231 results on '"Fesik SW"'
Search Results
2. Expanded profiling of WD repeat domain 5 inhibitors reveals actionable strategies for the treatment of hematologic malignancies.
- Author
-
Meyer CT, Smith BN, Wang J, Teuscher KB, Grieb BC, Howard GC, Silver AJ, Lorey SL, Stott GM, Moore WJ, Lee T, Savona MR, Weissmiller AM, Liu Q, Quaranta V, Fesik SW, and Tansey WP
- Subjects
- Humans, Animals, Mice, Cell Line, Tumor, Sulfonamides pharmacology, Sulfonamides therapeutic use, Antineoplastic Agents pharmacology, Antineoplastic Agents therapeutic use, Tumor Suppressor Protein p53 metabolism, Tumor Suppressor Protein p53 genetics, Bridged Bicyclo Compounds, Heterocyclic pharmacology, Bridged Bicyclo Compounds, Heterocyclic therapeutic use, Hematologic Neoplasms drug therapy, Hematologic Neoplasms genetics, Hematologic Neoplasms metabolism, Xenograft Model Antitumor Assays
- Abstract
WD40 Repeat Domain 5 (WDR5) is a highly conserved nuclear protein that recruits MYC oncoprotein transcription factors to chromatin to stimulate ribosomal protein gene expression. WDR5 is tethered to chromatin via an arginine-binding cavity known as the "WIN" site. Multiple pharmacological inhibitors of the WDR5-interaction site of WDR5 (WINi) have been described, including those with picomolar affinity and oral bioavailability in mice. Thus far, however, WINi have only been shown to be effective against a number of rare cancer types retaining wild-type p53. To explore the full potential of WINi for cancer therapy, we systematically profiled WINi across a panel of cancer cells, alone and in combination with other agents. We report that WINi are unexpectedly active against cells derived from both solid and blood-borne cancers, including those with mutant p53. Among hematologic malignancies, we find that WINi are effective as a single agent against leukemia and diffuse large B cell lymphoma xenograft models, and can be combined with the approved drug venetoclax to suppress disseminated acute myeloid leukemia in vivo. These studies reveal actionable strategies for the application of WINi to treat blood-borne cancers and forecast expanded utility of WINi against other cancer types., Competing Interests: Competing interests statement:Fesik, S. W., Stauffer, S. R., Salovich, J. M., Tansey, W. P., Wang, F., Phan, J., Olejniczak, E. T., inventors. WDR5 inhibitors and modulators. United States Patent US 10,501,466. 10 December 2019. Fesik, S. W., Stauffer, S. R., Tansey, W. P., Olejniczak, E. T., Phan, J., Wang, F., Jeon, K., Gogliotti, R. D., inventors. WDR5 inhibitors and modulators. United States Patent US 10,160,763. 25 December 2018. Lee. T.; Alvarado, J.; Tian, J.; Meyers, K. M.; Han, C.; Mills, J. J.; Teuscher, K. B.; Fesik, S. W. WDR5 inhibitors and modulators. WO 2020086857. 30 April 2020. Lee. T.; Han, C.; Mills, J. J.; Teuscher, K. B.; Tian, J.; Meyers, K. M.; Chowdhury, S.; Fesik, S. W. WDR5 inhibitors and modulators. WO 2020247679. 10 December 2020. Lee. T.; Teuscher, K. B.; Tian, J.; Meyers, K. M.; Chowdhury, S.; Fesik, S. W. WDR5 Inhibitors and modulators. WO 2021092525. 14 May 2021. Lee. T.; Teuscher, K. B.; Chowdhury, S.; Tian, J.; Meyers, K. M.; Fesik, S. W. WDR5 Inhibitors and modulators. WO2022236101. 10 November 2022. C.T.M. and V.Q. are co-founders of Duet BioSystems. M.R.S. has stock in Karyopharm and Ryvu; serves on advisory boards or consults for BMS, CTI, Forma, Geron, GSK, Karyopharm, Rigel, Ryvu, Taiho and Treadwell. All other authors declare no competing interest.
- Published
- 2024
- Full Text
- View/download PDF
3. Discovery of a Myeloid Cell Leukemia 1 (Mcl-1) Inhibitor That Demonstrates Potent In Vivo Activities in Mouse Models of Hematological and Solid Tumors.
- Author
-
Tarr JC, Salovich JM, Aichinger M, Jeon K, Veerasamy N, Sensintaffar JL, Arnhof H, Samwer M, Christov PP, Kim K, Wunberg T, Schweifer N, Trapani F, Arnold A, Martin F, Zhao B, Miriyala N, Sgubin D, Fogarty S, Moore WJ, Stott GM, Olejniczak ET, Engelhardt H, Rudolph D, Lee T, McConnell DB, and Fesik SW
- Subjects
- Animals, Humans, Mice, Cell Line, Tumor, Dogs, Structure-Activity Relationship, Female, Drug Discovery, Taxoids pharmacology, Taxoids pharmacokinetics, Taxoids therapeutic use, Taxoids chemistry, Docetaxel pharmacology, Docetaxel therapeutic use, Docetaxel pharmacokinetics, Docetaxel chemistry, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Antineoplastic Agents pharmacology, Antineoplastic Agents pharmacokinetics, Antineoplastic Agents therapeutic use, Antineoplastic Agents chemical synthesis, Antineoplastic Agents chemistry, Xenograft Model Antitumor Assays
- Abstract
Myeloid cell leukemia 1 (Mcl-1) is a key regulator of the intrinsic apoptosis pathway. Overexpression of Mcl-1 is correlated with high tumor grade, poor survival, and both intrinsic and acquired resistance to cancer therapies. Herein, we disclose the structure-guided design of a small molecule Mcl-1 inhibitor, compound 26 , that binds to Mcl-1 with subnanomolar affinity, inhibits growth in cell culture assays, and possesses low clearance in mouse and dog pharmacokinetic (PK) experiments. Evaluation of 26 as a single agent in Mcl-1 sensitive hematological and solid tumor xenograft models resulted in regressions. Co-treatment of Mcl-1-sensitive and Mcl-1 insensitive lung cancer derived xenografts with 26 and docetaxel or topotecan, respectively, resulted in an enhanced tumor response. These findings support the premise that pro-apoptotic priming of tumor cells by other therapies in combination with Mcl-1 inhibition may significantly expand the subset of cancers in which Mcl-1 inhibitors may prove beneficial.
- Published
- 2024
- Full Text
- View/download PDF
4. Fragment-Based Screen of SARS-CoV-2 Papain-like Protease (PL pro ).
- Author
-
Taylor AJ, Amporndanai K, Rietz TA, Zhao B, Thiruvaipati A, Wei Q, South TM, Crow MM, Apakama C, Sensintaffar JL, Phan J, Lee T, and Fesik SW
- Abstract
Coronaviruses have been responsible for numerous viral outbreaks in the past two decades due to the high transmission rate of this family of viruses. The deadliest outbreak is the recent Covid-19 pandemic, which resulted in over 7 million deaths worldwide. SARS-CoV-2 papain-like protease (PL
Pro ) plays a key role in both viral replication and host immune suppression and is highly conserved across the coronavirus family, making it an ideal drug target. Herein we describe a fragment-based screen against PLPro using protein-observed NMR experiments, identifying 77 hit fragments. Analyses of NMR perturbation patterns and X-ray cocrystallized structures reveal fragments bind to two distinct regions of the protein. Importantly none of the fragments identified belong to the same chemical class as the few reported inhibitors, allowing for the discovery of a novel class of PLPro inhibitors., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)- Published
- 2024
- Full Text
- View/download PDF
5. Ribosome subunit attrition and activation of the p53-MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition.
- Author
-
Howard GC, Wang J, Rose KL, Jones C, Patel P, Tsui T, Florian AC, Vlach L, Lorey SL, Grieb BC, Smith BN, Slota MJ, Reynolds EM, Goswami S, Savona MR, Mason FM, Lee T, Fesik SW, Liu Q, and Tansey WP
- Abstract
The chromatin-associated protein WD Repeat Domain 5 (WDR5) is a promising target for cancer drug discovery, with most efforts blocking an arginine-binding cavity on the protein called the "WIN" site that tethers WDR5 to chromatin. WIN site inhibitors (WINi) are active against multiple cancer cell types in vitro, the most notable of which are those derived from MLL-rearranged (MLLr) leukemias. Peptidomimetic WINi were originally proposed to inhibit MLLr cells via dysregulation of genes connected to hematopoietic stem cell expansion. Our discovery and interrogation of small molecule WIN site inhibitors, however, revealed that they act in MLLr cell lines to suppress ribosome protein gene (RPG) transcription, induce nucleolar stress, and activate p53. Because there is no precedent for an anti-cancer strategy that specifically targets RPG expression, we took an integrated multi-omics approach to further interrogate the mechanism of action of WINi in MLLr cancer cells. We show that WINi induce depletion of the stock of ribosomes, accompanied by a broad yet modest translational choke and changes in alternative mRNA splicing that inactivate the p53 antagonist MDM4. We also show that WINi are synergistic with agents including venetoclax and BET-bromodomain inhibitors. Together, these studies reinforce the concept that WINi are a novel type of ribosome-directed anti-cancer therapy and provide a resource to support their clinical implementation in MLLr leukemias and other malignancies., Competing Interests: Declarations of Interest Fesik, S. W., Stauffer, S. R., Salovich, J. M., Tansey, W. P., Wang, F., Phan, J., Olejniczak, E. T., inventors. WDR5 inhibitors and modulators. United States Patent US 10,501,466. 10 December 2019. Fesik, S. W., Stauffer, S. R., Tansey, W. P., Olejniczak, E. T., Phan, J., Wang, F., Jeon, K., Gogliotti, R. D., inventors. WDR5 inhibitors and modulators. United States Patent US 10,160,763. 25 December 2018.
- Published
- 2024
- Full Text
- View/download PDF
6. WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think.
- Author
-
Weissmiller AM, Fesik SW, and Tansey WP
- Abstract
WDR5 is a conserved nuclear protein that scaffolds the assembly of epigenetic regulatory complexes and moonlights in functions ranging from recruiting MYC oncoproteins to chromatin to facilitating the integrity of mitosis. It is also a high-value target for anti-cancer therapies, with small molecule WDR5 inhibitors and degraders undergoing extensive preclinical assessment. WDR5 inhibitors were originally conceived as epigenetic modulators, proposed to inhibit cancer cells by reversing oncogenic patterns of histone H3 lysine 4 methylation-a notion that persists to this day. This premise, however, does not withstand contemporary inspection and establishes expectations for the mechanisms and utility of WDR5 inhibitors that can likely never be met. Here, we highlight salient misconceptions regarding WDR5 inhibitors as epigenetic modulators and provide a unified model for their action as a ribosome-directed anti-cancer therapy that helps focus understanding of when and how the tumor-inhibiting properties of these agents can best be understood and exploited.
