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Wu D, Li Y, Zheng L, Xiao H, Ouyang L, Wang G, Sun Q. Small molecules targeting protein-protein interactions for cancer therapy. Acta Pharm Sin B 2023; 13:4060-4088. [PMID: 37799384 PMCID: PMC10547922 DOI: 10.1016/j.apsb.2023.05.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/22/2023] [Indexed: 10/07/2023] Open
Abstract
Protein-protein interactions (PPIs) are fundamental to many biological processes that play an important role in the occurrence and development of a variety of diseases. Targeting the interaction between tumour-related proteins with emerging small molecule drugs has become an attractive approach for treatment of human diseases, especially tumours. Encouragingly, selective PPI-based therapeutic agents have been rapidly advancing over the past decade, providing promising perspectives for novel therapies for patients with cancer. In this review we comprehensively clarify the discovery and development of small molecule modulators of PPIs from multiple aspects, focusing on PPIs in disease, drug design and discovery strategies, structure-activity relationships, inherent dilemmas, and future directions.
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Affiliation(s)
- Defa Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yang Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Lang Zheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Huan Xiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Qiu Sun
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
- West China Medical Publishers, West China Hospital, Sichuan University, Chengdu 610041, China
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2
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Farag M, Kieffer C, Guedeney N, Voisin-Chiret AS, Sopkova-de Oliveira Santos J. Computational Tool to Design Small Synthetic Inhibitors Selective for XIAP-BIR3 Domain. Molecules 2023; 28:5155. [PMID: 37446817 DOI: 10.3390/molecules28135155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) exercises its biological function by locking up and inhibiting essential caspase-3, -7 and -9 toward apoptosis execution. It is overexpressed in multiple human cancers, and it plays an important role in cancer cells' death skipping. Inhibition of XIAP-BIR3 domain and caspase-9 interaction was raised as a promising strategy to restore apoptosis in malignancy treatment. However, XIAP-BIR3 antagonists also inhibit cIAP1-2 BIR3 domains, leading to serious side effects. In this study, we worked on a theoretical model that allowed us to design and optimize selective synthetic XIAP-BIR3 antagonists. Firstly, we assessed various MM-PBSA strategies to predict the XIAP-BIR3 binding affinities of synthetic ligands. Molecular dynamics simulations using hydrogen mass repartition as an additional parametrization with and without entropic term computed by the interaction entropy approach produced the best correlations. These simulations were then exploited to generate 3D pharmacophores. Following an optimization with a training dataset, five features were enough to model XIAP-BIR3 synthetic ligands binding to two hydrogen bond donors, one hydrogen bond acceptor and two hydrophobic groups. The correlation between pharmacophoric features and computed MM-PBSA free energy revealed nine residues as crucial for synthetic ligand binding: Thr308, Glu314, Trp323, Leu307, Asp309, Trp310, Gly306, Gln319 and Lys297. Ultimately, and three of them seemed interesting to use to improve XIAP-BR3 versus cIAP-BIR3 selectivity: Lys297, Thr308 and Asp309.
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Affiliation(s)
- Marc Farag
- Normandie Univ., UNICAEN, CERMN, 14000 Caen, France
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3
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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4
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Hassan AHE, El-Sayed SM, Yamamoto M, Gohda J, Matsumoto T, Shirouzu M, Inoue JI, Kawaguchi Y, Mansour RMA, Anvari A, Farahat AA. In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases. Viruses 2023; 15:1171. [PMID: 37243257 PMCID: PMC10223987 DOI: 10.3390/v15051171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and influenza A virus, require the host proteases to mediate viral entry into cells. Rather than targeting the continuously mutating viral proteins, targeting the conserved host-based entry mechanism could offer advantages. Nafamostat and camostat were discovered as covalent inhibitors of TMPRSS2 protease involved in viral entry. To circumvent their limitations, a reversible inhibitor might be required. Considering nafamostat structure and using pentamidine as a starting point, a small set of structurally diverse rigid analogues were designed and evaluated in silico to guide selection of compounds to be prepared for biological evaluation. Based on the results of in silico study, six compounds were prepared and evaluated in vitro. At the enzyme level, compounds 10-12 triggered potential TMPRSS2 inhibition with low micromolar IC50 concentrations, but they were less effective in cellular assays. Meanwhile, compound 14 did not trigger potential TMPRSS2 inhibition at the enzyme level, but it showed potential cellular activity regarding inhibition of membrane fusion with a low micromolar IC50 value of 10.87 µM, suggesting its action could be mediated by another molecular target. Furthermore, in vitro evaluation showed that compound 14 inhibited pseudovirus entry as well as thrombin and factor Xa. Together, this study presents compound 14 as a hit compound that might serve as a starting point for developing potential viral entry inhibitors with possible application against coronaviruses.
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Affiliation(s)
- Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takehisa Matsumoto
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan
| | - Jun-Ichiro Inoue
- Infection and Advanced Research Center (UTOPIA), The University of Tokyo Pandemic Preparedness, Tokyo 108-8639, Japan
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Reem M A Mansour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abtin Anvari
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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5
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Morado J, Mortenson PN, Nissink JWM, Essex JW, Skylaris CK. Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins. J Chem Inf Model 2023; 63:2810-2827. [PMID: 37071825 PMCID: PMC10170518 DOI: 10.1021/acs.jcim.2c01510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
We present a comparative study that evaluates the performance of a machine learning potential (ANI-2x), a conventional force field (GAFF), and an optimally tuned GAFF-like force field in the modeling of a set of 10 γ-fluorohydrins that exhibit a complex interplay between intra- and intermolecular interactions in determining conformer stability. To benchmark the performance of each molecular model, we evaluated their energetic, geometric, and sampling accuracies relative to quantum-mechanical data. This benchmark involved conformational analysis both in the gas phase and chloroform solution. We also assessed the performance of the aforementioned molecular models in estimating nuclear spin-spin coupling constants by comparing their predictions to experimental data available in chloroform. The results and discussion presented in this study demonstrate that ANI-2x tends to predict stronger-than-expected hydrogen bonding and overstabilize global minima and shows problems related to inadequate description of dispersion interactions. Furthermore, while ANI-2x is a viable model for modeling in the gas phase, conventional force fields still play an important role, especially for condensed-phase simulations. Overall, this study highlights the strengths and weaknesses of each model, providing guidelines for the use and future development of force fields and machine learning potentials.
