Protein-protein interactions (PPIs) are critical regulatory events in physiology and pathology, and they represent an important target space for pharmacological intervention. However, targeting PPIs ...with small molecules is challenging owing to the large surface area involved in protein-protein binding and the lack of obvious small-molecule-binding pockets at many protein-protein interfaces. Nonetheless, successful examples of small-molecule modulators of PPIs have been growing in recent years. This article reviews some of the recent advances in the discovery of small-molecule regulators of PPIs that involve key oncogenic proteins. Our discussion focuses on the three key modes of action for these small-molecule modulators: orthosteric inhibition, allosteric regulation, and interfacial binding/stabilization. Understanding the opportunities and challenges of these diverse mechanisms will help guide future efforts in developing small-molecule modulators against PPIs.
Three decades after identification of the Ras oncogene, no effective treatments for Ras mutant tumors are available despite intensive drug discovery efforts. Here we critically review the attempts to ...inhibit Ras function via direct binding of small molecules at the Ras surface with the aim to disrupt its interaction with other proteins. Multiple binders at different binding sites have been discovered, and recent efforts afforded crystal structures of Ras–binder complexes. Albeit with low affinities, many of the binders were shown to impart inhibitory activities, and inhibition of nucleotide exchange as a consequence of disrupting the Ras–SOS interaction has been the most commonly identified mode of action. We see two key challenges in the development of these early starting points: Enhancing binding affinities and achieving selectivity, both against other GTPases and for mutant Ras over the wildtype form. In light of the large unmet medical need, we encourage the continued search for functionally active Ras binders, and we believe that integrated use of biophysical and biochemical tools will provide the highest chances for success. Given the failures experienced in the past and the significant hurdles ahead, we propose that this challenge be tackled through alliances between industry and academia.
Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to ...overactive Wnt signaling in subsets of pancreatic, ovarian, gastric, and colorectal tumors. Despite the progress in biochemical understanding of Wnt–FZD receptor interactions, the molecular basis for recognition of Wnt cis-unsaturated fatty acyl groups by the cysteine-rich domain (CRD) of FZD receptors remains elusive. Here, we determined a crystal structure of human FZD7 CRD unexpectedly bound to a 24-carbon fatty acid. We also report a crystal structure of human FZD5 CRD bound to C16:1 cis-Δ9 unsaturated fatty acid. Both structures reveal a dimeric arrangement of the CRD. The lipid-binding groove exhibits flexibility and spans both monomers, adopting a U-shaped geometry that accommodates the fatty acid. Re-evaluation of the published mouse FZD8 CRD structure reveals that it also shares the same architecture as FZD5 and FZD7 CRDs. Our results define a common molecular mechanism for recognition of the cis-unsaturated fatty acyl group, a necessary posttranslational modification of Wnts, by multiple FZD receptors. The fatty acid bridges two CRD monomers, implying that Wnt binding mediates FZD receptor dimerization. Our data uncover possibilities for the arrangement of Wnt–FZD CRD complexes and shed structural insights that could aide in the identification of pharmacological strategies to modulate FZD receptor function.
The conservativeness of unit commitment models-based robust optimization (RO) depends on the modeling of uncertainty sets. This paper proposes a new two-stage robust security-constrained unit ...commitment (SCUC) model, which aims at minimizing the operating cost in the base scenario while guaranteeing that the robust solution can be adaptively and safely adjusted according to the uncertainties of wind power, load, and <inline-formula> <tex-math notation="LaTeX">N </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">k </tex-math></inline-formula> fault. This new model has the following characteristics: 1) the temporal correlation of continuous uncertainties (i.e., wind power output and load) are studied and a time-correlation constraint is established to reduce the conservativeness of uncertainty sets in the proposed robust SCUC model; 2) the discrete characteristics of the uncertain set is used to describe the uncertainty of discrete <inline-formula> <tex-math notation="LaTeX">N </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">k </tex-math></inline-formula> fault; 3) the outage probability of units with different capacity is also considered with a proposed probability criterion; and 4) the constraint approximation is simplified to a linear constraint that can be applied to RO. The proposed model is solved by the Benders decomposition and dual theory. The simulation results on modified IEEE-RTS-96 system show that the proposed method can effectively reduce the conservativeness of uncertain sets and ensure the economic and security of the optimization results.
Recurrent R-spondin fusions in colon cancer SESHAGIRI, Somasekar; STAWISKI, Eric W; GUILLORY, Joseph ...
