scholarly journals Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5

2012 ◽  
Vol 449 (1) ◽  
pp. 151-159 ◽  
Author(s):  
Guillermo Senisterra ◽  
Hong Wu ◽  
Abdellah Allali-Hassani ◽  
Gregory A. Wasney ◽  
Dalia Barsyte-Lovejoy ◽  
...  
Keyword(s):  
Small Molecule ◽  
Catalytic Domain ◽  
Binding Pocket ◽  
Protein Protein Interaction ◽  
Small Molecule Inhibition ◽  
Histone 3 ◽  
Mixed Lineage Leukaemia ◽  
Biophysical Analysis ◽  
Lower Protein

WDR5 (WD40 repeat protein 5) is an essential component of the human trithorax-like family of SET1 [Su(var)3–9 enhancer-of-zeste trithorax 1] methyltransferase complexes that carry out trimethylation of histone 3 Lys4 (H3K4me3), play key roles in development and are abnormally expressed in many cancers. In the present study, we show that the interaction between WDR5 and peptides from the catalytic domain of MLL (mixed-lineage leukaemia protein) (KMT2) can be antagonized with a small molecule. Structural and biophysical analysis show that this antagonist binds in the WDR5 peptide-binding pocket with a Kd of 450 nM and inhibits the catalytic activity of the MLL core complex in vitro. The degree of inhibition was enhanced at lower protein concentrations consistent with a role for WDR5 in directly stabilizing the MLL multiprotein complex. Our data demonstrate inhibition of an important protein–protein interaction and form the basis for further development of inhibitors of WDR5-dependent enzymes implicated in MLL-rearranged leukaemias or other cancers.

Probing the Small-Molecule Inhibition of an Anticancer Therapeutic Protein-Protein Interaction Using a Solid-State Nanopore

2016 ◽  
Vol 128 (19) ◽  
pp. 5807-5811 ◽  
Author(s):  
Dong-Kyu Kwak ◽  
Hongsik Chae ◽  
Mi-Kyung Lee ◽  
Ji-Hyang Ha ◽  
Gaurav Goyal ◽  
...  
Keyword(s):  
Solid State ◽  
Small Molecule ◽  
Protein Interaction ◽  
Therapeutic Protein ◽  
Protein Protein Interaction ◽  
Small Molecule Inhibition

scholarly journals Solution NMR readily reveals distinct structural folds and interactions in doubly 13C- and 19F-labeled RNAs

2020 ◽  
Vol 6 (41) ◽  
pp. eabc6572
Author(s):  
Owen B. Becette ◽  
Guanghui Zong ◽  
Bin Chen ◽  
Kehinde M. Taiwo ◽  
David A. Case ◽  
...  
Keyword(s):  
Small Molecule ◽  
High Sensitivity ◽  
Binding Pocket ◽  
In Vitro Transcription ◽  
Rapid Identification ◽  
Spin Pair ◽  
Encapsidation Signal ◽  
Spin Pairs ◽  
Critical Components

RNAs form critical components of biological processes implicated in human diseases, making them attractive for small-molecule therapeutics. Expanding the sites accessible to nuclear magnetic resonance (NMR) spectroscopy will provide atomic-level insights into RNA interactions. Here, we present an efficient strategy to introduce 19F-13C spin pairs into RNA by using a 5-fluorouridine-5′-triphosphate and T7 RNA polymerase–based in vitro transcription. Incorporating the 19F-13C label in two model RNAs produces linewidths that are twice as sharp as the commonly used 1H-13C spin pair. Furthermore, the high sensitivity of the 19F nucleus allows for clear delineation of helical and nonhelical regions as well as GU wobble and Watson-Crick base pairs. Last, the 19F-13C label enables rapid identification of a small-molecule binding pocket within human hepatitis B virus encapsidation signal epsilon (hHBV ε) RNA. We anticipate that the methods described herein will expand the size limitations of RNA NMR and aid with RNA-drug discovery efforts.