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Affiliation(s)
- João Morado
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - J Willem M Nissink
- Computational Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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7
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Wang S, Ji T, Wang L, Qu Y, Wang X, Wang W, Lv M, Wang Y, Li X, Jiang P. Exploration of the mechanism by which Huangqi Guizhi Wuwu decoction inhibits Lps-induced inflammation by regulating macrophage polarization based on network pharmacology. BMC Complement Med Ther 2023; 23:8. [PMID: 36624435 PMCID: PMC9830836 DOI: 10.1186/s12906-022-03826-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Huangqi Guizhi Wuwu decoction (HQGZWWD) is a traditional Chinese herbal medicine formulation with significant anti-inflammatory activity. However, its underlying mechanism remains unknown. Through network pharmacology and experimental validation, this study aimed to examine the potential mechanism of HQGZWWD in regulating macrophage polarization and inflammation. METHODS The active components were obtained from the Traditional Chinese Medicine Systems Pharmacology database and Analysis Platform (TCMSP), whereas the corresponding targets were obtained from the TCMSP and Swiss Target Prediction database. The GeneCards database identified targets associated with macrophage polarization and inflammation. Multiple networks were developed to identify the key compounds, principal biological processes, and pathways of HQGZWWD that regulate macrophage polarization and inflammation. Autodock Vina is utilized to assess the binding ability between targets and active compounds. Finally, confirm the experiment's central hypothesis. Human histiocytic lymphoma (U-937) cells were transformed into M1 macrophages following stimulation with Lipopolysaccharide (LPS) to evaluate the effect of HQGZWWD drug-containing mouse serum (HQGZWWD serum) on regulating macrophage polarization and inflammation. RESULTS A total of 54 active components and 859 HQGZWWD targets were obtained. There were 9972 targets associated with macrophage polarization and 11,109 targets associated with inflammation. After screening, 34 overlapping targets were identified, of which 5 were identified as central targets confirmed by experiments, including the α7 nicotinic acetylcholine receptor (α7 nAchR), interleukin 6 (IL-6), Interleukin-1 beta (IL-1β), interleukin 10 (IL-10) and growth factor beta (TGF-β1). Pathway enrichment analysis revealed that 34 overlapping targets were enriched in multiple pathways associated with macrophage polarization and inflammation, including the TGF beta signaling pathway, NF-kappa B signaling pathway, JAK-STAT signaling pathway, and TNF signaling pathway. Molecular docking confirmed that the majority of HQGZWWD's compounds can bind to the target. In vitro experiments, HQGZWWD serum was shown to up-regulate the expression of α7 nAchR, reduce the number of M1 macrophages, stimulate the production of M2 macrophages, inhibit the expression of pro-inflammatory cytokines IL-6 and IL1-β, and increase the expression of anti-inflammatory cytokines IL-10 and TGF-β1. CONCLUSION HQGZWWD can regulate the number of M1/M2 macrophages and the level of inflammatory cytokines, and the underlying mechanism may be related to the up-regulation of α7 nAchR expression.
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Affiliation(s)
- Sutong Wang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Tianshu Ji
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Lin Wang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Yiwei Qu
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Xinhui Wang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Wenting Wang
- grid.464481.b0000 0004 4687 044XNational Clincial Research Center for Cardiovascular Diseases of Traditional Chinese Medicine, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091 China
| | - Mujie Lv
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, Jinan, 250014 Shandong China
| | - Yongcheng Wang
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011 China
| | - Xiao Li
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011 China
| | - Ping Jiang
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011 China
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8
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Shen M, Kang Y. Cancer fitness genes: emerging therapeutic targets for metastasis. Trends Cancer 2023; 9:69-82. [PMID: 36184492 DOI: 10.1016/j.trecan.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 12/31/2022]
Abstract
Development of cancer therapeutics has traditionally focused on targeting driver oncogenes. Such an approach is limited by toxicity to normal tissues and treatment resistance. A class of 'cancer fitness genes' with crucial roles in metastasis have been identified. Elevated or altered activities of these genes do not directly cause cancer; instead, they relieve the stresses that tumor cells encounter and help them adapt to a changing microenvironment, thus facilitating tumor progression and metastasis. Importantly, as normal cells do not experience high levels of stress under physiological conditions, targeting cancer fitness genes is less likely to cause toxicity to noncancerous tissues. Here, we summarize the key features and function of cancer fitness genes and discuss their therapeutic potential.
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Affiliation(s)
- Minhong Shen
- Department of Pharmacology, Wayne State University School of Medicine, Michigan, MI, USA; Department of Oncology, Wayne State University School of Medicine and Tumor Biology and Microenvironment Research Program, Barbara Ann Karmanos Cancer Institute, Michigan, MI, USA.
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; Ludwig Institute for Cancer Research Princeton Branch, Princeton, NJ, USA.
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Martin MP, Noble MEM. Exiting the tunnel of uncertainty: crystal soak to validated hit. Acta Crystallogr D Struct Biol 2022; 78:1294-1302. [PMID: 36322414 PMCID: PMC9629488 DOI: 10.1107/s2059798322009986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, it is suggested that hit validation and prioritization are best achieved by a `triangulation' approach in which the results of multiple available biochemical and biophysical techniques are correlated to develop qualitative structure-activity relationships (SARs). Such qualitative SARs may indeed be the only means by which to navigate a project through the tunnel of uncertainty that prevails before on-scale biophysical, biochemical and/or biological measurements become possible.
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Affiliation(s)
- Mathew P. Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Martin E. M. Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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10
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Lee J, Lee Y, Jung YM, Park JH, Yoo HS, Park J. Discovery of E3 Ligase Ligands for Target Protein Degradation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196515. [PMID: 36235052 PMCID: PMC9573645 DOI: 10.3390/molecules27196515] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 12/02/2022]
Abstract
Target protein degradation has emerged as a promising strategy for the discovery of novel therapeutics during the last decade. Proteolysis-targeting chimera (PROTAC) harnesses a cellular ubiquitin-dependent proteolysis system for the efficient degradation of a protein of interest. PROTAC consists of a target protein ligand and an E3 ligase ligand so that it enables the target protein degradation owing to the induced proximity with ubiquitin ligases. Although a great number of PROTACs has been developed so far using previously reported ligands of proteins for their degradation, E3 ligase ligands have been mostly limited to either CRBN or VHL ligands. Those PROTACs showed their limitation due to the cell type specific expression of E3 ligases and recently reported resistance toward PROTACs with CRBN ligands or VHL ligands. To overcome these hurdles, the discovery of various E3 ligase ligands has been spotlighted to improve the current PROTAC technology. This review focuses on currently reported E3 ligase ligands and their application in the development of PROTACs.
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Affiliation(s)
- Jaeseok Lee
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Youngjun Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Young Mee Jung
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
| | - Ju Hyun Park
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Hyuk Sang Yoo
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: ; Tel.: +82-33-250-8482
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11
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Kennedy C, McPhie K, Rittinger K. Targeting the ubiquitin system by fragment-based drug discovery. Front Mol Biosci 2022; 9:1019636. [PMID: 36275626 PMCID: PMC9580268 DOI: 10.3389/fmolb.2022.1019636] [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: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 11/22/2022] Open
Abstract
The ubiquitin system contains a wealth of potential drug targets for many diseases and conditions, including neurodegenerative, immune, metabolic and developmental diseases, as well as multiple cancers. Despite years of research, relatively few clinical inhibitors or specific chemical probes for proteins within the ubiquitin system exist, with many interesting target proteins yet to be explored. Fragment-based drug discovery (FBDD) offers efficient and broad coverage of chemical space with small libraries, using covalent and non-covalent approaches. Coupled with advances in structural biology and proteomics, FBDD now provides a thorough screening platform for inhibitor discovery within the ubiquitin system. In this mini review, we summarise the current scope of FBDD and how it has been applied to ubiquitin-activating (E1), ubiquitin-conjugating (E2), ubiquitin ligase (E3) and deubiquitinating (DUB) enzymes. We also discuss the newest frontiers of FBDD and how they could be applied to enable inhibitor and novel chemical probe discovery and provide functional insight into the ubiquitin system.
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12
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Martins V, Fazal L, Oganesian A, Shah A, Stow J, Walton H, Wilsher N. A commentary on the use of pharmacoenhancers in the pharmaceutical industry and the implication for DMPK drug discovery strategies. Xenobiotica 2022; 52:786-796. [PMID: 36537234 DOI: 10.1080/00498254.2022.2130838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Paxlovid, a drug combining nirmatrelvir and ritonavir, was designed for the treatment of COVID-19 and its rapid development has led to emergency use approval by the FDA to reduce the impact of COVID-19 infection on patients.In order to overcome potentially suboptimal therapeutic exposures, nirmatrelvir is dosed in combination with ritonavir to boost the pharmacokinetics of the active product.Here we consider examples of drugs co-administered with pharmacoenhancers.Pharmacoenhancers have been adopted for multiple purposes such as ensuring therapeutic exposure of the active product, reducing formation of toxic metabolites, changing the route of administration, and increasing the cost-effectiveness of a therapy.We weigh the benefits and risks of this approach, examining the impact of technology developments on drug design and how enhanced integration between cross-discipline teams can improve the outcome of drug discovery.