- Published
- 2024
- Full Text
- View/download PDF
7. Structure-Based Discovery of Potent, Orally Bioavailable Benzoxazepinone-Based WD Repeat Domain 5 Inhibitors.
- Author
-
Teuscher KB, Mills JJ, Tian J, Han C, Meyers KM, Sai J, South TM, Crow MM, Van Meveren M, Sensintaffar JL, Zhao B, Amporndanai K, Moore WJ, Stott GM, Tansey WP, Lee T, and Fesik SW
- Subjects
- Animals, Drug Discovery, WD40 Repeats, Antineoplastic Agents pharmacology
- Abstract
The chromatin-associated protein WDR5 (WD repeat domain 5) is an essential cofactor for MYC and a conserved regulator of ribosome protein gene transcription. It is also a high-profile target for anti-cancer drug discovery, with proposed utility against both solid and hematological malignancies. We have previously discovered potent dihydroisoquinolinone-based WDR5 WIN-site inhibitors with demonstrated efficacy and safety in animal models. In this study, we sought to optimize the bicyclic core to discover a novel series of WDR5 WIN-site inhibitors with improved potency and physicochemical properties. We identified the 3,4-dihydrobenzo[ f ][1,4]oxazepin-5(2 H )-one core as an alternative scaffold for potent WDR5 inhibitors. Additionally, we used X-ray structural analysis to design partially saturated bicyclic P
7 units. These benzoxazepinone-based inhibitors exhibited increased cellular potency and selectivity and favorable physicochemical properties compared to our best-in-class dihydroisoquinolinone-based counterparts. This study opens avenues to discover more advanced WDR5 WIN-site inhibitors and supports their development as novel anti-cancer therapeutics.- Published
- 2023
- Full Text
- View/download PDF
8. Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models.
- Author
-
Teuscher KB, Chowdhury S, Meyers KM, Tian J, Sai J, Van Meveren M, South TM, Sensintaffar JL, Rietz TA, Goswami S, Wang J, Grieb BC, Lorey SL, Howard GC, Liu Q, Moore WJ, Stott GM, Tansey WP, Lee T, and Fesik SW
- Subjects
- Animals, Humans, Mice, Chromatin, Models, Animal, Cell Line, Tumor, Intracellular Signaling Peptides and Proteins antagonists & inhibitors, Intracellular Signaling Peptides and Proteins metabolism, WD40 Repeats, Neoplasms drug therapy
- Abstract
WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P
7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high-dose regimen in rodents to demonstrate the safety of the WDR5 WIN-site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.- Published
- 2023
- Full Text
- View/download PDF
9. Discovery of Potent Orally Bioavailable WD Repeat Domain 5 (WDR5) Inhibitors Using a Pharmacophore-Based Optimization.
- Author
-
Teuscher KB, Meyers KM, Wei Q, Mills JJ, Tian J, Alvarado J, Sai J, Van Meveren M, South TM, Rietz TA, Zhao B, Moore WJ, Stott GM, Tansey WP, Lee T, and Fesik SW
- Subjects
- Humans, WD40 Repeats, Intracellular Signaling Peptides and Proteins
- Abstract
WD repeat domain 5 (WDR5) is a nuclear scaffolding protein that forms many biologically important multiprotein complexes. The WIN site of WDR5 represents a promising pharmacological target in a variety of human cancers. Here, we describe the optimization of our initial WDR5 WIN-site inhibitor using a structure-guided pharmacophore-based convergent strategy to improve its druglike properties and pharmacokinetic profile. The core of the previous lead remained constant while a focused SAR effort on the three pharmacophore units was combined to generate a new in vivo lead series. Importantly, this new series of compounds has picomolar binding affinity, improved cellular antiproliferative activity and selectivity, and increased kinetic aqueous solubility. They also exhibit a desirable oral pharmacokinetic profile with manageable intravenous clearance and high oral bioavailability. Thus, these new leads are useful probes toward studying the effects of WDR5 inhibition.
- Published
- 2022
- Full Text
- View/download PDF
10. Synergistic action of WDR5 and HDM2 inhibitors in SMARCB1-deficient cancer cells.
- Author
-
Florian AC, Woodley CM, Wang J, Grieb BC, Slota MJ, Guerrazzi K, Hsu CY, Matlock BK, Flaherty DK, Lorey SL, Fesik SW, Howard GC, Liu Q, Weissmiller AM, and Tansey WP
- Abstract
Rhabdoid tumors (RT) are rare and deadly pediatric cancers driven by loss of SMARCB1 , which encodes the SNF5 component of the SWI/SNF chromatin remodeler. Loss of SMARCB1 is associated with a complex set of phenotypic changes including vulnerability to inhibitors of protein synthesis and of the p53 ubiquitin-ligase HDM2. Recently, we discovered small molecule inhibitors of the 'WIN' site of WDR5, which in MLL-rearranged leukemia cells decrease the expression of a set of genes linked to protein synthesis, inducing a translational choke and causing p53-dependent inhibition of proliferation. Here, we characterize how WIN site inhibitors act in RT cells. As in leukemia cells, WIN site inhibition in RT cells causes the comprehensive displacement of WDR5 from chromatin, resulting in a decrease in protein synthesis gene expression. Unlike leukemia cells, however, the growth response of RT cells to WIN site blockade is independent of p53. Exploiting this observation, we demonstrate that WIN site inhibitor synergizes with an HDM2 antagonist to induce p53 and block RT cell proliferation in vitro . These data reveal a p53-independent action of WIN site inhibitors and forecast that future strategies to treat RT could be based on dual WDR5/HDM2 inhibition., (© The Author(s) 2022. Published by Oxford University Press on behalf of NAR Cancer.)
- Published
- 2022
- Full Text
- View/download PDF
11. WIN site inhibition disrupts a subset of WDR5 function.
- Author
-
Siladi AJ, Wang J, Florian AC, Thomas LR, Creighton JH, Matlock BK, Flaherty DK, Lorey SL, Howard GC, Fesik SW, Weissmiller AM, Liu Q, and Tansey WP
- Subjects
- Binding Sites, Cell Cycle drug effects, Cell Line, Tumor, Cell Proliferation drug effects, Chromatin Assembly and Disassembly, Gene Expression Regulation, Neoplastic, Histones metabolism, Humans, Intracellular Signaling Peptides and Proteins genetics, Intracellular Signaling Peptides and Proteins metabolism, Lymphoma, B-Cell genetics, Lymphoma, B-Cell metabolism, Methylation, Protein Binding, Protein Interaction Domains and Motifs, Proteolysis, Signal Transduction, Transcription, Genetic, Antineoplastic Agents pharmacology, Bridged Bicyclo Compounds, Heterocyclic pharmacology, Intracellular Signaling Peptides and Proteins antagonists & inhibitors, Lymphoma, B-Cell drug therapy
- Abstract
WDR5 nucleates the assembly of histone-modifying complexes and acts outside this context in a range of chromatin-centric processes. WDR5 is also a prominent target for pharmacological inhibition in cancer. Small-molecule degraders of WDR5 have been described, but most drug discovery efforts center on blocking the WIN site of WDR5, an arginine binding cavity that engages MLL/SET enzymes that deposit histone H3 lysine 4 methylation (H3K4me). Therapeutic application of WIN site inhibitors is complicated by the disparate functions of WDR5, but is generally guided by two assumptions-that WIN site inhibitors disable all functions of WDR5, and that changes in H3K4me drive the transcriptional response of cancer cells to WIN site blockade. Here, we test these assumptions by comparing the impact of WIN site inhibition versus WDR5 degradation on H3K4me and transcriptional processes. We show that WIN site inhibition disables only a specific subset of WDR5 activity, and that H3K4me changes induced by WDR5 depletion do not explain accompanying transcriptional responses. These data recast WIN site inhibitors as selective loss-of-function agents, contradict H3K4me as a relevant mechanism of action for WDR5 inhibitors, and indicate distinct clinical applications of WIN site inhibitors and WDR5 degraders., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
12. Fragment-Based Discovery of Small Molecules Bound to T-Cell Immunoglobulin and Mucin Domain-Containing Molecule 3 (TIM-3).
- Author
-
Rietz TA, Teuscher KB, Mills JJ, Gogliotti RD, Lepovitz LT, Scaggs WR, Yoshida K, Luong K, Lee T, and Fesik SW
- Subjects
- Crystallography, X-Ray, Fluorescence Polarization, Humans, Protein Binding, Protein Domains, Small Molecule Libraries chemistry, Structure-Activity Relationship, Drug Discovery, Hepatitis A Virus Cellular Receptor 2 metabolism, Small Molecule Libraries pharmacology, T-Lymphocytes metabolism
- Abstract
T-cell immunoglobulin and mucin domain-containing molecule 3 (TIM-3; HAVCR2) has emerged as an attractive immune checkpoint target for cancer immunotherapy. TIM-3 is a negative regulator of the systemic immune response to cancer and is expressed on several dysfunctional, or exhausted, immune cell subsets. Upregulation of TIM-3 is associated with tumor progression, poor survival rates, and acquired resistance to antibody-based immunotherapies in the clinic. Despite the potential advantages of small-molecule inhibitors over antibodies, the discovery of small-molecule inhibitors has lagged behind that of antibody therapeutics. Here, we describe the discovery of high-affinity small-molecule ligands for TIM-3 through an NMR-based fragment screen and structure-based lead optimization. These compounds represent useful tools to further study the biology of TIM-3 immune modulation in cancer and serve as a potentially useful starting point toward the discovery of TIM-3-targeted therapeutics.