Resistance to Selective FLT3 Inhibitors, Driven by FLT3 Ligand and FLT3 Point Mutations, Can Be Overcome with the Dual FLT3-Aurora Kinase Inhibitor CCT241736,

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3492-3492 ◽  
Author(s):  
Andrew S. Moore ◽  
Amir Faisal ◽  
Vassilios Bavetsias ◽  
David Gonzalez de Castro ◽  
Chongbo Sun ◽  
...  
Keyword(s):  
Cancer Research ◽  
Tyrosine Kinase ◽  
Small Molecule ◽  
Point Mutations ◽  
Flt3 Ligand ◽  
Aurora Kinases ◽  
Small Molecule Inhibition ◽  
Flt3 Inhibitors ◽  
Dual Inhibition

Abstract Abstract 3492 Mutations of the FLT3 gene, arising from internal tandem duplications (−ITD) or point mutations of the tyrosine kinase domain (−TKD), cause constitutive activation of the FLT3 receptor tyrosine kinase resulting in stimulation of leukemic proliferation. FLT3-ITD mutations confer a poor prognosis in acute myeloid leukemia (AML), whilst the prognostic impact of FLT3-TKD mutations remains unclear. Small molecule inhibition of FLT3 kinase has been a focus of AML drug development for the past decade, but sustained clinical benefits have been limited by pharmacokinetic failures and resistance. Important mechanisms of resistance to small molecule inhibition of FLT3 include the development of secondary mutations in the FLT3 gene, elevated levels of FLT3 ligand (FL) and over-expression of the anti-apoptotic protein, Survivin. We have previously reported that high FL levels induce resistance to the selective FLT3 inhibitor MLN518 (tandutinib) in vitro. Furthermore, prolonged treatment of human FLT3-ITD positive AML cells (MOLM-13) with MLN518 caused resistance and the selection of cells doubly-mutated with FLT3-ITD and a FLT3-TKD (D835Y) point mutation. These resistant cells, termed MOLM-13-RES, also over-express Survivin. Here we demonstrate that such doubly-mutated AML cells are also relatively resistant to the FLT3 inhibitors Sorafenib and AC220 but not the dual FLT3-Aurora inhibitor CCT241736. CCT241736 is a novel, orally bioavailable, imidazo[4,5-b]pyridine derivative discovered at our Institute, highly selective for FLT3 and Aurora kinases with an S(10) selectivity score using KINOMEscan™ technology of 0.057 (fraction of 386 non-mutant kinases inhibited >90% when screened at 1 uM of CCT241736; San Diego, CA). In biochemical kinase studies, CCT241736 has IC50 values against FLT3, Aurora A and Aurora B of 0.035, 0.015 and 0.1 uM respectively. Furthermore, CCT241736 inhibits a wide range of FLT3 mutants, including FLT3-ITD, -D835Y, -D835H, -K663Q and –N841I. In cellular assays, CCT241736 inhibits viability of the human FLT3-ITD positive AML cell lines MOLM-13 and MV-4-11 with EC50 values of 0.1 and 0.27 uM respectively. Unlike the selective FLT3 inhibitors MLN518 and AC220, the in vitro cellular efficacy of CCT241736 is not affected by high levels of FL. In vivo, mouse tumor xenograft models of MOLM-13, MV-4-11, and the doubly-mutated cell line MOLM-13-RES are also sensitive to CCT241736 at well tolerated oral doses, with biomarker modulation consistent with dual inhibition of FLT3 and Aurora kinases. Based on allometric scaling from mouse and rat data, CCT241736 has favorable predicted human pharmacokinetics and phase I clinical trials are planned. In summary, dual inhibition of FLT3 and the critical mitotic kinase Aurora by CCT241736 may represent a novel treatment strategy for FLT3-mutated AML by overcoming the effects of high FL levels and limiting resistance caused by secondary mutations of the FLT3 gene. Disclosures: Moore: The Institute of Cancer Research: Employment. Faisal:The Institute of Cancer Research: Employment. Bavetsias:The Institute of Cancer Research: Employment. Gonzalez de Castro:The Institute of Cancer Research: Employment. Sun:The Institute of Cancer Research: Employment. Atrash:The Institute of Cancer Research: Employment. Valenti:The Institute of Cancer Research: Employment. de Haven Brandon:The Institute of Cancer Research: Employment. Avery:The Institute of Cancer Research: Employment. Pearson:The Institute of Cancer Research: Employment. Workman:The Institute of Cancer Research: Employment. Blagg:The Institute of Cancer Research: Employment. Raynaud:The Institute of Cancer Research: Employment. Eccles:The Institute of Cancer Research: Employment. Linardopoulos:The Institute of Cancer Research: Employment.