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13
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Cons BD, Twigg DG, Kumar R, Chessari G. Electrostatic Complementarity in Structure-Based Drug Design. J Med Chem 2022; 65:7476-7488. [PMID: 35512344 DOI: 10.1021/acs.jmedchem.2c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimization of electrostatic complementarity is an important strategy in structure-based drug discovery for improving the affinity of molecules against a specific protein target. In this Miniperspective we identify examples where deliberate optimization of protein-ligand electrostatic complementarity or intramolecular electrostatic interactions gave improvements in target affinity (up to 250-fold), physicochemical properties, in vitro properties, and off-target selectivity. We also look retrospectively at a series of factor Xa inhibitors that show an almost 8000-fold range in potency that can be correlated with the calculated electrostatic potential (ESP) surfaces. Recent developments using a graph-convolutional deep neural network to rapidly generate high quality ESP surfaces have the potential to make this useful tool more accessible for a wider audience within the field of medicinal chemistry.
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Affiliation(s)
- Benjamin D Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Rajendra Kumar
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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14
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Sosič I, Bricelj A, Steinebach C. E3 ligase ligand chemistries: from building blocks to protein degraders. Chem Soc Rev 2022; 51:3487-3534. [PMID: 35393989 DOI: 10.1039/d2cs00148a] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, proteolysis-targeting chimeras (PROTACs), capable of achieving targeted protein degradation, have proven their great therapeutic potential and usefulness as molecular biology tools. These heterobifunctional compounds are comprised of a protein-targeting ligand, an appropriate linker, and a ligand binding to the E3 ligase of choice. A successful PROTAC induces the formation of a ternary complex, leading to the E3 ligase-mediated ubiquitination of the targeted protein and its proteasomal degradation. In over 20 years since the concept was first demonstrated, the field has grown substantially, mainly due to the advancements in the discovery of non-peptidic E3 ligase ligands. Development of small-molecule E3 binders with favourable physicochemical profiles aided the design of PROTACs, which are known for breaking the rules of established guidelines for discovering small molecules. Synthetic accessibility of the ligands and numerous successful applications led to the prevalent use of cereblon and von Hippel-Lindau as the hijacked E3 ligase. However, the pool of over 600 human E3 ligases is full of untapped potential, which is why expanding the artillery of E3 ligands could contribute to broadening the scope of targeted protein degradation. In this comprehensive review, we focus on the chemistry aspect of the PROTAC design process by providing an overview of liganded E3 ligases, their chemistries, appropriate derivatisation, and synthetic approaches towards their incorporation into heterobifunctional degraders. By covering syntheses of both established and underexploited E3 ligases, this review can serve as a chemistry blueprint for PROTAC researchers during their future ventures into the complex field of targeted protein degradation.
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Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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15
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Cruz Walma DA, Chen Z, Bullock AN, Yamada KM. Ubiquitin ligases: guardians of mammalian development. Nat Rev Mol Cell Biol 2022; 23:350-367. [DOI: 10.1038/s41580-021-00448-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/17/2022]
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16
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Morado J, Mortenson PN, Nissink JWM, Verdonk ML, Ward RA, Essex JW, Skylaris CK. Generation of Quantum Configurational Ensembles Using Approximate Potentials. J Chem Theory Comput 2021; 17:7021-7042. [PMID: 34644088 DOI: 10.1021/acs.jctc.1c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational analysis is of paramount importance in drug design: it is crucial to determine pharmacological properties, understand molecular recognition processes, and characterize the conformations of ligands when unbound. Molecular Mechanics (MM) simulation methods, such as Monte Carlo (MC) and molecular dynamics (MD), are usually employed to generate ensembles of structures due to their ability to extensively sample the conformational space of molecules. The accuracy of these MM-based schemes strongly depends on the functional form of the force field (FF) and its parametrization, components that often hinder their performance. High-level methods, such as ab initio MD, provide reliable structural information but are still too computationally expensive to allow for extensive sampling. Therefore, to overcome these limitations, we present a multilevel MC method that is capable of generating quantum configurational ensembles while keeping the computational cost at a minimum. We show that FF reparametrization is an efficient route to generate FFs that reproduce QM results more closely, which, in turn, can be used as low-cost models to achieve the gold standard QM accuracy. We demonstrate that the MC acceptance rate is strongly correlated with various phase space overlap measurements and that it constitutes a robust metric to evaluate the similarity between the MM and QM levels of theory. As a more advanced application, we present a self-parametrizing version of the algorithm, which combines sampling and FF parametrization in one scheme, and apply the methodology to generate the QM/MM distribution of a ligand in aqueous solution.
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Affiliation(s)
- João Morado
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - J Willem M Nissink
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Marcel L Verdonk
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Richard A Ward
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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17
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Douglas JJ, Tatton MR, de Bruin D, Buttar D, Cook C, Dai K, Ferrer C, Leslie K, Morrison J, Munday R, Ronson TO, Zhao H. Exploration of a Nitromethane-Carbonylation Strategy during Route Design of an Atropisomeric KRAS G12C Inhibitor. J Org Chem 2021; 87:2075-2086. [PMID: 34652911 DOI: 10.1021/acs.joc.1c01736] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Route design and proof of concept synthesis was conducted on a synthetically challenging atropisomeric KRASG12C inhibitor to support clinical API manufacture. Improvements to the synthesis of a chiral piperazine fragment gave reduced step count and streamlined protecting group strategy via the formation and methanol ring opening of an N-carboxy-anhydride (NCA). The complex atropisomeric nitroquinoline was accessed via an early stage salt-resolution followed by a formal two-part nitromethane-carbonylation, avoiding a high temperature Gould-Jacobs cyclization that previously led to atropisomer racemization. The substrate scope of the formal nitromethane-carbonylation strategy was further explored for a range of ortho-substituted bromo/iodo unprotected anilines.
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Affiliation(s)
- James J Douglas
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Matthew R Tatton
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Daniël de Bruin
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K.,Organic Chemistry & Catalysis, Institution Debye Institute for Nanomaterials Science, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - David Buttar
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Calum Cook
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Kuangchu Dai
- Changzhou SynTheAll Pharmaceutical Co. Ltd., No 589, North Yulong Road, Chunjiang Town, Xinbei District, Changzhou 213127, Jiangsu, PR China
| | | | - Kevin Leslie
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - James Morrison
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Rachel Munday
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Thomas O Ronson
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Hucheng Zhao
- Changzhou SynTheAll Pharmaceutical Co. Ltd., No 589, North Yulong Road, Chunjiang Town, Xinbei District, Changzhou 213127, Jiangsu, PR China
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18
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Chessari G, Grainger R, Holvey RS, Ludlow RF, Mortenson PN, Rees DC. C-H functionalisation tolerant to polar groups could transform fragment-based drug discovery (FBDD). Chem Sci 2021; 12:11976-11985. [PMID: 34667563 PMCID: PMC8457390 DOI: 10.1039/d1sc03563k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 12/28/2022] Open
Abstract
We have analysed 131 fragment-to-lead (F2L) examples targeting a wide variety of protein families published by academic and industrial laboratories between 2015-2019. Our assessment of X-ray structural data identifies the most common polar functional groups involved in fragment-protein binding are: N-H (hydrogen bond donors on aromatic and aliphatic N-H, amides and anilines; totalling 35%), aromatic nitrogen atoms (hydrogen bond acceptors; totalling 23%), and carbonyl oxygen group atoms (hydrogen bond acceptors on amides, ureas and ketones; totalling 22%). Furthermore, the elaboration of each fragment into its corresponding lead is analysed to identify the nominal synthetic growth vectors. In ∼80% of cases, growth originates from an aromatic or aliphatic carbon on the fragment and more than 50% of the total bonds formed are carbon-carbon bonds. This analysis reveals that growth from carbocentric vectors is key and therefore robust C-H functionalisation methods that tolerate the innate polar functionality on fragments could transform fragment-based drug discovery (FBDD). As a further resource to the community, we have provided the full data of our analysis as well as an online overlay page of the X-ray structures of the fragment hit and leads: https://astx.com/interactive/F2L-2021/.