- Published
- 2021
- Full Text
- View/download PDF
13. Impact of WIN site inhibitor on the WDR5 interactome.
- Author
-
Guarnaccia AD, Rose KL, Wang J, Zhao B, Popay TM, Wang CE, Guerrazzi K, Hill S, Woodley CM, Hansen TJ, Lorey SL, Shaw JG, Payne WG, Weissmiller AM, Olejniczak ET, Fesik SW, Liu Q, and Tansey WP
- Subjects
- 3-Phosphoinositide-Dependent Protein Kinases chemistry, 3-Phosphoinositide-Dependent Protein Kinases genetics, 3-Phosphoinositide-Dependent Protein Kinases metabolism, Amino Acid Sequence, Binding Sites, Drug Discovery, G2 Phase genetics, Gene Expression Regulation, HEK293 Cells, Humans, Immunoprecipitation, Intracellular Signaling Peptides and Proteins chemistry, Intracellular Signaling Peptides and Proteins genetics, Models, Molecular, Molecular Targeted Therapy, Protein Binding, Intracellular Signaling Peptides and Proteins antagonists & inhibitors
- Abstract
The chromatin-associated protein WDR5 is a promising pharmacological target in cancer, with most drug discovery efforts directed against an arginine-binding cavity in WDR5 called the WIN site. Despite a clear expectation that WIN site inhibitors will alter the repertoire of WDR5 interaction partners, their impact on the WDR5 interactome remains unknown. Here, we use quantitative proteomics to delineate how the WDR5 interactome is changed by WIN site inhibition. We show that the WIN site inhibitor alters the interaction of WDR5 with dozens of proteins, including those linked to phosphatidylinositol 3-kinase (PI3K) signaling. As proof of concept, we demonstrate that the master kinase PDPK1 is a bona fide high-affinity WIN site binding protein that engages WDR5 to modulate transcription of genes expressed in the G2 phase of the cell cycle. This dataset expands our understanding of WDR5 and serves as a resource for deciphering the action of WIN site inhibitors., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
14. Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on RAS Using Fragment-Based Methods.
- Author
-
Sarkar D, Olejniczak ET, Phan J, Coker JA, Sai J, Arnold A, Beesetty Y, Waterson AG, and Fesik SW
- Subjects
- Allosteric Regulation drug effects, Crystallography, X-Ray, Drug Design, Drug Discovery, Humans, Molecular Docking Simulation, SOS1 Protein chemistry, Guanosine Triphosphate metabolism, SOS1 Protein agonists, SOS1 Protein metabolism, Sulfonamides chemistry, Sulfonamides pharmacology, ras Proteins metabolism
- Abstract
The nucleotide exchange factor Son of Sevenless (SOS) catalyzes the activation of RAS by converting it from its inactive GDP-bound state to its active GTP-bound state. Recently, we have reported the discovery of small-molecule allosteric activators of SOS1 that can increase the amount of RAS-GTP in cells. The compounds can inhibit ERK phosphorylation at higher concentrations by engaging a feedback mechanism. To further study this process, we sought different chemical matter from an NMR-based fragment screen using selective methyl labeling. To aid this process, several Ile methyl groups located in different binding sites of the protein were assigned and used to categorize the NMR hits into different classes. Hit to lead optimization using an iterative structure-based design paradigm resulted in compounds with improvements in binding affinity. These improved molecules of a different chemical class increase SOS1
cat -mediated nucleotide exchange on RAS and display cellular action consistent with our prior results.- Published
- 2020
- Full Text
- View/download PDF
15. Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design.
- Author
-
Chacón Simon S, Wang F, Thomas LR, Phan J, Zhao B, Olejniczak ET, Macdonald JD, Shaw JG, Schlund C, Payne W, Creighton J, Stauffer SR, Waterson AG, Tansey WP, and Fesik SW
- Subjects
- Cell Line, Tumor, HEK293 Cells, Humans, Intracellular Signaling Peptides and Proteins metabolism, Protein Structure, Tertiary, Proto-Oncogene Proteins c-myc metabolism, Structure-Activity Relationship, Drug Design, Drug Discovery methods, Intracellular Signaling Peptides and Proteins antagonists & inhibitors, Proto-Oncogene Proteins c-myc antagonists & inhibitors, Sulfonamides chemical synthesis, Sulfonamides pharmacology
- Abstract
The frequent deregulation of MYC and its elevated expression via multiple mechanisms drives cells to a tumorigenic state. Indeed, MYC is overexpressed in up to ∼50% of human cancers and is considered a highly validated anticancer target. Recently, we discovered that WD repeat-containing protein 5 (WDR5) binds to MYC and is a critical cofactor required for the recruitment of MYC to its target genes and reported the first small molecule inhibitors of the WDR5-MYC interaction using structure-based design. These compounds display high binding affinity, but have poor physicochemical properties and are hence not suitable for in vivo studies. Herein, we conducted an NMR-based fragment screening to identify additional chemical matter and, using a structure-based approach, we merged a fragment hit with the previously reported sulfonamide series. Compounds in this series can disrupt the WDR5-MYC interaction in cells, and as a consequence, we observed a reduction of MYC localization to chromatin.
- Published
- 2020
- Full Text
- View/download PDF
16. WDR5 is a conserved regulator of protein synthesis gene expression.
- Author
-
Bryan AF, Wang J, Howard GC, Guarnaccia AD, Woodley CM, Aho ER, Rellinger EJ, Matlock BK, Flaherty DK, Lorey SL, Chung DH, Fesik SW, Liu Q, Weissmiller AM, and Tansey WP
- Subjects
- Base Sequence, Binding Sites genetics, Cell Line, Chromatin metabolism, Conserved Sequence genetics, Female, Humans, Male, Protein Binding, Transcription, Genetic, Tumor Suppressor Protein p53 metabolism, Gene Expression Regulation, Intracellular Signaling Peptides and Proteins metabolism, Protein Biosynthesis genetics
- Abstract
WDR5 is a highly-conserved nuclear protein that performs multiple scaffolding functions in the context of chromatin. WDR5 is also a promising target for pharmacological inhibition in cancer, with small molecule inhibitors of an arginine-binding pocket of WDR5 (the 'WIN' site) showing efficacy against a range of cancer cell lines in vitro. Efforts to understand WDR5, or establish the mechanism of action of WIN site inhibitors, however, are stymied by its many functions in the nucleus, and a lack of knowledge of the conserved gene networks-if any-that are under its control. Here, we have performed comparative genomic analyses to identify the conserved sites of WDR5 binding to chromatin, and the conserved genes regulated by WDR5, across a diverse panel of cancer cell lines. We show that a specific cohort of protein synthesis genes (PSGs) are invariantly bound by WDR5, demonstrate that the WIN site anchors WDR5 to chromatin at these sites, and establish that PSGs are bona fide, acute, and persistent targets of WIN site blockade. Together, these data reveal that WDR5 plays a predominant transcriptional role in biomass accumulation and provide further evidence that WIN site inhibitors act to repress gene networks linked to protein synthesis homeostasis., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2020
- Full Text
- View/download PDF
17. Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex.
- Author
-
Zhao B, Payne WG, Sai J, Lu Z, Olejniczak ET, and Fesik SW
- Subjects
- Adaptor Proteins, Signal Transducing chemistry, Adaptor Proteins, Signal Transducing genetics, Amino Acid Sequence, Amino Acid Substitution, Binding Sites, Humans, Mutation, Nuclear Magnetic Resonance, Biomolecular, Peptides chemistry, Protein Binding, Protein Domains, Adaptor Proteins, Signal Transducing metabolism, Peptides metabolism
- Abstract
KLHL-12 is a substrate specific adapter protein for a Cul3-Ring ligase complex. It is a member of the Kelch β-propeller domain subclass of Cullin-Ring substrate recognition domains. This E3 ubiquitin ligase complex has many activities, including acting as a negative regulator of the Wnt signaling pathway by mediating ubiquitination and subsequent proteolysis of Dvl3/Dsh3. KLHL-12 is also known to mediate the polyubiquitination of the dopamine D4 receptor (D4.2), the ubiquitination of KHSRP, a protein that is involved in IRES translation, and also the ubiquitination of Sec31, which is involved in endoplasmic reticulum-Golgi transport by regulating the size of COPII coats. Earlier studies broadly defined the substrate binding regions for D4.2 and Dvl3/Dsh3 to KLHL-12. We tested several peptides from these regions and succeeded in identifying a short peptide that bound to KLHL-12 with low micromolar affinity. To better understand the sequence specificity of this peptide, we used alanine substitutions to map the important residues and obtained an X-ray structure of this peptide bound to KLHL-12. This structure and our peptide affinity measurements suggest a sequence motif for peptides that bind to the top face of KLHL-12. Understanding this binding site on KLHL-12 may contribute to efforts to find small molecule ligands that can either directly inhibit the degradation of substrate proteins or be used in targeted protein degradation strategies using PROTACs.
- Published
- 2020
- Full Text
- View/download PDF
18. Reply to Tran et al.: Dimeric KRAS protein-protein interaction stabilizers.
- Author
-
Kessler D, Gollner A, Gmachl M, Mantoulidis A, Martin LJ, Zoephel A, Mayer M, Covini D, Fischer S, Gerstberger T, Gmaschitz T, Goodwin C, Greb P, Häring D, Hela W, Hoffmann J, Karolyi-Oezguer J, Knesl P, Kornigg S, Koegl M, Kousek R, Lamarre L, Moser F, Munico-Martinez S, Peinsipp C, Phan J, Rinnenthal J, Sai J, Salamon C, Scherbantin Y, Schipany K, Schnitzer R, Schrenk A, Sharps B, Siszler G, Sun Q, Waterson A, Wolkerstorfer B, Zeeb M, Pearson M, Fesik SW, and McConnell DB
- Subjects
- Proto-Oncogene Proteins p21(ras)
- Abstract
Competing Interests: Competing interest statement: D.K., A.G., M.G., A.M., L.J.M., A.Z., M.M., D.C., S.F., T. Gerstberger, T. Gmaschitz, P.G., D.H., W.H., J.H., J.K.-O., P.K., S.K., M.K., R.K., L.L., F.M., S.M.-M., C.P., J.R., C.S., Y.S., K.S., R.S., A.S., B.S., G.S., B.W., M.Z., M.P., and D.B.M. were employees of Boehringer Ingelheim at the time of the work.
- Published
- 2020
- Full Text
- View/download PDF
19. Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core.