Nature (London),
08/2012, Letnik:
488, Številka:
7413
Journal Article
Recenzirano
Odprti dostop
Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by ...applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory ...effects have not been uncovered to date. Through an NMR-based fragment screen, we identified a group of small molecules that all bind to a common site on Ras. High-resolution cocrystal structures delineated a unique ligand-binding pocket on the Ras protein that is adjacent to the switch I/II regions and can be expanded upon compound binding. Structure analysis predicts that compound-binding interferes with the Ras/SOS interactions. Indeed, selected compounds inhibit SOS-mediated nucleotide exchange and prevent Ras activation by blocking the formation of intermediates of the exchange reaction. The discovery of a small-molecule binding pocket on Ras with functional significance provides a new direction in the search of therapeutically effective inhibitors of the Ras oncoprotein.
Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T-cell receptor signaling and as such is an attractive target for cancer immunotherapy. Although the role of the HPK1 kinase domain ...(KD) has been extensively characterized, the function of its citron homology domain (CHD) remains elusive. Through a combination of structural, biochemical, and mechanistic studies, we characterize the structure-function of CHD in relationship to KD. Crystallography and hydrogen-deuterium exchange mass spectrometry reveal that CHD adopts a seven-bladed β-propellor fold that binds to KD. Mutagenesis associated with binding and functional studies show a direct correlation between domain-domain interaction and negative regulation of kinase activity. We further demonstrate that the CHD provides stability to HPK1 protein in cells as well as contributes to the docking of its substrate SLP76. Altogether, this study highlights the importance of the CHD in the direct and indirect regulation of HPK1 function.
Inositol requiring enzyme 1 (IRE1) mitigates endoplasmic-reticulum (ER) stress by orchestrating the unfolded-protein response (UPR). IRE1 spans the ER membrane, and signals through a cytosolic ...kinase-endoribonuclease module. The endoribonuclease generates the transcription factor XBP1s by intron excision between similar RNA stem-loop endomotifs, and depletes select cellular mRNAs through regulated IRE1-dependent decay (RIDD). Paradoxically, in mammals RIDD seems to target only mRNAs with XBP1-like endomotifs, while in flies RIDD exhibits little sequence restriction. By comparing nascent and total IRE1α-controlled mRNAs in human cells, we identify not only canonical endomotif-containing RIDD substrates, but also targets without such motifs-degraded by a process we coin RIDDLE, for RIDD lacking endomotif. IRE1α displays two basic endoribonuclease modalities: highly specific, endomotif-directed cleavage, minimally requiring dimers; and more promiscuous, endomotif-independent processing, requiring phospho-oligomers. An oligomer-deficient IRE1α mutant fails to support RIDDLE in vitro and in cells. Our results advance current mechanistic understanding of the UPR.
The membrane of the primary cilium is a highly specialized compartment that organizes proteins to achieve spatially ordered signaling. Disrupting ciliary organization leads to diseases called ...ciliopathies, with phenotypes ranging from retinal degeneration and cystic kidneys to neural tube defects. How proteins are selectively transported to and organized in the primary cilium remains unclear. Using a proteomic approach, we identified the ARL3 effector UNC119 as a binding partner of the myristoylated ciliopathy protein nephrocystin-3 (NPHP3). We mapped UNC119 binding to the N-terminal 200 residues of NPHP3 and found the interaction requires myristoylation. Creating directed mutants predicted from a structural model of the UNC119-myristate complex, we identified highly conserved phenylalanines within a hydrophobic β sandwich to be essential for myristate binding. Furthermore, we found that binding of ARL3-GTP serves to release myristoylated cargo from UNC119. Finally, we showed that ARL3, UNC119b (but not UNC119a), and the ARL3 GAP Retinitis Pigmentosa 2 (RP2) are required for NPHP3 ciliary targeting and that targeting requires UNC119b myristoyl-binding activity. Our results uncover a selective, membrane targeting GTPase cycle that delivers myristoylated proteins to the ciliary membrane and suggest that other myristoylated proteins may be similarly targeted to specialized membrane domains.
Robust optimization (RO) is an important tool to solve the security-constrained unit commitment (SCUC) problem for a power system with large-scale wind power. The main disadvantage of RO is that it ...is overly conservative, and the conservativeness of RO can be attributed to the uncertainty set used in the formulation. This paper proposes a two-stage robust SCUC model considering the spatiotemporal correlation of the uncertainty prediction error. First, based on the historical data, a polyhedral uncertainty set that can describe the spatial-temporal correlation of uncertainties is established, and the analytical relationship between confidence probability and the uncertain set is given. Second, a two-stage robust SCUC model with the objective of minimizing the operating cost under the forecasting scenarios is proposed based on the polyhedral set. Third, the Benders decomposition method is used to solve the proposed model according to its characteristics. The simulation results on the modified IEEE-30 and IEEE-118 bus system demonstrate that the proposed method can reduce the conservativeness of RO and guarantee the security and economy of the unit commitment.
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