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Affiliation(s)
- Gianni Chessari
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rachel Grainger
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rhian S Holvey
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Paul N Mortenson
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - David C Rees
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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19
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Miah AH, Smith IED, Rackham M, Mares A, Thawani AR, Nagilla R, Haile PA, Votta BJ, Gordon LJ, Watt G, Denyer J, Fisher DT, Dace P, Giffen P, Goncalves A, Churcher I, Scott-Stevens P, Harling JD. Optimization of a Series of RIPK2 PROTACs. J Med Chem 2021; 64:12978-13003. [PMID: 34432979 DOI: 10.1021/acs.jmedchem.1c01118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Receptor-interacting serine/threonine protein kinase 2 (RIPK2) is an important kinase of the innate immune system. Herein, we describe the optimization of a series of RIPK2 PROTACs which recruit members of the inhibitor of apoptosis (IAP) family of E3 ligases. Our PROTAC optimization strategy focused on reducing the lipophilicity of the early lead which resulted in the identification of analogues with improved solubility and increased human and rat microsomal stability. We identified a range of IAP binders that were successfully incorporated into potent RIPK2 PROTACs with attractive pharmacokinetic profiles. Compound 20 possessed the best overall profile with good solubility, potent degradation of RIPK2, and associated inhibition of TNFα release. A proof-of-concept study utilizing a slow release matrix demonstrated the feasibility of a long-acting parenteral formulation with >1 month duration. This represents an attractive alternative dosing paradigm to oral delivery, especially for chronic diseases where compliance can be challenging.
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Affiliation(s)
- Afjal H Miah
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian E D Smith
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Mark Rackham
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alina Mares
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Aditya R Thawani
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rakesh Nagilla
- Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Pamela A Haile
- Innate Immunity Research Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Bartholomew J Votta
- Clinical Biomarkers, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Laurie J Gordon
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gillian Watt
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jane Denyer
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Don T Fisher
- Drug Design and Selection, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Phoebe Dace
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Giffen
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrea Goncalves
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian Churcher
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Scott-Stevens
- Drug Metabolism and Pharmacokinetics, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - John D Harling
- Medicine Design, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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20
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Hamilton C, Fox JP, Longley DB, Higgins CA. Therapeutics Targeting the Core Apoptotic Machinery. Cancers (Basel) 2021; 13:cancers13112618. [PMID: 34073507 PMCID: PMC8198123 DOI: 10.3390/cancers13112618] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/09/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancer develops when the balance between cell death and cell division in tissues is dysregulated. A key focus of cancer drug discovery is identifying therapeutic agents which will selectively kill and eliminate cancer cells from the body. A number of proteins can prevent the death of cancer cells and developing inhibitors against these proteins to promote cancer cell death is a focus of recent drug discovery efforts. This review aims to summarize the key targets being explored, the drug development approaches being adopted, and the success or limitations of agents currently approved or in clinical development. Abstract Therapeutic targeting of the apoptotic pathways for the treatment of cancer is emerging as a valid and exciting approach in anti-cancer therapeutics. Accumulating evidence demonstrates that cancer cells are typically “addicted” to a small number of anti-apoptotic proteins for their survival, and direct targeting of these proteins could provide valuable approaches for directly killing cancer cells. Several approaches and agents are in clinical development targeting either the intrinsic mitochondrial apoptotic pathway or the extrinsic death receptor mediated pathways. In this review, we discuss the main apoptosis pathways and the key molecular targets which are the subject of several drug development approaches, the clinical development of these agents and the emerging resistance factors and combinatorial treatment approaches for this class of agents with existing and emerging novel targeted anti-cancer therapeutics.
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21
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Kannt A, Đikić I. Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chem Biol 2021; 28:1014-1031. [PMID: 33945791 DOI: 10.1016/j.chembiol.2021.04.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Efficacy and selectivity of molecules inducing protein degradation depend on their affinity to the target protein but also on the type of E3 ubiquitin ligase that is recruited to trigger proteasomal degradation. While tremendous progress has been made on the former, the latter-the arsenal of E3 ligases that can be hijacked for targeted protein degradation-is still largely unexplored. Only about 2% of the more than 600 E3 ligases have been utilized to date. Exploiting additional E3 ligases that are, for example, selectively expressed in specific tissues or cells, or regulated under certain conditions, can considerably broaden the applicability of molecular degraders as a therapeutic modality. Here, we provide an overview of major classes of E3 ligases, review the enzymes that have been exploited for induced protein degradation and approaches used to identify or design E3 ligands, and highlight challenges and opportunities for targeting new E3 ligases.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ivan Đikić
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
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22
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Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
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Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
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23
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Knoll G, Ehrenschwender M. The non-peptidomimetic IAP antagonist ASTX660 sensitizes colorectal cancer cells for extrinsic apoptosis. FEBS Open Bio 2021; 11:714-723. [PMID: 33484626 PMCID: PMC7931242 DOI: 10.1002/2211-5463.13096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/13/2021] [Accepted: 01/21/2021] [Indexed: 01/16/2023] Open
Abstract
Apoptosis resistance worsens treatment response in cancer and is associated with poor prognosis. Inhibition of anti-apoptotic proteins can restore cell death and improve treatment efficacy. cIAP1, cIAP2, and XIAP belong to the inhibitor of apoptosis protein (IAP) family and block apoptosis. Targeting IAPs with peptides or peptidomimetics mimicking the IAP-antagonizing activity of the cell's endogenous IAP antagonist SMAC (SMAC mimetics) showed promising results and fueled development of novel compounds. ASTX660 belongs to the recently introduced class of non-peptidomimetic IAP antagonists and successfully completed phase I clinical trials. However, ASTX660 has thus far only been evaluated in few cancer entities. Here, we demonstrate that ASTX660 has cell death-promoting activity in colorectal cancer and provide a head-to-head comparison with birinapant, the clinically most advanced peptidomimetic IAP antagonist. ASTX660 facilitates activation of the extrinsic apoptosis pathway upon stimulation with the death ligands TNF and TRAIL and boosts effector caspase activation and subsequent apoptosis. Mechanistically, ASTX660 enhances amplification of death receptor-generated apoptotic signals in a mitochondria-dependent manner. Failure to activate the mitochondria-associated (intrinsic) apoptosis pathway attenuated the apoptosis-promoting effect of ASTX660. Further clinical studies are warranted to highlight the therapeutic potential of ASTX660 in colorectal cancer.