- Author
-
Tian J, Teuscher KB, Aho ER, Alvarado JR, Mills JJ, Meyers KM, Gogliotti RD, Han C, Macdonald JD, Sai J, Shaw JG, Sensintaffar JL, Zhao B, Rietz TA, Thomas LR, Payne WG, Moore WJ, Stott GM, Kondo J, Inoue M, Coffey RJ, Tansey WP, Stauffer SR, Lee T, and Fesik SW
- Subjects
- Cell Cycle drug effects, Cell Line, Tumor, Cell Proliferation, Chromatin drug effects, Chromatin genetics, Crystallography, X-Ray, Drug Design, Drug Discovery, Epigenetic Repression drug effects, Genes, myc drug effects, Humans, Structure-Activity Relationship, Antineoplastic Agents chemical synthesis, Antineoplastic Agents pharmacology, Bridged Bicyclo Compounds, Heterocyclic chemical synthesis, Bridged Bicyclo Compounds, Heterocyclic pharmacology, Intracellular Signaling Peptides and Proteins antagonists & inhibitors, Quinolones chemical synthesis, Quinolones pharmacology, WD40 Repeats drug effects
- Abstract
WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple chromatin-centric processes. Overexpression of WDR5 correlates with a poor clinical outcome in many human cancers, and WDR5 itself has emerged as an attractive target for therapy. Most drug-discovery efforts center on the WIN site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe discovery of a novel WDR5 WIN site antagonists containing a dihydroisoquinolinone bicyclic core using a structure-based design. These compounds exhibit picomolar binding affinity and selective concentration-dependent antiproliferative activities in sensitive MLL-fusion cell lines. Furthermore, these WDR5 WIN site binders inhibit proliferation in MYC-driven cancer cells and reduce MYC recruitment to chromatin at MYC/WDR5 co-bound genes. Thus, these molecules are useful probes to study the implication of WDR5 inhibition in cancers and serve as a potential starting point toward the discovery of anti-WDR5 therapeutics.
- Published
- 2020
- Full Text
- View/download PDF
20. Targeting MYC through WDR5.
- Author
-
Thomas LR, Adams CM, Fesik SW, Eischen CM, and Tansey WP
- Abstract
The oncoprotein transcription factor MYC is overexpressed in most cancers and is responsible for hundreds of thousands of cancer deaths worldwide every year. MYC is also a highly validated - but currently undruggable - anti-cancer target. We recently showed that breaking the interaction of MYC with its chromatin co-factor WD repeat-containing protein 5 (WDR5) promotes tumor regression in mouse xenografts, laying the foundation for a new strategy to inhibit MYC in the clinic., (© 2020 The Author(s). Published with license by Taylor & Francis Group, LLC.)
- Published
- 2020
- Full Text
- View/download PDF
21. Discovery and Optimization of Salicylic Acid-Derived Sulfonamide Inhibitors of the WD Repeat-Containing Protein 5-MYC Protein-Protein Interaction.
- Author
-
Macdonald JD, Chacón Simon S, Han C, Wang F, Shaw JG, Howes JE, Sai J, Yuh JP, Camper D, Alicie BM, Alvarado J, Nikhar S, Payne W, Aho ER, Bauer JA, Zhao B, Phan J, Thomas LR, Rossanese OW, Tansey WP, Waterson AG, Stauffer SR, and Fesik SW
- Subjects
- DNA-Binding Proteins antagonists & inhibitors, DNA-Binding Proteins metabolism, HEK293 Cells, High-Throughput Screening Assays, Humans, Intracellular Signaling Peptides and Proteins metabolism, Protein Binding, Protein Conformation, Proto-Oncogene Proteins c-myc metabolism, WD40 Repeats, Drug Discovery, Intracellular Signaling Peptides and Proteins antagonists & inhibitors, Protein Interaction Domains and Motifs drug effects, Proto-Oncogene Proteins c-myc antagonists & inhibitors, Salicylic Acid chemistry, Small Molecule Libraries pharmacology, Sulfonamides pharmacology
- Abstract
The treatment of tumors driven by overexpression or amplification of MYC oncogenes remains a significant challenge in drug discovery. Here, we present a new strategy toward the inhibition of MYC via the disruption of the protein-protein interaction between MYC and its chromatin cofactor WD Repeat-Containing Protein 5. Blocking the association of these proteins is hypothesized to disrupt the localization of MYC to chromatin, thus disrupting the ability of MYC to sustain tumorigenesis. Utilizing a high-throughput screening campaign and subsequent structure-guided design, we identify small-molecule inhibitors of this interaction with potent in vitro binding affinity and report structurally related negative controls that can be used to study the effect of this disruption. Our work suggests that disruption of this protein-protein interaction may provide a path toward an effective approach for the treatment of multiple tumors and anticipate that the molecules disclosed can be used as starting points for future efforts toward compounds with improved drug-like properties.
- Published
- 2019
- Full Text
- View/download PDF
22. Interaction of the oncoprotein transcription factor MYC with its chromatin cofactor WDR5 is essential for tumor maintenance.
- Author
-
Thomas LR, Adams CM, Wang J, Weissmiller AM, Creighton J, Lorey SL, Liu Q, Fesik SW, Eischen CM, and Tansey WP
- Subjects
- Animals, Burkitt Lymphoma genetics, Carcinogenesis, Cell Line, Tumor, Chromatin genetics, Humans, Intracellular Signaling Peptides and Proteins genetics, Mice, Mice, Nude, Protein Binding, Proto-Oncogene Proteins c-myc genetics, Burkitt Lymphoma metabolism, Chromatin metabolism, Intracellular Signaling Peptides and Proteins metabolism, Proto-Oncogene Proteins c-myc metabolism
- Abstract
The oncoprotein transcription factor MYC is overexpressed in the majority of cancers. Key to its oncogenic activity is the ability of MYC to regulate gene expression patterns that drive and maintain the malignant state. MYC is also considered a validated anticancer target, but efforts to pharmacologically inhibit MYC have failed. The dependence of MYC on cofactors creates opportunities for therapeutic intervention, but for any cofactor this requires structural understanding of how the cofactor interacts with MYC, knowledge of the role it plays in MYC function, and demonstration that disrupting the cofactor interaction will cause existing cancers to regress. One cofactor for which structural information is available is WDR5, which interacts with MYC to facilitate its recruitment to chromatin. To explore whether disruption of the MYC-WDR5 interaction could potentially become a viable anticancer strategy, we developed a Burkitt's lymphoma system that allows replacement of wild-type MYC for mutants that are defective for WDR5 binding or all known nuclear MYC functions. Using this system, we show that WDR5 recruits MYC to chromatin to control the expression of genes linked to biomass accumulation. We further show that disrupting the MYC-WDR5 interaction within the context of an existing cancer promotes rapid and comprehensive tumor regression in vivo. These observations connect WDR5 to a core tumorigenic function of MYC and establish that, if a therapeutic window can be established, MYC-WDR5 inhibitors could be developed as anticancer agents., Competing Interests: Competing interest statement: S.W.F., S. R. Stauffer, W.P.T., E. T. Olejniczak, J. Phan, F. Wang, K. Jeon, and R. D. Gogliotti were granted US Patent 10,160,763, “WDR5 Inhibitors and Modulators,” on December 25, 2018., (Copyright © 2019 the Author(s). Published by PNAS.)
- Published
- 2019
- Full Text
- View/download PDF
23. Drugging an undruggable pocket on KRAS.
- Author
-
Kessler D, Gmachl M, Mantoulidis A, Martin LJ, Zoephel A, Mayer M, Gollner A, Covini D, Fischer S, Gerstberger T, Gmaschitz T, Goodwin C, Greb P, Häring D, Hela W, Hoffmann J, Karolyi-Oezguer J, Knesl P, Kornigg S, Koegl M, Kousek R, Lamarre L, Moser F, Munico-Martinez S, Peinsipp C, Phan J, Rinnenthal J, Sai J, Salamon C, Scherbantin Y, Schipany K, Schnitzer R, Schrenk A, Sharps B, Siszler G, Sun Q, Waterson A, Wolkerstorfer B, Zeeb M, Pearson M, Fesik SW, and McConnell DB
- Subjects
- Guanosine Triphosphate metabolism, Humans, Models, Molecular, Nanoparticles chemistry, Drug Discovery, Pharmaceutical Preparations chemistry, Proto-Oncogene Proteins p21(ras) chemistry
- Abstract
The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRAS
G12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS., Competing Interests: Conflict of interest statement: D.K., M.G., A.M., L.J.M., A.Z., M.M., A.G., D.C., S.F., T. Gerstberger, T. Gmashitz, P.G., D.H., W.H., J.H., J.K.-O., P.K., S.K., M.K., R.K., L.L., F.M., S.M.-M., C.P., J.R., C.S., Y.S., K.S., R.S., A.S., B.S., G.S., B.W., M.Z., M.P., and D.B.M. were employees of Boehringer Ingelheim at the time of this work., (Copyright © 2019 the Author(s). Published by PNAS.)- Published
- 2019
- Full Text
- View/download PDF
24. Targeting WDR5: A WINning Anti-Cancer Strategy?
- Author
-
Aho ER, Weissmiller AM, Fesik SW, and Tansey WP
- Abstract
WDR5 is a component of multiple epigenetic regulatory complexes, including the mixed lineage leukemia (MLL)/SET complexes that deposit histone H3 lysine 4 methylation. Inhibitors of an arginine-binding cavity in WDR5, known as the WDR5-interaction (WIN) site, have been proposed to selectively kill MLL-rearranged malignancies via an epigenetic mechanism. We discovered potent WIN site inhibitors and found that they kill MLL cancer cells not through changes in histone methylation, but by displacing WDR5 from chromatin at protein synthesis genes, choking the translational capacity of these cells, and inducing death via a nucleolar stress response. The mechanism of action of WIN site inhibitors reveals new aspects of WDR5 function and forecasts broad therapeutic utility as anti-cancer agents., Competing Interests: Declaration of Conflicting Interests:S.W.F., S.R. Stauffer, W.P.T., E.T. Olejniczak, J. Phan, F. Wang, K. Jeon, and R.D. Gogliotti. were granted US Patent 10,160,763, “WDR5 Inhibitors and Modulators,” on December 25, 2018.
- Published
- 2019
- Full Text
- View/download PDF
25. Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors That Demonstrate in Vivo Activity in Mouse Xenograft Models of Human Cancer.