The Small Molecule Inhibitor of VLA4 TBC3486 Sensitizes Resistant ALL to Chemotherapy

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1500-1500 ◽  
Author(s):  
Yao-Te Hsieh ◽  
Eun Ji Gang ◽  
Halvard Bonig ◽  
Ronald J Biediger ◽  
Peter Vanderslice ◽  
...  
Keyword(s):  
Cell Viability ◽  
Small Molecule ◽  
Conflicts Of Interest ◽  
Lymphoblastic Leukemia ◽  
Chemotherapy Resistance ◽  
Leukemia Cell ◽  
The Novel ◽  
Small Molecule Inhibition

Abstract Abstract 1500 Significant progress notwithstanding, drug resistant acute lymphoblastic leukemia (ALL) remains a therapeutic challenge, as well as acute and long-term off-target toxicity of anti-ALL therapies can be dose-limiting or debilitating. Therefore, the development of more targeted therapies is desirable. We recently provided evidence that chemotherapy resistance of ALL cells can be partly overcome by interfering with the function of VLA4, the alpha4beta1 integrin, in vivo. In those studies, we used the anti-functional antibody Natalizumab. We extended our studies to an alternative VLA4 inhibitor, the novel non-peptidic small molecule TBC3486. Previous in vitro assays and molecular modeling studies indicate that TBC3486 behaves as a ligand mimetic, competing with VCAM-1 for the MIDAS site of VLA-4. As such, the compound has been shown to be efficacious in VLA-4 dependent models of inflammatory and autoimmune disease. The potential usefulness of this novel inhibitor in leukemia treatment was tested in our established in vitro and in vivo assays. LAX7R cells, primary pre-B-ALL with a normal karyotype from a patient with an early relapse, were used throughout for the studies reported here. LAX7R cells were treated with 25μM TBC3486 or THI0012 control, the inactive enantiomer of TBC3486, and seeded onto plates coated with human VCAM-1. Adhesion, scored after 2 days, was significantly inhibited by TBC3486 compared to control treated cells (7.9%±4.0 vs 95.4%±8.0; p=0.003). Proliferation rate and cell viability were unaffected by the treatments. In a co-culture system of LAX7R cells with OP9 stroma cells, which we use as an in vitro model of stroma-mediated chemotherapy resistance, we assessed differential effects of VDL (Vincristine, Dexamethasone, L-Asparaginase) on leukemia cell survival in the presence or absence of TBC3486. Stromal adhesion significantly protected LAX7R cells against VDL chemotherapy; this effect was significantly attenuated by TBC3486 compared to the control as determined by Trypan blue exclusion of dead cells (Cell viability of 39.9%±5.1 vs. 57.2±1.8; p=0.02). After these encouraging observations, we next evaluated the benefit of TBC3486 on leukemia progression in a xenotransplant assay. LAX7R cells were lentivirally labelled with luciferase for in vivo tracking and injected into NOD/SCID hosts. Three days after leukemia cell transfer, mice received either TBC3486 or THI0012 (control) (10mg/kg/d) daily for 2 weeks (intraperitoneally), with or without VDL chemotherapy. This experiment is in progress, but already survival of leukemia-bearing mice was significantly prolonged, from a median survival time (MST) for control mice of 33 days post-leukemia injection to a MST of 47 days post-leukemia injection for TBC3486 treated mice (p=0.02). Similarly, bioluminescence imaging revealed a marked delay of leukemia cell dissemination (p<0.0001). Taken together, our data demonstrate that small molecule inhibition of VLA4 using the novel TBC3486 is a suitable approach for targeting of chemotherapy-resistant leukemia. Further studies are warranted to understand and evaluate preclinically adjuvant small molecule inhibition of integrins to overcome relapse of ALL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Investigating the NRAS 5' UTR as a Target for Small Molecules

2022 ◽  
Author(s):  
Sumirtha Balaratnam ◽  
Zachary R Torrey ◽  
David R. Calabrese ◽  
Michael T Banco ◽  
Kamyar Yazdani ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cell Lines ◽  
Small Molecule ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Small Molecule Inhibition ◽  
Ras Family ◽  
Control Translation ◽  
Rapid Amplification