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Affiliation(s)
- Gertrud Knoll
- Institute of Clinical Microbiology and HygieneUniversity Hospital RegensburgGermany
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24
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Yan P, Lai Q, Li M, Jin X, Wie G, Chen W, Ye L. New Anticancer Agents: Design, Synthesis, Biological Activity, and Molecular Docking of Bicyclic Phloroglucinol Derivatives. ChemistrySelect 2021. [DOI: 10.1002/slct.202004442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Pei Yan
- School of Pharmacy Guangdong Pharmaceutical University Guangzhou 510006 China
| | - Qingfu Lai
- School of Pharmacy Guangdong Pharmaceutical University Guangzhou 510006 China
| | - Ming Li
- School of Life Sciences and Biopharmaceutics Guangdong Pharmaceutical University Guangzhou 510006 China
| | - Xiaobao Jin
- School of Life Sciences and Biopharmaceutics Guangdong Pharmaceutical University Guangzhou 510006 China
- Guangdong Key Laboratory of Pharmaceutical Bioactive Substances Guangdong Pharmaceutical University Guangzhou 510006 China
| | - Gao Wie
- School of Pharmacy Guangdong Pharmaceutical University Guangzhou 510006 China
| | - Weiqiang Chen
- School of Life Sciences and Biopharmaceutics Guangdong Pharmaceutical University Guangzhou 510006 China
| | - Lianbao Ye
- School of Pharmacy Guangdong Pharmaceutical University Guangzhou 510006 China
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25
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Bogaerts J, Atilaw Y, Peintner S, Aerts R, Kihlberg J, Johannessen C, Erdélyi M. Employing complementary spectroscopies to study the conformations of an epimeric pair of side-chain stapled peptides in aqueous solution. RSC Adv 2021; 11:4200-4208. [PMID: 35424346 PMCID: PMC8694311 DOI: 10.1039/d0ra10167b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding the conformational preferences of free ligands in solution is often necessary to rationalize structure-activity relationships in drug discovery. Herein, we examine the conformational behavior of an epimeric pair of side-chain stapled peptides that inhibit the FAD dependent amine oxidase lysine specific demethylase 1 (LSD1). The peptides differ only at a single stereocenter, but display a major difference in binding affinity. Their Raman optical activity (ROA) spectra are most likely dominated by the C-terminus, obscuring the analysis of the epimeric macrocycle. By employing NMR spectroscopy, we show a difference in conformational behavior between the two compounds and that the LSD1 bound conformation of the most potent compound is present to a measurable extent in aqueous solution. In addition, we illustrate that Molecular Dynamics (MD) simulations produce ensembles that include the most important solution conformations, but that it remains problematic to identify relevant conformations with no a priori knowledge from the large conformational pool. Furthermore, this work highlights the importance of understanding the scope and limitations of the available techniques for conducting conformational analyses. It also emphasizes the importance of conformational selection of a flexible ligand in molecular recognition.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | - Roy Aerts
- Department of Chemistry, University of Antwerp 2020 Antwerp Belgium
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University SE-751 23 Uppsala Sweden
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26
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Schiemer J, Horst R, Meng Y, Montgomery JI, Xu Y, Feng X, Borzilleri K, Uccello DP, Leverett C, Brown S, Che Y, Brown MF, Hayward MM, Gilbert AM, Noe MC, Calabrese MF. Snapshots and ensembles of BTK and cIAP1 protein degrader ternary complexes. Nat Chem Biol 2020; 17:152-160. [PMID: 33199914 DOI: 10.1038/s41589-020-00686-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/30/2020] [Indexed: 02/05/2023]
Abstract
Heterobifunctional chimeric degraders are a class of ligands that recruit target proteins to E3 ubiquitin ligases to drive compound-dependent protein degradation. Advancing from initial chemical tools, protein degraders represent a mechanism of growing interest in drug discovery. Critical to the mechanism of action is the formation of a ternary complex between the target, degrader and E3 ligase to promote ubiquitination and subsequent degradation. However, limited insights into ternary complex structures exist, including a near absence of studies on one of the most widely co-opted E3s, cellular inhibitor of apoptosis 1 (cIAP1). In this work, we use a combination of biochemical, biophysical and structural studies to characterize degrader-mediated ternary complexes of Bruton's tyrosine kinase and cIAP1. Our results reveal new insights from unique ternary complex structures and show that increased ternary complex stability or rigidity need not always correlate with increased degradation efficiency.
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Affiliation(s)
- James Schiemer
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Reto Horst
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Yilin Meng
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Justin I Montgomery
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Yingrong Xu
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Xidong Feng
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Kris Borzilleri
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Daniel P Uccello
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Carolyn Leverett
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Stephen Brown
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Ye Che
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew F Brown
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew M Hayward
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Mark C Noe
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew F Calabrese
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA.
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27
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XIAP's Profile in Human Cancer. Biomolecules 2020; 10:biom10111493. [PMID: 33138314 PMCID: PMC7692959 DOI: 10.3390/biom10111493] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/17/2022] Open
Abstract
XIAP, the X-linked inhibitor of apoptosis protein, regulates cell death signaling pathways through binding and inhibiting caspases. Mounting experimental research associated with XIAP has shown it to be a master regulator of cell death not only in apoptosis, but also in autophagy and necroptosis. As a vital decider on cell survival, XIAP is involved in the regulation of cancer initiation, promotion and progression. XIAP up-regulation occurs in many human diseases, resulting in a series of undesired effects such as raising the cellular tolerance to genetic lesions, inflammation and cytotoxicity. Hence, anti-tumor drugs targeting XIAP have become an important focus for cancer therapy research. RNA-XIAP interaction is a focus, which has enriched the general profile of XIAP regulation in human cancer. In this review, the basic functions of XIAP, its regulatory role in cancer, anti-XIAP drugs and recent findings about RNA-XIAP interactions are discussed.
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28
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Udvarhelyi A, Rodde S, Wilcken R. ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules. J Comput Aided Mol Des 2020; 35:399-415. [PMID: 32803515 DOI: 10.1007/s10822-020-00337-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022]
Abstract
Conformational equilibria are at the heart of drug design, yet their energetic description is often hampered by the insufficient accuracy of low-cost methods. Here we present a flexible and semi-automatic workflow based on quantum chemistry, ReSCoSS, designed to identify relevant conformers and predict their equilibria across different solvent environments in the Conductor-like Screening Model for Real Solvents (COSMO-RS) framework. We demonstrate the utility and accuracy of the workflow through conformational case studies on several drug-like molecules from literature where relevant conformations are known. We further show that including ReSCoSS conformers significantly improves COSMO-RS based predictions of physicochemical properties over single-conformation approaches. ReSCoSS has found broad adoption in the in-house drug discovery and development work streams and has contributed to establishing quantum-chemistry methods as a strategic pillar in ligand discovery.
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Affiliation(s)
- Anikó Udvarhelyi
- Technical Research and Development, Novartis Pharma AG, 4002, Basel, Switzerland.
| | - Stephane Rodde
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 4002, Basel, Switzerland
| | - Rainer Wilcken
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 4002, Basel, Switzerland.
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29
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Mamriev D, Abbas R, Klingler FM, Kagan J, Kfir N, Donald A, Weidenfeld K, Sheppard DW, Barkan D, Larisch S. A small-molecule ARTS mimetic promotes apoptosis through degradation of both XIAP and Bcl-2. Cell Death Dis 2020; 11:483. [PMID: 32587235 PMCID: PMC7316745 DOI: 10.1038/s41419-020-2670-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Many human cancers over-express B cell lymphoma 2 (Bcl-2) or X-linked inhibitor of apoptosis (IAP) proteins to evade cell death. The pro-apoptotic ARTS (Sept4_i2) protein binds directly to both Bcl-2 and XIAP and promotes apoptosis by stimulating their degradation via the ubiquitin-proteasome system (UPS). Here we describe a small molecule, A4, that mimics the function of ARTS. Microscale thermophoresis assays showed that A4 binds XIAP, but not cellular inhibitor of apoptosis protein 1 (cIAP1). A4 binds to a distinct ARTS binding pocket in the XIAP-BIR3 (baculoviral IAP repeat 3) domain. Like ARTS, A4 stimulated poly-ubiquitylation and UPS-mediated degradation of XIAP and Bcl-2, but not cIAP1, resulting in caspase-9 and -3 activation and apoptosis. In addition, over-expression of XIAP rescued HeLa cells from A4-induced apoptosis, consistent with the idea that A4 kills by antagonizing XIAP. On the other hand, treatment with the SMAC-mimetic Birinapant induced secretion of tumour necrosis factor-α (TNFα) and killed ~50% of SKOV-3 cells, and addition of A4 to Birinapant-treated cells significantly reduced secretion of TNFα and blocked Birinapant-induced apoptosis. This suggests that A4 acts by specifically targeting XIAP. The effect of A4 was selective as peripheral blood mononuclear cells and normal human breast epithelial cells were unaffected. Furthermore, proteome analysis revealed that cancer cell lines with high levels of XIAP were particularly sensitive to the killing effect of A4. These results provide proof of concept that the ARTS binding site in XIAP is "druggable". A4 represents a novel class of dual-targeting compounds stimulating apoptosis by UPS-mediated degradation of important anti-apoptotic oncogenes.