- Author
-
Lee T, Christov PP, Shaw S, Tarr JC, Zhao B, Veerasamy N, Jeon KO, Mills JJ, Bian Z, Sensintaffar JL, Arnold AL, Fogarty SA, Perry E, Ramsey HE, Cook RS, Hollingshead M, Davis Millin M, Lee KM, Koss B, Budhraja A, Opferman JT, Kim K, Arteaga CL, Moore WJ, Olejniczak ET, Savona MR, and Fesik SW
- Subjects
- Animals, Antineoplastic Agents metabolism, Antineoplastic Agents pharmacology, Antineoplastic Agents therapeutic use, Azepines chemistry, Binding Sites, Cell Line, Tumor, Cell Survival drug effects, Crystallography, X-Ray, Drug Evaluation, Preclinical, Female, Humans, Mice, Mice, Inbred NOD, Mice, SCID, Molecular Dynamics Simulation, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Neoplasms drug therapy, Neoplasms pathology, Protein Structure, Tertiary, Small Molecule Libraries metabolism, Small Molecule Libraries pharmacology, Small Molecule Libraries therapeutic use, Structure-Activity Relationship, Xenograft Model Antitumor Assays, Antineoplastic Agents chemistry, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors, Small Molecule Libraries chemistry
- Abstract
Overexpression of myeloid cell leukemia-1 (Mcl-1) in cancers correlates with high tumor grade and poor survival. Additionally, Mcl-1 drives intrinsic and acquired resistance to many cancer therapeutics, including B cell lymphoma 2 family inhibitors, proteasome inhibitors, and antitubulins. Therefore, Mcl-1 inhibition could serve as a strategy to target cancers that require Mcl-1 to evade apoptosis. Herein, we describe the use of structure-based design to discover a novel compound (42) that robustly and specifically inhibits Mcl-1 in cell culture and animal xenograft models. Compound 42 binds to Mcl-1 with picomolar affinity and inhibited growth of Mcl-1-dependent tumor cell lines in the nanomolar range. Compound 42 also inhibited the growth of hematological and triple negative breast cancer xenografts at well-tolerated doses. These findings highlight the use of structure-based design to identify small molecule Mcl-1 inhibitors and support the use of 42 as a potential treatment strategy to block Mcl-1 activity and induce apoptosis in Mcl-1-dependent cancers.
- Published
- 2019
- Full Text
- View/download PDF
26. Small Molecule SOS1 Agonists Modulate MAPK and PI3K Signaling via Independent Cellular Responses.
- Author
-
Akan DT, Howes JE, Sai J, Arnold AL, Beesetty Y, Phan J, Olejniczak ET, Waterson AG, and Fesik SW
- Subjects
- Benzimidazoles metabolism, CRISPR-Associated Protein 9 metabolism, Clustered Regularly Interspaced Short Palindromic Repeats genetics, Gene Editing, Humans, Indoles metabolism, Quinazolines metabolism, Benzimidazoles chemistry, Indoles chemistry, Mitogen-Activated Protein Kinase Kinases metabolism, Phosphatidylinositol 3-Kinases metabolism, Quinazolines chemistry, SOS1 Protein agonists
- Abstract
Activating mutations in RAS can lead to oncogenesis by enhancing downstream signaling, such as through the MAPK and PI3K pathways. Therefore, therapeutically targeting RAS may perturb multiple signaling pathways simultaneously. One method for modulating RAS signaling is to target the activity of the guanine nucleotide exchange factor SOS1. Our laboratory has discovered compounds that bind to SOS1 and activate RAS. Interestingly, these SOS1 agonist compounds elicit biphasic modulation of ERK phosphorylation and simultaneous inhibition of AKT phosphorylation levels. Here, we utilized multiple chemically distinct compounds to elucidate whether these effects on MAPK and PI3K signaling by SOS1 agonists were mechanistically linked. In addition, we used CRISPR/Cas9 gene-editing to generate clonally derived SOS1 knockout cells and identified a potent SOS1 agonist that rapidly elicited on-target molecular effects at substantially lower concentrations than those causing off-target effects. Our findings will allow us to further define the on-target utility of SOS1 agonists.
- Published
- 2019
- Full Text
- View/download PDF
27. Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity.
- Author
-
Aho ER, Wang J, Gogliotti RD, Howard GC, Phan J, Acharya P, Macdonald JD, Cheng K, Lorey SL, Lu B, Wenzel S, Foshage AM, Alvarado J, Wang F, Shaw JG, Zhao B, Weissmiller AM, Thomas LR, Vakoc CR, Hall MD, Hiebert SW, Liu Q, Stauffer SR, Fesik SW, and Tansey WP
- Subjects
- Binding Sites, Cell Line, Tumor, Enzyme Inhibitors chemical synthesis, Female, HEK293 Cells, Humans, Intracellular Signaling Peptides and Proteins antagonists & inhibitors, Intracellular Signaling Peptides and Proteins chemistry, Male, Protein Binding drug effects, Chromatin metabolism, Enzyme Inhibitors pharmacology, Intracellular Signaling Peptides and Proteins metabolism
- Abstract
The chromatin-associated protein WDR5 is a promising target for pharmacological inhibition in cancer. Drug discovery efforts center on the blockade of the "WIN site" of WDR5, a well-defined pocket that is amenable to small molecule inhibition. Various cancer contexts have been proposed to be targets for WIN site inhibitors, but a lack of understanding of WDR5 target genes and of the primary effects of WIN site inhibitors hampers their utility. Here, by the discovery of potent WIN site inhibitors, we demonstrate that the WIN site links WDR5 to chromatin at a small cohort of loci, including a specific subset of ribosome protein genes. WIN site inhibitors rapidly displace WDR5 from chromatin and decrease the expression of associated genes, causing translational inhibition, nucleolar stress, and p53 induction. Our studies define a mode by which WDR5 engages chromatin and forecast that WIN site blockade could have utility against multiple cancer types., (Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2019
- Full Text
- View/download PDF
28. A Novel MCL1 Inhibitor Combined with Venetoclax Rescues Venetoclax-Resistant Acute Myelogenous Leukemia.
- Author
-
Ramsey HE, Fischer MA, Lee T, Gorska AE, Arrate MP, Fuller L, Boyd KL, Strickland SA, Sensintaffar J, Hogdal LJ, Ayers GD, Olejniczak ET, Fesik SW, and Savona MR
- Subjects
- Acute Disease, Animals, Antineoplastic Agents chemistry, Apoptosis drug effects, Cell Line, Tumor, Drug Synergism, HL-60 Cells, Humans, Indoles chemistry, K562 Cells, Leukemia, Myeloid metabolism, Mice, Inbred NOD, Mice, Knockout, Mice, SCID, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Proto-Oncogene Proteins c-bcl-2 antagonists & inhibitors, Proto-Oncogene Proteins c-bcl-2 metabolism, Pyrazines chemistry, Pyrazoles chemistry, THP-1 Cells, U937 Cells, Xenograft Model Antitumor Assays, Antineoplastic Agents pharmacology, Bridged Bicyclo Compounds, Heterocyclic pharmacology, Drug Resistance, Neoplasm drug effects, Indoles pharmacology, Leukemia, Myeloid drug therapy, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors, Pyrazines pharmacology, Pyrazoles pharmacology, Sulfonamides pharmacology
- Abstract
Suppression of apoptosis by expression of antiapoptotic BCL2 family members is a hallmark of acute myeloblastic leukemia (AML). Induced myeloid leukemia cell differentiation protein (MCL1), an antiapoptotic BCL2 family member, is commonly upregulated in AML cells and is often a primary mode of resistance to treatment with the BCL2 inhibitor venetoclax. Here, we describe VU661013, a novel, potent, selective MCL1 inhibitor that destabilizes BIM/MCL1 association, leads to apoptosis in AML, and is active in venetoclax-resistant cells and patient-derived xenografts. In addition, VU661013 was safely combined with venetoclax for synergy in murine models of AML. Importantly, BH3 profiling of patient samples and drug-sensitivity testing ex vivo accurately predicted cellular responses to selective inhibitors of MCL1 or BCL2 and showed benefit of the combination. Taken together, these data suggest a strategy of rationally using BCL2 and MCL1 inhibitors in sequence or in combination in AML clinical trials. SIGNIFICANCE: Targeting antiapoptotic proteins in AML is a key therapeutic strategy, and MCL1 is a critical antiapoptotic oncoprotein. Armed with novel MCL1 inhibitors and the potent BCL2 inhibitor venetoclax, it may be possible to selectively induce apoptosis by combining or thoughtfully sequencing these inhibitors based on a rational evaluation of AML. See related commentary by Leber et al., p. 1511 . This article is highlighted in the In This Issue feature, p. 1494 ., (©2018 American Association for Cancer Research.)
- Published
- 2018
- Full Text
- View/download PDF
29. Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
- Author
-
Hodges TR, Abbott JR, Little AJ, Sarkar D, Salovich JM, Howes JE, Akan DT, Sai J, Arnold AL, Browning C, Burns MC, Sobolik T, Sun Q, Beesetty Y, Coker JA, Scharn D, Stadtmueller H, Rossanese OW, Phan J, Waterson AG, McConnell DB, and Fesik SW
- Subjects
- Benzimidazoles chemistry, Extracellular Signal-Regulated MAP Kinases metabolism, Guanine Nucleotide Exchange Factors chemistry, Guanosine Diphosphate metabolism, Guanosine Triphosphate metabolism, HeLa Cells, Humans, Phosphorylation, Protein Conformation, Proto-Oncogene Proteins p21(ras) chemistry, Structure-Activity Relationship, Benzimidazoles pharmacology, Drug Discovery standards, Guanine Nucleotide Exchange Factors metabolism, Proto-Oncogene Proteins p21(ras) metabolism, SOS1 Protein agonists, SOS1 Protein metabolism
- Abstract
Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.
- Published
- 2018
- Full Text
- View/download PDF
30. Understanding the Species Selectivity of Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors.
- Author
-
Zhao B, Arnold AL, Coronel MA, Lee JH, Lee T, Olejniczak ET, and Fesik SW
- Subjects
- Amino Acid Sequence, Animals, Crystallography, X-Ray, Dogs, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, Humans, Mice, Molecular Sequence Data, Protein Binding drug effects, Rabbits, Rats, Sequence Homology, Amino Acid, Structure-Activity Relationship, Myeloid Cell Leukemia Sequence 1 Protein chemistry, Myeloid Cell Leukemia Sequence 1 Protein metabolism
- Abstract
To test for on target toxicity of a new chemical entity, it is important to have comparable binding affinities of the compound in the target proteins from humans and the test species. To evaluate our myeloid cell leukemia-1 (Mcl-1) inhibitors, we tested them against rodent Mcl-1 and found a significant loss of binding affinity when compared to that seen with human Mcl-1. To understand the affinity loss, we used sequence alignments and structures of human Mcl-1/inhibitor complexes to identify the important differences in the amino acid sequences. One difference is human L246 (F226 in rat, F227 in mouse) in the ligand binding pocket. Mutating rat F226 to a Leu restores affinity, but the mouse F227L mutant still has a ligand affinity that is lower than that of human Mcl-1. Another mutation of mouse F267, located ∼12 Å from the ligand pocket, to the human/rat cysteine, F267C, improved the affinity and combined with F227L resulted in a mutant mouse protein with a binding affinity similar to that of human Mcl-1. To help understand the structural components of the affinity loss, we obtained an X-ray structure of a mouse Mcl-1/inhibitor complex and identified how the residue changes reduced compound complementarity. Finally, we tested Mcl-1 of other preclinical animal models (canine, monkey, rabbit, and ferret) that are identical to humans in terms of these two residues and found that their Mcl-1 bound our compounds with affinities comparable to that of human Mcl-1. These results have implications for understanding ligand selectivity for similar proteins and for the interpretation of preclinical toxicology studies with Mcl-1 inhibitors.
