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Nutt MJ, Stewart SG. Strengthening Molecular Glues: Design Strategies for Improving Thalidomide Analogs as Cereblon Effectors and Anticancer Agents. Drug Discov Today 2024; 29:104010. [PMID: 38704021 DOI: 10.1016/j.drudis.2024.104010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024]
Abstract
In the two decades since a novel thalidomide analog was last approved, many promising drug candidates have emerged with remarkable potency as targeted protein degraders. Likewise, the advent of PROTACs for suppressing 'undruggable' protein targets reinforces the need for new analogs with improved cereblon affinity, target selectivity and drug-like properties. However, thalidomide and its approved derivatives remain plagued by several shortcomings, such as structural instability and poor solubility. Herein, we present a review of strategies for mitigating these shortcomings and highlight contemporary drug discovery approaches that have generated novel thalidomide analogs with enhanced efficacy as cereblon effectors and/or anticancer agents.
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Affiliation(s)
- Michael J Nutt
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley 6009, Australia.
| | - Scott G Stewart
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley 6009, Australia.
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Nayek U, Basheer Ahamed SI, Mansoor Hussain UH, Unnikrishnan MK, Abdul Salam AA. Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component. Comput Biol Chem 2022; 101:107776. [PMID: 36252444 DOI: 10.1016/j.compbiolchem.2022.107776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cereblon, an extensively studied multifunctional protein, is a Cullin 4-RING E3 ubiquitin ligase complex component. Cereblon is a well-known target of thalidomide and its derivatives. Cereblon is involved in multiple myeloma cell apoptosis. When ligands such as thalidomide and lenalidomide bind to cereblon, it recognizes various neosubstrates based on the ligand shape and properties. We have identified novel CRBN inhibitors, namely DHFO and its analogs, with structural features that are slightly different from thalidomide but stronger cereblon-binding affinity. We selected indanedione and indanone derivatives from the literature to understand and compare their cereblon-mediated substrate recognition potential. METHODS Computational investigations of possible CRBN inhibitors were investigated by molecular docking with Autodock Vina and DockThor programs. The properties of the compounds' ADME/T and drug-likeness were investigated. A molecular dynamics study was carried out for four selected molecules, and the molecular interactions were analyzed using PCA-based FEL methods. The binding affinity was calculated using the MM/PBSA method. RESULTS We conducted computational investigations on 68 indanedione and indanone derivatives binding with cereblon. Ten molecules showed better CRBN binding affinity than thalidomide. We studied the drug-likeness properties of the selected ten molecules, and four of the most promising molecules (DHFO, THOH, DIMS, and DTIN) were chosen for molecular dynamics studies. The MM/PBSA calculations showed that the DHFO, already shown to be a 5-LOX/COX2 inhibitor, has the highest binding affinity of - 163.16 kJ/mol with cereblon. CONCLUSION The selected CRBN inhibitor DHFO has demonstrated the highest binding affinity with cereblon protein compared to other molecules. Thalidomide and its derivatives have a new substitute in the form of DHFO, which produces an interaction hotspot on the surface of the cereblon. Ease of chemical synthesis, low toxicity, versatile therapeutic options, and pleiotropism of DHFO analogs provide an opportunity for exploring clinical alternatives with versatile therapeutic potential for a new category of indanedione molecules as novel modulators of E3 ubiquitin ligases.
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Nguyen TD, Ho Ba NM, Phan DC, Vu BD. Microwave Assisted Synthesis of Thalidomide on Hectogram Scale. ORG PREP PROCED INT 2022. [DOI: 10.1080/00304948.2021.2024681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Trong Diep Nguyen
- Institue of Pharmaceutical Education, Vietnam Military Medical University, Hanoi, Vietnam
| | - Ngoc Minh Ho Ba
- Drug R&D Center, Vietnam Military Medical University, Hanoi, Vietnam
| | - Dinh Chau Phan
- School of Chemical Engineering, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Binh Duong Vu
- Drug R&D Center, Vietnam Military Medical University, Hanoi, Vietnam
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Bricelj A, Steinebach C, Kuchta R, Gütschow M, Sosič I. E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points. Front Chem 2021; 9:707317. [PMID: 34291038 PMCID: PMC8287636 DOI: 10.3389/fchem.2021.707317] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/04/2021] [Indexed: 12/16/2022] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) have received tremendous attention as a new and exciting class of therapeutic agents that promise to significantly impact drug discovery. These bifunctional molecules consist of a target binding unit, a linker, and an E3 ligase binding moiety. The chemically-induced formation of ternary complexes leads to ubiquitination and proteasomal degradation of target proteins. Among the plethora of E3 ligases, only a few have been utilized for the novel PROTAC technology. However, extensive knowledge on the preparation of E3 ligands and their utilization for PROTACs has already been acquired. This review provides an in-depth analysis of synthetic entries to functionalized ligands for the most relevant E3 ligase ligands, i.e. CRBN, VHL, IAP, and MDM2. Less commonly used E3 ligase and their ligands are also presented. We compare different preparative routes to E3 ligands with respect to feasibility and productivity. A particular focus was set on the chemistry of the linker attachment by discussing the synthetic opportunities to connect the E3 ligand at an appropriate exit vector with a linker to assemble the final PROTAC. This comprehensive review includes many facets involved in the synthesis of such complex molecules and is expected to serve as a compendium to support future synthetic attempts towards PROTACs.