Neuroblastoma RAS (NRAS) is an oncogene that is deregulated and highly mutated in cancers including melanomas and acute myeloid leukemias. Constitutively activated NRAS induces the MAPK and AKT signaling pathways and leads to uncontrolled proliferation and cell growth, making it an attractive target for small molecule inhibition. Like all RAS-family proteins, it has proven difficult to identify small molecules that directly inhibit the protein. An alternative approach would involve targeting the NRAS mRNA. The 5′ untranslated region (5′ UTR) of the NRAS mRNA is reported to contain a G-quadruplex (G4) that regulates translation of NRAS mRNA. Stabilizing the G4 structure with small molecules could reduce NRAS protein expression in cancer cells by impacting translation. Here we report a novel class of small molecule that binds to the G4 structure located in the 5′ UTR of the NRAS mRNA. We used a small molecule microarray (SMM) screen to identify molecules that selectively bind to the NRAS-G4. Biophysical studies demonstrated that compound 18 binds reversibly to the NRAS-G4 structure with submicromolar affinity. A Luciferase based reporter assay indicated that 18 inhibits the translation of NRAS via stabilizing the NRAS-G4 in vitro but showed only moderate effects on the NRAS levels in cellulo. Rapid Amplification of cDNA Ends (RACE), RT-PCR analysis on 14 different NRAS-expressing cell lines, coupled with analysis of publicly available CAGE seq experiments, revealed that predominant NRAS transcript does not possess the G4 structure. Further analysis of published rG4 and G4 sequencing data indicated the presence of G4 structure in the promoter region of NRAS gene (DNA) but not in the mRNA. Thus, although many NRAS transcripts lack a G4 in many cell lines the broader concept of targeting folded regions within 5' UTRs to control translation remains a highly attractive strategy and this work represents an intriguing example of transcript heterogeneity impacting targetability.

scholarly journals Compensatory Substitutions in the HIV-1 Capsid Reduce the Fitness Cost Associated with Resistance to a Capsid-Targeting Small-Molecule Inhibitor

2014 ◽  
Vol 89 (1) ◽  
pp. 208-219 ◽  
Author(s):  
Jiong Shi ◽  
Jing Zhou ◽  
Upul D. Halambage ◽  
Vaibhav B. Shah ◽  
Mallori J. Burse ◽  
...  
Keyword(s):  
Amino Acid ◽  
Small Molecule ◽  
Therapeutic Target ◽  
Binding Pocket ◽  
Host Protein ◽  
Viral Capsid ◽  
Inhibitory Protein ◽  
Hiv 1 ◽  
Ca Protein

ABSTRACTThe HIV-1 capsid plays multiple roles in infection and is an emerging therapeutic target. The small-molecule HIV-1 inhibitor PF-3450074 (PF74) blocks HIV-1 at an early postentry stage by binding the viral capsid and interfering with its function. Selection for resistance resulted in accumulation of five amino acid changes in the viral CA protein, which collectively reduced binding of the compound to HIV-1 particles. In the present study, we dissected the individual and combinatorial contributions of each of the five substitutions Q67H, K70R, H87P, T107N, and L111I to PF74 resistance, PF74 binding, and HIV-1 infectivity. Q67H, K70R, and T107N each conferred low-level resistance to PF74 and collectively conferred strong resistance. The substitutions K70R and L111I impaired HIV-1 infectivity, which was partially restored by the other substitutions at positions 67 and 107. PF74 binding to HIV-1 particles was reduced by the Q67H, K70R, and T107N substitutions, consistent with the location of these positions in the inhibitor-binding pocket. Replication of the 5Mut virus was markedly impaired in cultured macrophages, reminiscent of the previously reported N74D CA mutant. 5Mut substitutions also reduced the binding of the host protein CPSF6 to assembled CA complexesin vitroand permitted infection of cells expressing the inhibitory protein CPSF6-358. Our results demonstrate that strong resistance to PF74 requires accumulation of multiple substitutions in CA to inhibit PF74 binding and compensate for fitness impairments associated with some of the sequence changes.IMPORTANCEThe HIV-1 capsid is an emerging drug target, and several small-molecule compounds have been reported to inhibit HIV-1 infection by targeting the capsid. Here we show that resistance to the capsid-targeting inhibitor PF74 requires multiple amino acid substitutions in the binding pocket of the CA protein. Three changes in CA were necessary to inhibit binding of PF74 while maintaining viral infectivity. Replication of the PF74-resistant HIV-1 mutant was impaired in macrophages, likely owing to altered interactions with host cell factors. Our results suggest that HIV-1 resistance to capsid-targeting inhibitors will be limited by functional constraints on the viral capsid protein. Therefore, this work enhances the attractiveness of the HIV-1 capsid as a therapeutic target.