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Affiliation(s)
- Dana Mamriev
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel.,The Laboratory of Tumor Dormancy and Metastasis, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel
| | - Ruqaia Abbas
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel
| | | | - Juliana Kagan
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel
| | - Nir Kfir
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel
| | | | - Keren Weidenfeld
- The Laboratory of Tumor Dormancy and Metastasis, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel
| | | | - Dalit Barkan
- The Laboratory of Tumor Dormancy and Metastasis, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel
| | - Sarit Larisch
- Cell Death and Cancer Research Laboratory, Department of Human Biology and Medical Sciences, University of Haifa, Haifa, 31905, Israel.
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30
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Blaquiere N, Villemure E, Staben ST. Medicinal Chemistry of Inhibiting RING-Type E3 Ubiquitin Ligases. J Med Chem 2020; 63:7957-7985. [PMID: 32142281 DOI: 10.1021/acs.jmedchem.9b01451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The ubiquitin proteasome system (UPS) presents many opportunities for pharmacological intervention. Key players in the UPS are E3 ubiquitin ligases, responsible for conjugation of ubiquitin to specific cognate substrates. Numbering more than 600 members, these ligases represent the most selective way to intervene within this physiologically important system. This Perspective highlights some of the dedicated medicinal chemistry efforts directed at inhibiting the function of specific single-protein and multicomponent RING-type E3 ubiquitin ligases. We present opportunities and challenges associated with targeting this important class of enzymes.
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Affiliation(s)
- Nicole Blaquiere
- Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Elisia Villemure
- Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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31
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Bugera MY, Tarasenko KV, Kondratov IS, Gerus II, Vashchenko BV, Ivasyshyn VE, Grygorenko OO. (Het)aryl Difluoromethyl-Substituted β-Alkoxyenones: Synthesis and Heterocyclizations. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Maksym Ya. Bugera
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry; NAS of Ukraine; Murmanska Street 1 02660 Kyiv Ukraine
| | - Karen V. Tarasenko
- V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry; NAS of Ukraine; Murmanska Street 1 02660 Kyiv Ukraine
- Chemspace; Ilukstes iela 38-5 1082 Riga Latvia
| | - Ivan S. Kondratov
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry; NAS of Ukraine; Murmanska Street 1 02660 Kyiv Ukraine
| | - Igor I. Gerus
- V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry; NAS of Ukraine; Murmanska Street 1 02660 Kyiv Ukraine
| | - Bohdan V. Vashchenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
| | - Viktor E. Ivasyshyn
- V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry; NAS of Ukraine; Murmanska Street 1 02660 Kyiv Ukraine
| | - Oleksandr O. Grygorenko
- Enamine Ltd.; Chervonotkatska Street 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Volodymyrska Street 60 01601 Kyiv Ukraine
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32
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Erlanson DA, de Esch IJP, Jahnke W, Johnson CN, Mortenson PN. Fragment-to-Lead Medicinal Chemistry Publications in 2018. J Med Chem 2020; 63:4430-4444. [PMID: 31913033 DOI: 10.1021/acs.jmedchem.9b01581] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This Perspective, the fourth in an annual series, summarizes fragment-to-lead (F2L) success stories published during 2018. Topics such as target class, screening methods, physicochemical properties, and ligand efficiency are discussed for the 2018 examples as well as for the combined 111 F2L examples covering 2015-2018. While the overall properties of fragments and leads have remained constant, a number of new trends are noted, for example, broadening of target class coverage and application of FBDD to covalent inhibitors. Moreover, several studies make use of fragment hits that were previously described in the literature, illustrating that fragments are versatile starting points that can be optimized to structurally diverse leads. By focusing on success stories, the hope is that this Perspective will identify and inform best practices in fragment-based drug discovery.
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Affiliation(s)
- Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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33
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Mita MM, LoRusso PM, Papadopoulos KP, Gordon MS, Mita AC, Ferraldeschi R, Keer H, Oganesian A, Su XY, Jueliger S, Tolcher AW. A Phase I Study of ASTX660, an Antagonist of Inhibitors of Apoptosis Proteins, in Adults with Advanced Cancers or Lymphoma. Clin Cancer Res 2020; 26:2819-2826. [DOI: 10.1158/1078-0432.ccr-19-1430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022]
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34
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Thakur A, Singh A, Kaur N, Ojha R, Nepali K. Steering the antitumor drug discovery campaign towards structurally diverse indolines. Bioorg Chem 2020; 94:103436. [DOI: 10.1016/j.bioorg.2019.103436] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 12/13/2022]
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35
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Dewis L, Crouch R, Russell D, Butts C. Improving the accuracy of 1 H- 19 F internuclear distance measurement using 2D 1 H- 19 F HOESY. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:1143-1149. [PMID: 31237710 DOI: 10.1002/mrc.4904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
With the rise in fluorinated pharmaceuticals, it is becoming increasingly important to develop new 19 F NMR-based methods to assist in their analysis. Crucially, obtaining information regarding the conformational dynamics of a molecule in solution can aid the design of strongly binding therapeutics. Herein, we report the development of a 2D 1 H-19 F Heteronuclear Overhauser Spectroscopy (HOESY) experiment to measure 1 H-19 F internuclear distances, with accuracies of ~5% when compared with 1 H-19 F internuclear distances calculated by quantum chemical methods. We demonstrate that correcting for cross-relaxation of 1 H, using the diagonal peaks from the 2D 1 H-1 H Nuclear Overhauser Enhancement Spectroscopy (NOESY), is critical in obtaining accurate values for 1 H-19 F internuclear distances. Finally, we show that by using the proposed method to measure 1 H-19 F internuclear distances, we are able to determine the relative stereochemistry of two fluorinated pharmaceuticals.
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Affiliation(s)
- Lydia Dewis
- Genentech Inc, South San Francisco, CA, USA
- School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Craig Butts
- School of Chemistry, University of Bristol, Bristol, UK
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36
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Targeted protein degradation: expanding the toolbox. Nat Rev Drug Discov 2019; 18:949-963. [PMID: 31666732 DOI: 10.1038/s41573-019-0047-y] [Citation(s) in RCA: 471] [Impact Index Per Article: 94.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/19/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) and related molecules that induce targeted protein degradation by the ubiquitin-proteasome system represent a new therapeutic modality and are the focus of great interest, owing to potential advantages over traditional occupancy-based inhibitors with respect to dosing, side effects, drug resistance and modulating 'undruggable' targets. However, the technology is still maturing, and the design elements for successful PROTAC-based drugs are currently being elucidated. Importantly, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been exploited for targeted protein degradation, and expansion of knowledge in this area is a key opportunity. Here, we briefly discuss lessons learned about targeted protein degradation in chemical biology and drug discovery and systematically review the expression profile, domain architecture and chemical tractability of human E3 ligases that could expand the toolbox for PROTAC discovery.