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Affiliation(s)
- Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Robert Kuchta
- Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | | | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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Nutt MJ, Yee YS, Buyan A, Andrewartha N, Corry B, Yeoh GCT, Stewart SG. In pursuit of a selective hepatocellular carcinoma therapeutic agent: Novel thalidomide derivatives with antiproliferative, antimigratory and STAT3 inhibitory properties. Eur J Med Chem 2021; 217:113353. [PMID: 33773263 DOI: 10.1016/j.ejmech.2021.113353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/24/2022]
Abstract
Advanced stage liver cancer is predominantly treated with the multi-kinase inhibitor sorafenib; however, this therapeutic agent lacks selectivity in its cytotoxic actions and is associated with poor survival outcomes. Herein we report the design and preparation of several thalidomide derivatives, including a variety of novel thioether-containing forms that are especially rare in the literature. Importantly, two of the derivatives described are potent antiproliferative agents with dose-dependent selectivity for tumorigenic liver progenitor cells (LPC) growth inhibition (up to 36% increase in doubling time at 10 μM) over non-tumorigenic cells (no effect at 10 μM). Furthermore, these putative anti-liver cancer agents were also found to be potent inhibitors of tumorigenic LPC migration. This report also describes these derivatives' effects on several key signalling pathways in our novel liver cell lines by immunofluorescence and AlphaLISA assays. Aryl thioether derivative 7f significantly reduced STAT3 phosphorylation (23%) and its nuclear localisation (16%) at 10 μM in tumorigenic LPCs, implicating the IL-6/JAK/STAT3 axis is central in the mode of action of our derivatives.
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Affiliation(s)
- Michael J Nutt
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia; The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
| | - Yeung Sing Yee
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Amanda Buyan
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| | - Neil Andrewartha
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia; The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
| | - Ben Corry
- Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| | - George C T Yeoh
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia; The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA, 6009, Australia
| | - Scott G Stewart
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
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Affiliation(s)
- Binh Duong Vu
- The R&D Drug Center, Vietnam Military Medical University, No.160, Phung Hung str., Phuc La Ward, Ha Dong District, Hanoi 10000, Vietnam
| | - Ngoc Minh Ho Ba
- The R&D Drug Center, Vietnam Military Medical University, No.160, Phung Hung str., Phuc La Ward, Ha Dong District, Hanoi 10000, Vietnam
| | - Dinh Chau Phan
- School of Chemical Engineering, Hanoi University of Science and Technology, No.1, Dai Co Viet str., Bach Khoa Ward, Hai Ba Trung District, Hanoi 10000, Vietnam
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Frlan R, Gobec S. Evaluation of US 2016/0115161 A1: isoindoline compounds and methods of their use. Expert Opin Ther Pat 2017; 27:637-641. [PMID: 28452243 DOI: 10.1080/13543776.2017.1322954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Immunomodulatory drugs (IMIDs®) are small orally available molecules that modulate the immune system and other biological targets through multiple mechanisms of action and have been successfully used in the treatment of myelodysplastic syndrome and multiple myeloma. However, recent studies of their complex mechanism of action revealed their potential in autoimmune diseases and solid tumors, which intensified scientific interest in these compounds. Areas covered: This patent application claims new IMIDs for the treatment of cancer and disorders associated with angiogenesis and inflammation. Substitution of isoindolinone ring on position 5 with urea and amide linkers connected to different aromatic rings lead to very potent inhibitors of TNF-α production with antiproliferative activities against Nemalwa cells and against colorectal, pancreatic, prostate and breast cancer cell lines in sub-nano to low-nanomolar concentration range. Expert opinion: Substitution of position 5 on the isoindolinone ring, which is presented in this invention, is currently the hot spot of Celgene's research. Results of biological tests, which are superior over those of presently used IMIDs lenalidomide and pomalidomide, make these compounds viable leads for future development of new anticancer drugs against blood and solid cancers.