scholarly journals Targeting a binding pocket within the trimer-of-hairpins: Small-molecule inhibition of viral fusion

2004 ◽  
Vol 101 (42) ◽  
pp. 15046-15051 ◽  
Author(s):  
C. Cianci ◽  
D. R. Langley ◽  
D. D. Dischino ◽  
Y. Sun ◽  
K.-L. Yu ◽  
...  
Keyword(s):  
Small Molecule ◽  
Binding Pocket ◽  
Viral Fusion ◽  
Small Molecule Inhibition

scholarly journals Small-molecule inhibitor targeting the Hsp90-Cdc37 protein-protein interaction in colorectal cancer

2019 ◽  
Vol 5 (9) ◽  
pp. eaax2277 ◽  
Author(s):  
Lei Wang ◽  
Lixiao Zhang ◽  
Li Li ◽  
Jingsheng Jiang ◽  
Zhen Zheng ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Small Molecule ◽  
Protein Interaction ◽  
Small Molecule Inhibitor ◽  
Protein Protein Interaction ◽  
Molecule Inhibitor ◽  
Dependent Cell ◽  
Hsp90 Chaperone

Disrupting the interactions between Hsp90 and Cdc37 is emerging as an alternative and specific way to regulate the Hsp90 chaperone cycle in a manner not involving adenosine triphosphatase inhibition. Here, we identified DDO-5936 as a small-molecule inhibitor of the Hsp90-Cdc37 protein-protein interaction (PPI) in colorectal cancer. DDO-5936 disrupted the Hsp90-Cdc37 PPI both in vitro and in vivo via binding to a previously unknown site on Hsp90 involving Glu47, one of the binding determinants for the Hsp90-Cdc37 PPI, leading to selective down-regulation of Hsp90 kinase clients in HCT116 cells. In addition, inhibition of Hsp90-Cdc37 complex formation by DDO-5936 resulted in a remarkable cyclin-dependent kinase 4 decrease and consequent inhibition of cell proliferation through Cdc37-dependent cell cycle arrest. Together, our results demonstrated DDO-5936 as an identified specific small-molecule inhibitor of the Hsp90-Cdc37 PPI that could be used to comprehensively investigate alternative approaches targeting Hsp90 chaperone cycles for cancer therapy.

scholarly journals Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle

2008 ◽  
Vol 82 (20) ◽  
pp. 10262-10270 ◽  
Author(s):  
Christina Bourne ◽  
Sejin Lee ◽  
Bollu Venkataiah ◽  
Angela Lee ◽  
Brent Korba ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Small Molecule ◽  
Self Assembly ◽  
Binding Pocket ◽  
Hbv Replication ◽  
B Virus ◽  
In Vitro Assembly ◽  
Kinetics Of

ABSTRACT The relationship between the physical chemistry and biology of self-assembly is poorly understood, but it will be critical to quantitatively understand infection and for the design of antivirals that target virus genesis. Here we take advantage of heteroaryldihydropyrimidines (HAPs), which affect hepatitis B virus (HBV) assembly, to gain insight and correlate in vitro assembly with HBV replication in culture. Based on a low-resolution crystal structure of a capsid-HAP complex, a closely related series of HAPs were designed and synthesized. These differentially strengthen the association between neighboring capsid proteins, alter the kinetics of assembly, and give rise to aberrant structures incompatible with a functional capsid. The chemical nature of the HAP variants correlated well with the structure of the HAP binding pocket. The thermodynamics and kinetics of in vitro assembly had strong and predictable effects on product morphology. However, only the kinetics of in vitro assembly had a strong correlation with inhibition of HBV replication in HepG2.2.15 cells; there was at best a weak correlation between assembly thermodynamics and replication. The correlation between assembly kinetics and virus suppression implies a competition between successful assembly and misassembly, small molecule induced or otherwise. This is a predictive and testable model for the mechanism of action of assembly effectors.

Sign in / Sign up

Export Citation Format

Share Document