- Published
- 2018
- Full Text
- View/download PDF
31. Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS.
- Author
-
Abbott JR, Patel PA, Howes JE, Akan DT, Kennedy JP, Burns MC, Browning CF, Sun Q, Rossanese OW, Phan J, Waterson AG, and Fesik SW
- Abstract
Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One approach for modulating RAS signaling is to target proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report hit-to-lead studies on quinazoline-containing compounds that bind to SOS1 and activate nucleotide exchange on RAS. Using structure-based design, we refined the substituents attached to the quinazoline nucleus and built in additional interactions not present in the initial HTS hit. Optimized compounds activate nucleotide exchange at single-digit micromolar concentrations in vitro. In HeLa cells, these quinazolines increase the levels of RAS-GTP and cause signaling changes in the mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway., Competing Interests: The authors declare the following competing financial interest(s): RAS activator compounds have been licensed to Boehringer Ingelheim.
- Published
- 2018
- Full Text
- View/download PDF
32. Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling.
- Author
-
Abbott JR, Hodges TR, Daniels RN, Patel PA, Kennedy JP, Howes JE, Akan DT, Burns MC, Sai J, Sobolik T, Beesetty Y, Lee T, Rossanese OW, Phan J, Waterson AG, and Fesik SW
- Subjects
- HeLa Cells, Humans, Models, Molecular, Protein Conformation, SOS1 Protein chemistry, Structure-Activity Relationship, ras Proteins chemistry, Drug Design, Indoles chemistry, Indoles pharmacology, Piperidines chemistry, SOS1 Protein metabolism, Signal Transduction drug effects, ras Proteins metabolism
- Abstract
Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS activity is to target and affect the activity of proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report on structure-activity relationships (SAR) in an indole series of compounds. Using structure-based design, we systematically explored substitution patterns on the indole nucleus, the pendant amino acid moiety, and the linker unit that connects these two fragments. Best-in-class compounds activate the nucleotide exchange process at submicromolar concentrations in vitro, increase levels of active RAS-GTP in HeLa cells, and elicit signaling changes in the mitogen-activated protein kinase-extracellular regulated kinase (MAPK-ERK) pathway, resulting in a decrease in pERK1/2
T202/Y204 protein levels at higher compound concentrations.- Published
- 2018
- Full Text
- View/download PDF
33. Discovery of Potent 2-Aryl-6,7-dihydro-5 H-pyrrolo[1,2- a]imidazoles as WDR5-WIN-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design.
- Author
-
Wang F, Jeon KO, Salovich JM, Macdonald JD, Alvarado J, Gogliotti RD, Phan J, Olejniczak ET, Sun Q, Wang S, Camper D, Yuh JP, Shaw JG, Sai J, Rossanese OW, Tansey WP, Stauffer SR, and Fesik SW
- Subjects
- Amino Acid Motifs, Amino Acid Sequence, Binding Sites, Cell Line, Tumor, Cell Proliferation drug effects, Histone-Lysine N-Methyltransferase metabolism, Humans, Intracellular Signaling Peptides and Proteins, Structure-Activity Relationship, Drug Design, Histone-Lysine N-Methyltransferase antagonists & inhibitors, Histone-Lysine N-Methyltransferase chemistry, Imidazoles chemistry, Imidazoles pharmacology
- Abstract
WDR5 is a chromatin-regulatory scaffold protein overexpressed in various cancers and a potential epigenetic drug target for the treatment of mixed-lineage leukemia. Here, we describe the discovery of potent and selective WDR5-WIN-site inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified several chemically distinct hit series that bind to the WIN site within WDR5. Members of a 6,7-dihydro-5 H-pyrrolo[1,2- a]imidazole fragment class were expanded using a structure-based design approach to arrive at lead compounds with dissociation constants <10 nM and micromolar cellular activity against an AML-leukemia cell line. These compounds represent starting points for the discovery of clinically useful WDR5 inhibitors for the treatment of cancer.
- Published
- 2018
- Full Text
- View/download PDF
34. Small Molecule-Mediated Activation of RAS Elicits Biphasic Modulation of Phospho-ERK Levels that Are Regulated through Negative Feedback on SOS1.
- Author
-
Howes JE, Akan DT, Burns MC, Rossanese OW, Waterson AG, and Fesik SW
- Subjects
- Cell Line, Tumor, Enzyme Activation drug effects, HCT116 Cells, HEK293 Cells, HeLa Cells, Humans, Molecular Structure, Mutation, Missense, Phosphorylation drug effects, Protein Binding, SOS1 Protein genetics, Small Molecule Libraries chemistry, ras Proteins genetics, Extracellular Signal-Regulated MAP Kinases metabolism, Feedback, Physiological drug effects, SOS1 Protein metabolism, Small Molecule Libraries pharmacology, ras Proteins metabolism
- Abstract
Oncogenic mutation of RAS results in aberrant cellular signaling and is responsible for more than 30% of all human tumors. Therefore, pharmacologic modulation of RAS has attracted great interest as a therapeutic strategy. Our laboratory has recently discovered small molecules that activate Son of Sevenless (SOS)-catalyzed nucleotide exchange on RAS and inhibit downstream signaling. Here, we describe how pharmacologically targeting SOS1 induced biphasic modulation of RAS-GTP and ERK phosphorylation levels, which we observed in a variety of cell lines expressing different RAS-mutant isoforms. We show that compound treatment caused an increase in phosphorylation at ERK consensus motifs on SOS1 that was not observed with the expression of a non-phosphorylatable S1178A SOS1 mutant or after pretreatment with an ERK inhibitor. Phosphorylation at S1178 on SOS1 is known to inhibit the association between SOS1 and GRB2 and disrupt SOS1 membrane localization. Consistent with this, we show that wild-type SOS1 and GRB2 dissociated in a time-dependent fashion in response to compound treatment, and conversely, this interaction was enhanced with the expression of an S1178A SOS1 mutant. Furthermore, in cells expressing either S1178A SOS1 or a constitutively membrane-bound CAAX box tagged SOS1 mutant, we observed elevated RAS-GTP levels over time in response to compound, as compared with the biphasic changes in RAS-GTP exhibited in cells expressing wild-type SOS1. These results suggest that small molecule targeting of SOS1 can elicit a biphasic modulation of RAS-GTP and phospho-ERK levels through negative feedback on SOS1 that regulates the interaction between SOS1 and GRB2. Mol Cancer Ther; 17(5); 1051-60. ©2018 AACR ., (©2018 American Association for Cancer Research.)
- Published
- 2018
- Full Text
- View/download PDF
35. High-throughput screening identifies small molecules that bind to the RAS:SOS:RAS complex and perturb RAS signaling.
- Author
-
Burns MC, Howes JE, Sun Q, Little AJ, Camper DV, Abbott JR, Phan J, Lee T, Waterson AG, Rossanese OW, and Fesik SW
- Subjects
- HeLa Cells, Humans, Proto-Oncogene Proteins p21(ras) chemistry, Proto-Oncogene Proteins p21(ras) genetics, SOS1 Protein chemistry, SOS1 Protein genetics, MAP Kinase Signaling System, Proto-Oncogene Proteins p21(ras) metabolism, SOS1 Protein metabolism
- Abstract
K-RAS is mutated in approximately 30% of human cancers, resulting in increased RAS signaling and tumor growth. Thus, RAS is a highly validated therapeutic target, especially in tumors of the pancreas, lung and colon. Although directly targeting RAS has proven to be challenging, it may be possible to target other proteins involved in RAS signaling, such as the guanine nucleotide exchange factor Son of Sevenless (SOS). We have previously reported on the discovery of small molecules that bind to SOS1, activate SOS-mediated nucleotide exchange on RAS, and paradoxically inhibit ERK phosphorylation (Burns et al., PNAS, 2014). Here, we describe the discovery of additional, structurally diverse small molecules that also bind to SOS1 in the same pocket and elicit similar biological effects. We tested >160,000 compounds in a fluorescence-based assay to assess their effects on SOS-mediated nucleotide exchange. X-Ray structures revealed that these small molecules bind to the CDC25 domain of SOS1. Compounds that elicited high levels of nucleotide exchange activity in vitro increased RAS-GTP levels in cells, and inhibited phospho ERK levels at higher treatment concentrations. The identification of structurally diverse SOS1 binding ligands may assist in the discovery of new molecules designed to target RAS-driven tumors., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
- Full Text
- View/download PDF
36. Optimization of Potent and Selective Tricyclic Indole Diazepinone Myeloid Cell Leukemia-1 Inhibitors Using Structure-Based Design.
- Author
-
Shaw S, Bian Z, Zhao B, Tarr JC, Veerasamy N, Jeon KO, Belmar J, Arnold AL, Fogarty SA, Perry E, Sensintaffar JL, Camper DV, Rossanese OW, Lee T, Olejniczak ET, and Fesik SW
- Subjects
- Apoptosis, Caspases metabolism, Cell Division drug effects, Cell Line, Tumor, Crystallography, X-Ray, Drug Design, Enzyme Activators chemical synthesis, Enzyme Activators pharmacology, Humans, Models, Molecular, Molecular Structure, Proto-Oncogene Proteins c-bcl-2 antagonists & inhibitors, Structure-Activity Relationship, Azepines chemical synthesis, Azepines pharmacology, Indoles chemical synthesis, Indoles pharmacology, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors
- Abstract
Myeloid cell leukemia 1 (Mcl-1), an antiapoptotic member of the Bcl-2 family of proteins, has emerged as an attractive target for cancer therapy. Mcl-1 upregulation is often found in many human cancers and is associated with high tumor grade, poor survival, and resistance to chemotherapy. Here, we describe a series of potent and selective tricyclic indole diazepinone Mcl-1 inhibitors that were discovered and further optimized using structure-based design. These compounds exhibit picomolar binding affinity and mechanism-based cellular efficacy, including growth inhibition and caspase induction in Mcl-1-sensitive cells. Thus, they represent useful compounds to study the implication of Mcl-1 inhibition in cancer and serve as potentially useful starting points toward the discovery of anti-Mcl-1 therapeutics.