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Affiliation(s)
- Rok Frlan
- a The Chair of Pharmaceutical Chemistry , University of Ljubljana , Ljubljana , Slovenia
| | - Stanislav Gobec
- a The Chair of Pharmaceutical Chemistry , University of Ljubljana , Ljubljana , Slovenia
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Woo K, Stewart SG, Kong GS, Finch-Edmondson ML, Dwyer BJ, Yeung SY, Abraham LJ, Kampmann SS, Diepeveen LA, Passman AM, Elsegood CL, Tirnitz-Parker JEE, Callus BA, Olynyk JK, Yeoh GCT. Identification of a thalidomide derivative that selectively targets tumorigenic liver progenitor cells and comparing its effects with lenalidomide and sorafenib. Eur J Med Chem 2016; 120:275-83. [PMID: 27208658 DOI: 10.1016/j.ejmech.2016.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/18/2016] [Accepted: 03/04/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS The availability of non-tumorigenic and tumorigenic liver progenitor cell (LPC) lines affords a method to screen putative anti-liver cancer agents to identify those that are selectively effective. To prove this principle we tested thalidomide and a range of its derivatives and compared them to lenalidomide and sorafenib, to assess their growth-inhibitory effects. METHODS Cell growth, the mitotic and apoptotic index of cell cultures were measured using the Cellavista instrument (SynenTec) using commercially available reagents. RESULTS Neither lenalidomide nor thalidomide (100 μM) affected tumorigenic LPCs but killed their non-tumorigenic counterparts. Sorafenib arrested growth in both cell types. All but two derivatives of thalidomide were ineffective; of the two effective derivatives, one (thalidomide C1) specifically affected the tumorigenic cell line (10 μM). Mitotic and apoptotic analyses revealed that thalidomide C1 induced apoptotic cell death and not mitotic arrest. CONCLUSIONS This study shows that screens incorporating non-tumorigenic and tumorigenic liver cell lines are a sound approach to identify agents that are effective and selective. A high throughput instrument such as the Cellavista affords robust and reproducible objective measurements with a large number of replicates that are reliable. These experiments show that neither lenalidomide nor thalidomide are potentially useful for anti-liver cancer therapy as they kill non-tumorigenic liver cells and not their tumorigenic counterparts. Sorafenib in contrast, is highly effective, but not selective. One tested thalidomide derivative has potential as an anti-tumor drug since it induced growth arrest; and importantly, it selectively induced apoptotic cell death only in tumorigenic liver progenitor cells.
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Affiliation(s)
- Ken Woo
- The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Scott G Stewart
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Geraldine S Kong
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Megan L Finch-Edmondson
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Benjamin J Dwyer
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia; The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Sing Y Yeung
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Lawrence J Abraham
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Sven S Kampmann
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Luke A Diepeveen
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia; The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Adam M Passman
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Caryn L Elsegood
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia; School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
| | - Janina E E Tirnitz-Parker
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia; School of Medicine and Pharmacology, University of Western Australia, Fremantle, WA 6959, Australia
| | - Bernard A Callus
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia; School of Health Sciences, The University of Notre Dame Australia, WA 6959, Australia
| | - John K Olynyk
- Department of Gastroenterology & Hepatology, Fiona Stanley Hospital, Bull Creek, WA, Australia; School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia; School of Veterinary Sciences, Murdoch University, Murdoch, WA, Australia
| | - George C T Yeoh
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia; The Centre for Medical Research, The Perkins Institute of Medical Research, Nedlands, WA 6009, Australia.