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37
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Taheri S, Nazifi M, Mansourian M, Hosseinzadeh L, Shokoohinia Y. Ugi efficient synthesis, biological evaluation and molecular docking of coumarin-quinoline hybrids as apoptotic agents through mitochondria-related pathways. Bioorg Chem 2019; 91:103147. [DOI: 10.1016/j.bioorg.2019.103147] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022]
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38
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XIAP as a Target of New Small Organic Natural Molecules Inducing Human Cancer Cell Death. Cancers (Basel) 2019; 11:cancers11091336. [PMID: 31505859 PMCID: PMC6770071 DOI: 10.3390/cancers11091336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) is an emerging crucial therapeutic target in cancer. We report on the discovery and characterisation of small organic molecules from Piper genus plants exhibiting XIAP antagonism, namely erioquinol, a quinol substituted in the 4-position with an alkenyl group and the alkenylphenols eriopodols A–C. Another isolated compound was originally identified as gibbilimbol B. Erioquinol was the most potent inhibitor of human cancer cell viability when compared with gibbilimbol B and eriopodol A was listed as intermediate. Gibbilimbol B and eriopodol A induced apoptosis through mitochondrial permeabilisation and caspase activation while erioquinol acted on cell fate via caspase-independent/non-apoptotic mechanisms, likely involving mitochondrial dysfunctions and aberrant generation of reactive oxygen species. In silico modelling and molecular approaches suggested that all molecules inhibit XIAP by binding to XIAP-baculoviral IAP repeat domain. This demonstrates a novel aspect of XIAP as a key determinant of tumour control, at the molecular crossroad of caspase-dependent/independent cell death pathway and indicates molecular aspects to develop tumour-effective XIAP antagonists.
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39
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Jarvis A, Ouvry G. Essential ingredients for rational drug design. Bioorg Med Chem Lett 2019; 29:126674. [PMID: 31521476 DOI: 10.1016/j.bmcl.2019.126674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023]
Abstract
This short review focuses on three aspects of rational drug design that we consider of utmost importance: the conformation of small molecules in solid form, the conformation of small molecules in solution and lesser studied interactions in protein-ligand complexes. Using examples from recent literature, we will illustrate these different aspects and how they have contributed to the discovery of potent modulators.
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Affiliation(s)
- Ashley Jarvis
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.
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40
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Polykretis P, Luchinat E, Bonucci A, Giachetti A, Graewert MA, Svergun DI, Banci L. Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach. IUCRJ 2019; 6:948-957. [PMID: 31576227 PMCID: PMC6760453 DOI: 10.1107/s205225251901073x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
The X-chromosome-linked inhibitor of apoptosis protein (XIAP) is a multidomain protein whose main function is to block apoptosis by caspase inhibition. XIAP is also involved in other signalling pathways, including NF-κB activation and copper homeostasis. XIAP is overexpressed in tumours, potentiating cell survival and resistance to chemotherapeutics, and has therefore become an important target for the treatment of malignancy. Despite the fact that the structure of each single domain is known, the conformation of the full-length protein has never been determined. Here, the first structural model of the full-length XIAP dimer, determined by an integrated approach using nuclear magnetic resonance, small-angle X-ray scattering and electron paramagnetic resonance data, is presented. It is shown that XIAP adopts a compact and relatively rigid conformation, implying that the spatial arrangement of its domains must be taken into account when studying the interactions with its physiological partners and in developing effective inhibitors.
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Affiliation(s)
- Panagis Polykretis
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Luchinat
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences ‘Mario Serio’, University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Alessio Bonucci
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Andrea Giachetti
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Melissa A. Graewert
- EMBL, Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitri I. Svergun
- EMBL, Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lucia Banci
- CERM – Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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41
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Investigation of Hot Spot Region in XIAP Inhibitor Binding Site by Fragment Molecular Orbital Method. Comput Struct Biotechnol J 2019; 17:1217-1225. [PMID: 31673305 PMCID: PMC6816037 DOI: 10.1016/j.csbj.2019.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 11/23/2022] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) is an important regulator of cancer cell survival whose BIR3 domain (XIAP-BIR3) recognizes the Smac N-terminal tetrapeptide sequence (AVPI), making it an attractive protein-protein interaction (PPI) target for cancer therapies. We used the fragment molecular orbital (FMO) method to study the binding modes and affinities between XIAP-BIR3 and a series of its inhibitors (1–8) that mimic the AVPI binding motif; the inhibitors had common interactions with key residues in a hot spot region of XIAP-BIR3 (P1–P4 subpockets) with increased binding affinity mainly attributed to specific interactions with the P1 and P4 subpockets. Based on the structural information from FMO results, we proposed a novel XIAP natural product inhibitor, neoeriocitrin 10, which was derived from our preciously reported XIAP-BIR3 inhibitor 9, can be used as a highly potent candidate for XIAP-BIR3 inhibition. We also performed pair interaction energy decomposition analysis to investigate the binding energies between specific binding residues and individual ligands, showing that the novel natural product neoeriocitrin 10 had a higher binding affinity than epicatechin gallate 9. Molecular docking and dynamics simulations were performed to explore the mode of binding between 10 and XIAP-BIR3, demonstrating that 10 binds more strongly to the P1 and P4 pockets than 9. Overall, we present a novel natural product, neoeriocitrin 10, and demonstrate that the FMO method can be used to identify hot spots in PPIs and design new compounds for XIAP inhibition.
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42
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Chen J, Chen X, Chen X, Sun H, Yang D. SM‑164 enhances the antitumor activity of adriamycin in human U2‑OS cells via downregulation of X‑linked inhibitor of apoptosis protein. Mol Med Rep 2019; 19:5079-5086. [PMID: 31059038 PMCID: PMC6522877 DOI: 10.3892/mmr.2019.10181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 02/28/2019] [Indexed: 11/05/2022] Open
Abstract
The antitumor effects of SM‑164 and adriamycin (ADM) on human osteosarcoma U2‑OS cells, the underlying mechanism are yet to be investigated. In the present study, U2‑OS cells were divided into control, ADM, SM‑164, and ADM + SM‑164 groups. In addition, cells treated with both SM‑164 and ADM were further divided into three subgroups: SM‑164 + ADM, SM‑164 + ADM + vector and SM‑164 + ADM + X‑linked inhibitor of apoptosis protein (XIAP) silencing groups. XIAP expression was achieved via transfection with shRNA lentiviral vectors. Reverse transcription‑quantitative polymerase chain reaction and western blotting were used to detect the expression of caspases‑7, ‑9, and ‑3, poly ADP‑ribose polymerase (PARP), XIAP, cellular inhibitor of apoptosis protein‑1 (cIAP‑1) and survivin. Cell viability and apoptosis were evaluated using MTT and flow cytometry assays, respectively. Compared with the control group, cell viability decreased, while apoptosis was increased in the ADM and SM‑164‑treatment group. ADM and SM‑164 treatment promoted the expression of caspases‑7, ‑9 and ‑3, and PARP, but reduced the expression of XIAP, survivin and cIAP‑1. Compared with ADM + SM‑164 group, XIAP silencing with ADM + SM‑164 treatment further reduced cell viability, promoted apoptosis, increased caspase‑7, ‑9 and ‑3, and PARP expression; however the expression of survivin and cIAP‑1 were reduced. Combined ADM and SM‑164 treatment may be considered as potential therapeutic agent in the treatment of osteosarcoma, possibly via reductions XIAP expression.