- Published
- 2018
- Full Text
- View/download PDF
37. Structure of a Myeloid cell leukemia-1 (Mcl-1) inhibitor bound to drug site 3 of Human Serum Albumin.
- Author
-
Zhao B, Sensintaffar J, Bian Z, Belmar J, Lee T, Olejniczak ET, and Fesik SW
- Subjects
- Binding Sites, Cell Line, Crystallography, X-Ray, Humans, Ligands, Molecular Docking Simulation, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Neoplasms drug therapy, Neoplasms metabolism, Protein Binding, Serum Albumin chemistry, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors, Serum Albumin metabolism
- Abstract
Amplification of the gene encoding Myeloid cell leukemia-1 (Mcl-1) is one of the most common genetic aberrations in human cancer and is associated with high tumor grade and poor survival. Recently, we reported on the discovery of high affinity Mcl-1 inhibitors that elicit mechanism-based cell activity. These inhibitors are lipophilic and contain an acidic functionality which is a common chemical profile for compounds that bind to albumin in plasma. Indeed, these Mcl-1 inhibitors exhibited reduced in vitro cell activity in the presence of serum. Here we describe the structure of a lead Mcl-1 inhibitor when bound to Human Serum Albumin (HSA). Unlike many acidic lipophilic compounds that bind to drug site 1 or 2, we found that this Mcl-1 inhibitor binds predominantly to drug site 3. Site 3 of HSA may be able to accommodate larger, more rigid compounds that do not fit into the smaller drug site 1 or 2. Structural studies of molecules that bind to this third site may provide insight into how some higher molecular weight compounds bind to albumin and could be used to aid in the design of compounds with reduced albumin binding., (Copyright © 2017. Published by Elsevier Ltd.)
- Published
- 2017
- Full Text
- View/download PDF
38. Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors.
- Author
-
Lee T, Bian Z, Zhao B, Hogdal LJ, Sensintaffar JL, Goodwin CM, Belmar J, Shaw S, Tarr JC, Veerasamy N, Matulis SM, Koss B, Fischer MA, Arnold AL, Camper DV, Browning CF, Rossanese OW, Budhraja A, Opferman J, Boise LH, Savona MR, Letai A, Olejniczak ET, and Fesik SW
- Subjects
- Animals, Antineoplastic Agents chemistry, Bcl-2-Like Protein 11 metabolism, Cell Line, Tumor, Cell Proliferation drug effects, Cell Survival drug effects, Drug Design, Drug Discovery, Humans, Immunoprecipitation, Membrane Potential, Mitochondrial drug effects, Mice, Myeloid Cell Leukemia Sequence 1 Protein metabolism, bcl-X Protein metabolism, Antineoplastic Agents pharmacology, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors
- Abstract
Myeloid cell leukemia 1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that when overexpressed is associated with high tumor grade, poor survival, and resistance to chemotherapy. Mcl-1 is amplified in many human cancers, and knockdown of Mcl-1 using RNAi can lead to apoptosis. Thus, Mcl-1 is a promising cancer target. Here, we describe the discovery of picomolar Mcl-1 inhibitors that cause caspase activation, mitochondrial depolarization, and selective growth inhibition. These compounds represent valuable tools to study the role of Mcl-1 in cancer and serve as useful starting points for the discovery of clinically useful Mcl-1 inhibitors., Pdb Id Codes: Comp. 2: 5IEZ; Comp. 5: 5IF4., (© 2016 Federation of European Biochemical Societies.)
- Published
- 2017
- Full Text
- View/download PDF
39. Recent advancements in the discovery of protein-protein interaction inhibitors of replication protein A.
- Author
-
Patrone JD, Waterson AG, and Fesik SW
- Abstract
Due to the relatively high rate of DNA damage that can occur during cell cycle progression, the DNA damage response (DDR) pathway is critical for the survival of eukaryotic cells. Replication protein A (RPA) is an essential cell cycle checkpoint protein that mediates the initiation of the DDR by binding to single-stranded DNA (ssDNA) and recruiting response partners via protein-protein interactions (PPIs). This important role of RPA in initiating the DDR and cell survival has led to interest within the scientific community to investigate RPA as a potential cancer drug discovery target. To this end, RPA inhibitors have been explored via a variety of methods. This review summarizes the structure and function of RPA and highlights recent efforts to discover inhibitors of RPA-protein interactions.
- Published
- 2016
- Full Text
- View/download PDF
40. Twenty years on: the impact of fragments on drug discovery.
- Author
-
Erlanson DA, Fesik SW, Hubbard RE, Jahnke W, and Jhoti H
- Subjects
- Clinical Trials as Topic, Computational Biology, High-Throughput Screening Assays, Humans, Peptide Library, Protein Conformation, Small Molecule Libraries, Drug Discovery trends, Peptide Fragments pharmacology
- Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
- Published
- 2016
- Full Text
- View/download PDF
41. Identification and Optimization of Anthranilic Acid Based Inhibitors of Replication Protein A.
- Author
-
Patrone JD, Pelz NF, Bates BS, Souza-Fagundes EM, Vangamudi B, Camper DV, Kuznetsov AG, Browning CF, Feldkamp MD, Frank AO, Gilston BA, Olejniczak ET, Rossanese OW, Waterson AG, Chazin WJ, and Fesik SW
- Subjects
- Anisotropy, Dose-Response Relationship, Drug, Fluorescence Polarization, High-Throughput Screening Assays, Models, Molecular, Molecular Structure, Structure-Activity Relationship, ortho-Aminobenzoates chemical synthesis, Replication Protein A antagonists & inhibitors, ortho-Aminobenzoates chemistry, ortho-Aminobenzoates pharmacology
- Abstract
Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that initiates the DNA damage response pathway through protein-protein interactions (PPIs) mediated by its 70N domain. The identification and use of chemical probes that can specifically disrupt these interactions is important for validating RPA as a cancer target. A high-throughput screen (HTS) to identify new chemical entities was conducted, and 90 hit compounds were identified. From these initial hits, an anthranilic acid based series was optimized by using a structure-guided iterative medicinal chemistry approach to yield a cell-penetrant compound that binds to RPA70N with an affinity of 812 nm. This compound, 2-(3- (N-(3,4-dichlorophenyl)sulfamoyl)-4-methylbenzamido)benzoic acid (20 c), is capable of inhibiting PPIs mediated by this domain., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2016
- Full Text
- View/download PDF
42. Discovery of 2-Indole-acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods.
- Author
-
Pelz NF, Bian Z, Zhao B, Shaw S, Tarr JC, Belmar J, Gregg C, Camper DV, Goodwin CM, Arnold AL, Sensintaffar JL, Friberg A, Rossanese OW, Lee T, Olejniczak ET, and Fesik SW
- Subjects
- Crystallography, X-Ray, Dose-Response Relationship, Drug, Humans, Indoles chemical synthesis, Indoles chemistry, Models, Molecular, Molecular Structure, Structure-Activity Relationship, Sulfonamides chemical synthesis, Sulfonamides chemistry, Drug Discovery, Indoles pharmacology, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors, Sulfonamides pharmacology
- Abstract
Myeloid cell leukemia-1 (Mcl-1) is a member of the Bcl-2 family of proteins responsible for the regulation of programmed cell death. Amplification of Mcl-1 is a common genetic aberration in human cancer whose overexpression contributes to the evasion of apoptosis and is one of the major resistance mechanisms for many chemotherapies. Mcl-1 mediates its effects primarily through interactions with pro-apoptotic BH3 containing proteins that achieve high affinity for the target by utilizing four hydrophobic pockets in its binding groove. Here we describe the discovery of Mcl-1 inhibitors using fragment-based methods and structure-based design. These novel inhibitors exhibit low nanomolar binding affinities to Mcl-1 and >500-fold selectivity over Bcl-xL. X-ray structures of lead Mcl-1 inhibitors when complexed to Mcl-1 provided detailed information on how these small-molecules bind to the target and were used extensively to guide compound optimization.
- Published
- 2016
- Full Text
- View/download PDF
43. Myeloid cell leukemia-1 is an important apoptotic survival factor in triple-negative breast cancer.
- Author
-
Goodwin CM, Rossanese OW, Olejniczak ET, and Fesik SW
- Subjects
- Apoptosis drug effects, Apoptosis Regulatory Proteins genetics, Apoptosis Regulatory Proteins metabolism, Bcl-2-Like Protein 11, Bridged Bicyclo Compounds, Heterocyclic pharmacology, Cell Line, Tumor, Cell Survival drug effects, Female, Humans, Membrane Proteins genetics, Membrane Proteins metabolism, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors, Myeloid Cell Leukemia Sequence 1 Protein genetics, Proto-Oncogene Proteins genetics, Proto-Oncogene Proteins metabolism, Proto-Oncogene Proteins c-bcl-2 genetics, Proto-Oncogene Proteins c-bcl-2 metabolism, RNA Interference, RNA, Small Interfering metabolism, Sulfonamides pharmacology, Triple Negative Breast Neoplasms metabolism, Triple Negative Breast Neoplasms pathology, bcl-2 Homologous Antagonist-Killer Protein genetics, bcl-2 Homologous Antagonist-Killer Protein metabolism, bcl-2-Associated X Protein genetics, bcl-2-Associated X Protein metabolism, bcl-X Protein antagonists & inhibitors, bcl-X Protein genetics, Myeloid Cell Leukemia Sequence 1 Protein metabolism, bcl-X Protein metabolism
- Abstract
Breast cancer is the second-most frequently diagnosed malignancy in US women. The triple-negative breast cancer (TNBC) subtype, which lacks expression of the estrogen receptor, progesterone receptor and human epidermal growth factor receptor-2, afflicts 15% of patients and is refractory to current targeted therapies. Like many cancers, TNBC cells often deregulate programmed cell death by upregulating anti-apoptotic proteins of the B-cell CLL/lymphoma 2 (Bcl-2) family. One family member, myeloid cell leukemia-1 (Mcl-1), is commonly amplified in TNBC and correlates with a poor clinical prognosis. Here we show the effect of silencing Mcl-1 and Bcl-2-like protein 1 isoform 1 (Bcl-xL) expression on viability in a panel of seventeen TNBC cell lines. Cell death was observed in a subset upon Mcl-1 knockdown. In contrast, Bcl-xL knockdown only modestly reduced viability, indicating that Mcl-1 is a more important survival factor. However, dual silencing of both Mcl-1 and Bcl-xL reduced viability in most cell lines tested. These proliferation results were recapitulated by BH3 profiling experiments. Treatment with a Bcl-xL and Bcl-2 peptide had only a moderate effect on any of the TNBC cell lines, however, co-dosing an Mcl-1-selective peptide with a peptide that inhibits Bcl-xL and Bcl-2 was effective in each line tested. Similarly, the selective Bcl-xL inhibitor WEHI-539 was only weakly cytotoxic across the panel, but sensitization by Mcl-1 knockdown markedly improved its EC50. ABT-199, which selectively inhibits Bcl-2, did not synergize with Mcl-1 knockdown, indicating the relatively low importance of Bcl-2 in these lines. Mcl-1 sensitivity is not predicted by mRNA or protein levels of a single Bcl-2 family member, except for only a weak correlation for Bak and Bax protein expression. However, a more comprehensive index composed of Mcl-1, Bcl-xL, Bim, Bak and Noxa protein or mRNA expression correlates well with Mcl-1 sensitivity in TNBC and can also predict Mcl-1 dependency in non-small cell lung cancer cell lines.
