 17:2188-2200. [PMID: 35833657 PMCID: PMC9773236 DOI: 10.1021/acschembio.2c00330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Regeneration of myelin in the central nervous system is being pursued as a potential therapeutic approach for multiple sclerosis. Several labs have reported small molecules that promote oligodendrocyte formation and remyelination in vivo. Recently, we reported that many such molecules function by inhibiting a narrow window of enzymes in the cholesterol biosynthesis pathway. Here we describe a new high-throughput screen of 1,836 bioactive molecules and a thorough re-analysis of more than 60 molecules previously identified as promoting oligodendrocyte formation from human, rat, or mouse oligodendrocyte progenitor cells. These studies highlight that an overwhelming fraction of validated screening hits, including several molecules being evaluated clinically for remyelination, inhibit cholesterol pathway enzymes like emopamil-binding protein (EBP). To rationalize these findings, we suggest a model that relies on the high druggability of sterol-metabolizing enzymes and the ability of cationic amphiphiles to mimic the transition state of EBP. These studies further establish cholesterol pathway inhibition as a dominant mechanism among screening hits that enhance human, rat, or mouse oligodendrocyte formation.
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Affiliation(s)
- Joel L Sax
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Samantha N Hershman
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Zita Hubler
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Dharmaraja Allimuthu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Matthew S Elitt
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Ilya Bederman
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Drew J Adams
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
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