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Kampmann SS, Skelton BW, Yeoh GC, Abraham LJ, Lengkeek NA, Stubbs KA, Heath CH, Stewart SG. The synthesis and fluorescence profile of novel thalidomide analogues. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.08.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Buccini M, Punch KA, Kaskow B, Flematti GR, Skelton BW, Abraham LJ, Piggott MJ. Ethynylbenzenoid metabolites of Antrodia camphorata: synthesis and inhibition of TNF expression. Org Biomol Chem 2014; 12:1100-13. [PMID: 24385001 DOI: 10.1039/c3ob42333f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An improved synthesis of the anti-inflammatory natural product antrocamphin A (2), involving a key Castro-Stephens reaction, is presented, along with the first total synthesis of its congener antrocamphin B (3). Approaches towards the more complex co-metabolite antrodioxolanone (4) were unsuccessful, but a samarium diiodide-mediated pinacol coupling of antrocamphin B did provide the chiral epimers (51). Antrocamphin A (2) inhibits Tumour Necrosis Factor (TNF) reporter gene expression, but its development as an anti-inflammatory agent may be limited by cytotoxicity.
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Affiliation(s)
- Marco Buccini
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA, Australia.
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Kampmann SS, Sobolev AN, Koutsantonis GA, Stewart SG. Stable Nickel(0) Phosphites as Catalysts for CN Cross-Coupling Reactions. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400201] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Kindahl T, Chorell E. Efficient one-step synthesis of 4-amino substituted phthalimides and evaluation of their potential as fluorescent probes. Org Biomol Chem 2014; 12:4461-70. [DOI: 10.1039/c4ob00342j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tomas Kindahl
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.
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Chen J, Natte K, Spannenberg A, Neumann H, Beller M, Wu XF. Efficient palladium-catalyzed double carbonylation of o-dibromobenzenes: synthesis of thalidomide. Org Biomol Chem 2014; 12:5578-81. [DOI: 10.1039/c4ob00796d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A convenient and mild procedure for double carbonylation of o-dibromobenzene with various 2-amino pyridines and naturally occurring amines has been developed. N-Substituted phthalimides were produced in good to excellent yields. Furthermore, thalidomide was produced in excellent yield under these conditions.
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Affiliation(s)
- Jianbin Chen
- Leibniz-Institut für Katalyse an der Universität Rostock
- 18059 Rostock, Germany
| | - Kishore Natte
- Leibniz-Institut für Katalyse an der Universität Rostock
- 18059 Rostock, Germany
| | - Anke Spannenberg
- Leibniz-Institut für Katalyse an der Universität Rostock
- 18059 Rostock, Germany
| | - Helfried Neumann
- Leibniz-Institut für Katalyse an der Universität Rostock
- 18059 Rostock, Germany
| | - Matthias Beller
- Leibniz-Institut für Katalyse an der Universität Rostock
- 18059 Rostock, Germany
| | - Xiao-Feng Wu
- Leibniz-Institut für Katalyse an der Universität Rostock
- 18059 Rostock, Germany
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Coêlho LCD, Cardoso MVDO, Moreira DRM, Gomes PATDM, Cavalcanti SMT, Oliveira AR, Filho GBDO, Siqueira LRPD, Barbosa MDO, Borba EFDO, Silva TGD, Kaskow B, Karimi M, Abraham LJ, Leite ACL. Novel phthalimide derivatives with TNF-α and IL-1β expression inhibitory and apoptotic inducing properties. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00070f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
24 compounds were synthesized and their immunomodulation of TNF-α and IL-1β was evaluated.
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Affiliation(s)
- Lucas Cunha Duarte Coêlho
- Departamento de Ciências Farmacêuticas
- Centro de Ciências da Saúde
- Universidade Federal de Pernambuco
- Recife, Brazil
| | | | | | | | | | - Arsenio Rodrigues Oliveira
- Departamento de Ciências Farmacêuticas
- Centro de Ciências da Saúde
- Universidade Federal de Pernambuco
- Recife, Brazil
| | | | | | - Miria de Oliveira Barbosa
- Departamento de Ciências Farmacêuticas
- Centro de Ciências da Saúde
- Universidade Federal de Pernambuco
- Recife, Brazil
| | | | | | - Belinda Kaskow
- The School of Chemistry & Biochemistry
- The University of Western Australia
- Crawley, Australia
| | - Mahdad Karimi
- The School of Chemistry & Biochemistry
- The University of Western Australia
- Crawley, Australia
| | - Lawrence J. Abraham
- School of Pathology & Laboratory Medicine
- The University of Western Australia
- Crawley, Australia
| | - Ana Cristina Lima Leite
- Departamento de Ciências Farmacêuticas
- Centro de Ciências da Saúde
- Universidade Federal de Pernambuco
- Recife, Brazil
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