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Affiliation(s)
- Jiangwei Chen
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xuanyin Chen
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xiaodong Chen
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Haiying Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangxi 210009, P.R. China
| | - Dong Yang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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Heightman TD, Callahan JF, Chiarparin E, Coyle JE, Griffiths-Jones C, Lakdawala AS, McMenamin R, Mortenson PN, Norton D, Peakman TM, Rich SJ, Richardson C, Rumsey WL, Sanchez Y, Saxty G, Willems HMG, Wolfe L, Woolford AJA, Wu Z, Yan H, Kerns JK, Davies TG. Structure–Activity and Structure–Conformation Relationships of Aryl Propionic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1/Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1/NRF2) Protein–Protein Interaction. J Med Chem 2019; 62:4683-4702. [DOI: 10.1021/acs.jmedchem.9b00279] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - James F. Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Ami S. Lakdawala
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Rachel McMenamin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Paul N. Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Torren M. Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J. Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William L. Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hongxing Yan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Jeffrey K. Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G. Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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44
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Clinical candidates modulating protein-protein interactions: The fragment-based experience. Eur J Med Chem 2019; 167:76-95. [DOI: 10.1016/j.ejmech.2019.01.084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/23/2022]
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45
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Grainger R, Heightman TD, Ley SV, Lima F, Johnson CN. Enabling synthesis in fragment-based drug discovery by reactivity mapping: photoredox-mediated cross-dehydrogenative heteroarylation of cyclic amines. Chem Sci 2019; 10:2264-2271. [PMID: 30881651 PMCID: PMC6385880 DOI: 10.1039/c8sc04789h] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
In fragment-based drug discovery (FBDD), a weakly binding fragment hit is elaborated into a potent ligand by bespoke functionalization along specific directions (growth vectors) from the fragment core in order to complement the 3D structure of the target protein. This structure-based design approach can present significant synthetic challenges, as growth vectors often originate on sp2 or sp3 ring carbons which are not the most synthetically accessible points on the fragment. To address this issue and expedite synthesis in FBDD, we established a nanogram-to-gram workflow for the development of enabling synthetic transformations, such as the direct C-H functionalization of heterocycles. This novel approach deploys high-throughput experimentation (HTE) in 1536-well microtiter plates (MTPs) facilitated by liquid handling robots to screen reaction conditions on the nanomolar scale; subsequently the reaction is upscaled in a continuous flow to generate gram-quantities of the material. In this paper, we disclose the use of this powerful workflow for the development of a photoredox-mediated cross-dehydrogenative coupling of fragments and medicinally relevant heterocyclic precursors via Minisci-type addition of α-amino radicals to electron-deficient heteroarenes. The optimized reaction conditions were employed on the milligram-scale on a diverse set of 112 substrates to map out structure-reactivity relationships (SRRs) of the transformation. The coupling exhibits excellent tolerance to a variety of functional groups and N-rich heteroarenes relevant to FBDD and was upscaled in a continuous flow to afford gram-quantities of pharmaceutically relevant sp2-sp3 privileged architectures.
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Affiliation(s)
- Rachel Grainger
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
| | - Steven V Ley
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Fabio Lima
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
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46
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Arshad F, Khan MF, Akhtar W, Alam MM, Nainwal LM, Kaushik SK, Akhter M, Parvez S, Hasan SM, Shaquiquzzaman M. Revealing quinquennial anticancer journey of morpholine: A SAR based review. Eur J Med Chem 2019; 167:324-356. [PMID: 30776694 DOI: 10.1016/j.ejmech.2019.02.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 02/07/2023]
Abstract
Morpholine, a six-membered heterocycle containing one nitrogen and one oxygen atom, is a moiety of great significance. It forms an important intermediate in many industrial and organic syntheses. Morpholine containing drugs are of high therapeutic value. Its wide array of pharmacological activity includes anti-diabetic, anti-emetic, growth stimulant, anti-depressant, bronchodilator and anticancer. Multi-drug resistance in cancer cases have emerged in the last few years and have led to the failure of many chemotherapeutic drugs. Newer treatment methods and drugs are being developed to overcome this problem. Target based drug discovery is an effective method to develop novel anticancer drugs. To develop newer drugs, previously reported work needs to be studied. Keeping this in mind, last five year's literature on morpholine used as anticancer agents has been reviewed and summarized in the paper herein.
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Affiliation(s)
- Fatima Arshad
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohemmed Faraz Khan
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Wasim Akhtar
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohammad Mumtaz Alam
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Lalit Mohan Nainwal
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Sumit Kumar Kaushik
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mymoona Akhter
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | | | - Mohammad Shaquiquzzaman
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
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47
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Cong H, Xu L, Wu Y, Qu Z, Bian T, Zhang W, Xing C, Zhuang C. Inhibitor of Apoptosis Protein (IAP) Antagonists in Anticancer Agent Discovery: Current Status and Perspectives. J Med Chem 2019; 62:5750-5772. [DOI: 10.1021/acs.jmedchem.8b01668] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hui Cong
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Lijuan Xu
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Yougen Wu
- College of Tropical Agriculture and Forestry, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Department of Medicinal Chemistry, University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Zhuo Qu
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
| | - Tengfei Bian
- Department of Medicinal Chemistry, University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Wannian Zhang
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Chengguo Xing
- Department of Medicinal Chemistry, University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Chunlin Zhuang
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
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48
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Experimental free ligand conformations: a missing link in structure-based drug discovery. Future Med Chem 2019; 11:79-82. [PMID: 30648432 DOI: 10.4155/fmc-2018-0339] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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49
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From Discovery to Bedside: Targeting the Ubiquitin System. Cell Chem Biol 2018; 26:156-177. [PMID: 30554913 DOI: 10.1016/j.chembiol.2018.10.022] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/21/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022]
Abstract
The ubiquitin/proteasome system is a primary conduit for selective intracellular protein degradation. Since its discovery over 30 years ago, this highly regulated system continues to be an active research area for drug discovery that is exemplified by several approved drugs. Here we review compounds in preclinical testing, clinical trials, and approved drugs, with the aim of highlighting innovative discoveries and breakthrough therapies that target the ubiquitin system.
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50
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Biological Potential and Mechanism of Prodigiosin from Serratia marcescens Subsp. lawsoniana in Human Choriocarcinoma and Prostate Cancer Cell Lines. Int J Mol Sci 2018; 19:ijms19113465. [PMID: 30400387 PMCID: PMC6274741 DOI: 10.3390/ijms19113465] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/11/2022] Open
Abstract
Tripyrrole molecules have received renewed attention due to reports of numerous biological activities, including antifungal, antibacterial, antiprotozoal, antimalarial, immunosuppressive, and anticancer activities. In a screen of bacterial strains with known toxicities to termites, a red pigment-producing strain, HDZK-BYSB107, was isolated from Chamaecyparis lawsoniana, which grows in Oregon, USA. Strain HDZK-BYSB107 was identified as Serratia marcescens subsp. lawsoniana. The red pigment was identified as prodigiosin using ultraviolet absorption, LC-MS, and 1H-NMR spectroscopy. The bacterial prodigiosin had an inhibitory effect on both Gram-negative and Gram-positive bacteria. The main objective of this study was to explore the anticancer activities and mechanism of strain HDZK-BYSB107 prodigiosin by using human choriocarcinoma (JEG3) and prostate cancer cell lines (PC3) in vitro and JEG3 and PC3 tumor-bearing nude mice in vivo. In vitro anticancer activities showed that the bacterial prodigiosin induced apoptosis in JEG3 cells. In vivo anticancer activities indicated that the prodigiosin significantly inhibited the growth of JEG3 and PC3 cells, and the inhibitory activity was dose and time dependent. The anticancer efficacy of the bacterial prodigiosin on JEG3 and PC3 cells, JEG3 and PC3 tumor exhibited a correlation with the down regulation of the inhibitor of IAP family, including XIAP, cIAP-1 and cIAP-2, and the activation of caspase-9 and caspase-3 accompanied by proteolytic degradation of poly (ADP-ribose)-polymerase. The expressions of P53 and Bax/Bcl-2 in JEG3 and PC3 cells were significantly higher than in untreated groups. Our results indicated that the bacterial prodigiosin extracted from C. lawsoniana is a promising molecule due to its potential for therapeutic applications.
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