- Published
- 2015
- Full Text
- View/download PDF
44. Discovery of tricyclic indoles that potently inhibit Mcl-1 using fragment-based methods and structure-based design.
- Author
-
Burke JP, Bian Z, Shaw S, Zhao B, Goodwin CM, Belmar J, Browning CF, Vigil D, Friberg A, Camper DV, Rossanese OW, Lee T, Olejniczak ET, and Fesik SW
- Subjects
- Crystallography, X-Ray, Heterocyclic Compounds, 3-Ring chemical synthesis, Heterocyclic Compounds, 3-Ring pharmacology, Humans, Indoles chemical synthesis, Indoles pharmacology, K562 Cells, Models, Molecular, Molecular Conformation, Myeloid Cell Leukemia Sequence 1 Protein metabolism, Protein Binding, Structure-Activity Relationship, bcl-X Protein chemistry, bcl-X Protein metabolism, Heterocyclic Compounds, 3-Ring chemistry, Indoles chemistry, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors
- Abstract
Myeloid cell leukemia-1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that is overexpressed and amplified in many cancers. Overexpression of Mcl-1 allows cancer cells to evade apoptosis and contributes to the resistance of cancer cells to be effectively treated with various chemotherapies. From an NMR-based screen of a large fragment library, several distinct chemical scaffolds that bind to Mcl-1 were discovered. Here, we describe the discovery of potent tricyclic 2-indole carboxylic acid inhibitors that exhibit single digit nanomolar binding affinity to Mcl-1 and greater than 1700-fold selectivity over Bcl-xL and greater than 100-fold selectivity over Bcl-2. X-ray structures of these compounds when complexed to Mcl-1 provide detailed information on how these small-molecules bind to the target, which was used to guide compound optimization.
- Published
- 2015
- Full Text
- View/download PDF
45. Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC.
- Author
-
Thomas LR, Wang Q, Grieb BC, Phan J, Foshage AM, Sun Q, Olejniczak ET, Clark T, Dey S, Lorey S, Alicie B, Howard GC, Cawthon B, Ess KC, Eischen CM, Zhao Z, Fesik SW, and Tansey WP
- Subjects
- Amino Acid Motifs, Amino Acid Sequence, Animals, Anisotropy, Binding Sites genetics, Carcinogenesis genetics, Chromatin chemistry, Chromatin genetics, Fluorescence Polarization, HEK293 Cells, Humans, Intracellular Signaling Peptides and Proteins, Mice, Mice, Nude, Models, Molecular, Molecular Sequence Data, Mutation, NIH 3T3 Cells, Protein Binding, Protein Structure, Tertiary, Proteins chemistry, Proteins genetics, Proto-Oncogene Proteins c-myc chemistry, Proto-Oncogene Proteins c-myc genetics, Sequence Homology, Amino Acid, Two-Hybrid System Techniques, Carcinogenesis metabolism, Chromatin metabolism, Proteins metabolism, Proto-Oncogene Proteins c-myc metabolism
- Abstract
MYC is an oncoprotein transcription factor that is overexpressed in the majority of malignancies. The oncogenic potential of MYC stems from its ability to bind regulatory sequences in thousands of target genes, which depends on interaction of MYC with its obligate partner, MAX. Here, we show that broad association of MYC with chromatin also depends on interaction with the WD40-repeat protein WDR5. MYC binds WDR5 via an evolutionarily conserved "MYC box IIIb" motif that engages a shallow, hydrophobic cleft on the surface of WDR5. Structure-guided mutations in MYC that disrupt interaction with WDR5 attenuate binding of MYC at ∼80% of its chromosomal locations and disable its ability to promote induced pluripotent stem cell formation and drive tumorigenesis. Our data reveal WDR5 as a key determinant for MYC recruitment to chromatin and uncover a tractable target for the discovery of anticancer therapies against MYC-driven tumors., (Copyright © 2015 Elsevier Inc. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
46. Small molecule Mcl-1 inhibitors for the treatment of cancer.
- Author
-
Belmar J and Fesik SW
- Subjects
- Antineoplastic Agents therapeutic use, Humans, Neoplasms drug therapy, Neoplasms metabolism, Antineoplastic Agents pharmacology, Myeloid Cell Leukemia Sequence 1 Protein antagonists & inhibitors
- Abstract
The Bcl-2 family of proteins serves as primary regulators of apoptosis. Myeloid cell leukemia 1 (Mcl-1), a pro-survival member of the Bcl-2 family of proteins, is overexpressed and the Mcl-1 gene is amplified in many tumor types. Moreover, the overexpression of Mcl-1 is the cause of resistance to several chemotherapeutic agents. Thus, Mcl-1 is a promising cancer target. This review highlights the current progress on the discovery of small molecule Mcl-1 inhibitors., (Copyright © 2014 Elsevier Inc. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
47. Fragment-based screening of the bromodomain of ATAD2.
- Author
-
Harner MJ, Chauder BA, Phan J, and Fesik SW
- Subjects
- ATPases Associated with Diverse Cellular Activities, Antineoplastic Agents chemistry, Binding Sites, Crystallography, X-Ray methods, Humans, Kinetics, Ligands, Magnetic Resonance Spectroscopy methods, Molecular Conformation, Neoplasms drug therapy, Protein Structure, Tertiary, Adenosine Triphosphatases chemistry, Chemistry, Pharmaceutical methods, DNA-Binding Proteins chemistry
- Abstract
Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. Fragment hits were identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.
- Published
- 2014
- Full Text
- View/download PDF
48. Diphenylpyrazoles as replication protein a inhibitors.
- Author
-
Waterson AG, Kennedy JP, Patrone JD, Pelz NF, Feldkamp MD, Frank AO, Vangamudi B, Souza-Fagundes EM, Rossanese OW, Chazin WJ, and Fesik SW
- Abstract
Replication Protein A is the primary eukaryotic ssDNA binding protein that has a central role in initiating the cellular response to DNA damage. RPA recruits multiple proteins to sites of DNA damage via the N-terminal domain of the 70 kDa subunit (RPA70N). Here we describe the optimization of a diphenylpyrazole carboxylic acid series of inhibitors of these RPA-protein interactions. We evaluated substituents on the aromatic rings as well as the type and geometry of the linkers used to combine fragments, ultimately leading to submicromolar inhibitors of RPA70N protein-protein interactions.
- Published
- 2014
- Full Text
- View/download PDF
49. Drugging the undruggable RAS: Mission possible?
- Author
-
Cox AD, Fesik SW, Kimmelman AC, Luo J, and Der CJ
- Subjects
- Animals, Antineoplastic Agents pharmacology, Antineoplastic Agents therapeutic use, Humans, Oncogene Proteins antagonists & inhibitors, Oncogene Proteins metabolism, Signal Transduction drug effects, ras Proteins antagonists & inhibitors, ras Proteins metabolism
- Abstract
Despite more than three decades of intensive effort, no effective pharmacological inhibitors of the RAS oncoproteins have reached the clinic, prompting the widely held perception that RAS proteins are 'undruggable'. However, recent data from the laboratory and the clinic have renewed our hope for the development of RAS-inhibitory molecules. In this Review, we summarize the progress and the promise of five key approaches. Firstly, we focus on the prospects of using direct inhibitors of RAS. Secondly, we address the issue of whether blocking RAS membrane association is a viable approach. Thirdly, we assess the status of targeting RAS downstream effector signalling, which is arguably the most favourable current approach. Fourthly, we address whether the search for synthetic lethal interactors of mutant RAS still holds promise. Finally, RAS-mediated changes in cell metabolism have recently been described and we discuss whether these changes could be exploited for new therapeutic directions. We conclude with perspectives on how additional complexities, which are not yet fully understood, may affect each of these approaches.
- Published
- 2014
- Full Text
- View/download PDF
50. A method for the second-site screening of K-Ras in the presence of a covalently attached first-site ligand.
- Author
-
Sun Q, Phan J, Friberg AR, Camper DV, Olejniczak ET, and Fesik SW
- Subjects
- Cysteine chemistry, Cysteine metabolism, Ligands, Nuclear Magnetic Resonance, Biomolecular methods, Protein Binding, Proto-Oncogene Proteins p21(ras) metabolism, Drug Discovery methods, Models, Molecular, Proto-Oncogene Proteins p21(ras) chemistry
- Abstract
K-Ras is a well-validated cancer target but is considered to be "undruggable" due to the lack of suitable binding pockets. We previously discovered small molecules that bind weakly to K-Ras but wanted to improve their binding affinities by identifying ligands that bind near our initial hits that we could link together. Here we describe an approach for identifying second site ligands that uses a cysteine residue to covalently attach a compound for tight binding to the first site pocket followed by a fragment screen for binding to a second site. This approach could be very useful for targeting Ras and other challenging drug targets.
- Published
- 2014
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.