The aberrant upregulation of exon 10-inclusive SREK1 through SRSF10 acts as an oncogenic driver in human hepatocellular carcinoma.

Deregulation of alternative splicing is implicated as a relevant source of molecular heterogeneity in cancer. However, the targets and intrinsic mechanisms of splicing in hepatocarcinogenesis are largely unknown. Here, we report a functional impact of a Splicing Regulatory Glutamine/Lysine-Rich Protein 1 (SREK1) variant and its regulator, Serine/arginine-rich splicing factor 10 (SRSF10). HCC patients with poor prognosis express higher levels of exon 10-inclusive SREK1 (SREK1L). SREK1L can sustain BLOC1S5-TXNDC5 (B-T) expression, a targeted gene of nonsense-mediated mRNA decay through inhibiting exon-exon junction complex binding with B-T to exert its oncogenic role. B-T plays its competing endogenous RNA role by inhibiting miR-30c-5p and miR-30e-5p, and further promoting the expression of downstream oncogenic targets SRSF10 and TXNDC5. Interestingly, SRSF10 can act as a splicing regulator for SREK1L to promote hepatocarcinogenesis via the formation of a SRSF10-associated complex. In summary, we demonstrate a SRSF10/SREK1L/B-T signalling loop to accelerate the hepatocarcinogenesis.

2-Trifluoromethylthiazole-5-carboxamides: Analogues of a Stilbene-Based Anti-HIV Agent that Impact HIV mRNA Processing.

The observation that stilbene 3 (5350150) blocks HIV replication through its impact on HIV mRNA processing prompted a program to develop non-cytotoxic analogues that maintain its mechanism of action. This initially involved replacement of the central double bond in 3 by an amide function and the quinoline motif by a 2-aminobenzothiazole subunit, as in 12jj (R' = Cl), 12pp (R = NO2), and 12vv (R = CF3). On the basis of the possible CF3 ↔ NO2 bioisostere relationship in 12vv and 12pp, compound 23 was prepared and also found to be active. In the final step, the thiazole compounds 28 (GPS488) (EC50 = 1.66 µM) and 29 (GPS491) (EC50 = 0.47 µM) were prepared and evaluated. Similar activity and cell viability values (therapeutic index (TI = CC50/EC50) values of 50-100) were observed in primary peripheral blood mononuclear cells. Furthermore, they remained active against a panel of HIV mutant strains displaying resistance to individual drugs used in antiretroviral therapy. It was determined that compound 29 suppressed expression of the HIV-1 structural protein Gag and altered HIV-1 RNA accumulation, decreasing the abundance of RNAs encoding the structural proteins while increasing levels of viral RNAs encoding the regulatory proteins, a pattern similar to that seen for compound 3.

A novel class of inhibitors that target SRSF10 and promote p53-mediated cytotoxicity on human colorectal cancer cells.

The elevated expression of the splicing regulator SRSF10 in metastatic colorectal cancer (CRC) stimulates the production of the pro-tumorigenic BCLAF1-L splice variant. We discovered a group of small molecules with an aminothiazole carboxamide core (GPS167, GPS192 and others) that decrease production of BCLAF1-L. While additional alternative splicing events regulated by SRSF10 are affected by GPS167/192 in HCT116 cells (e.g. in MDM4, WTAP, SLK1 and CLK1), other events are shifted in a SRSF10-independent manner (e.g. in MDM2, NAB2 and TRA2A). GPS167/192 increased the interaction of SRSF10 with the CLK1 and CLK4 kinases, leading us to show that GPS167/192 can inhibit CLK kinases preferentially impacting the activity of SRSF10. Notably, GPS167 impairs the growth of CRC cell lines and organoids, inhibits anchorage-independent colony formation, cell migration, and promotes cytoxicity in a manner that requires SRSF10 and p53. In contrast, GPS167 only minimally affects normal colonocytes and normal colorectal organoids. Thus, GPS167 reprograms the tumorigenic activity of SRSF10 in CRC cells to elicit p53-dependent apoptosis.

Reaction of 3-Cl/OMe-Substituted 5-Nitrobenzisothiazoles with Hydrazine: Structural and Computational Evidence for Rearrangement Pathways Implicating Intramolecular Formation of Pivotal Meisenheimer Complexes.

In projected structure-activity relationship studies of the novel diheteroarylamide-based anti-HIV agent 2 (1C8), one objective was to evaluate the influence of incorporating the central amide motif in 2 into a five-membered pyrazolone ring, as found in 3. It was envisaged that compound 3 could be prepared through reaction of 3-hydrazino-5-nitrobenzisothiazole 5 with the methyl ester of 4-chloropyridine-3-carboxylic acid, followed by N-methylation of the pyridine nitrogen. However, the reaction of 3-methoxyl-5-nitrobenzisothiazole with hydrazine resulted in formation of ring-opened hydrazonate product 18. In the corresponding reaction with 3-chloro-5-nitrobenzisothiazole, a different rearrangement product 19 was formed, in which two 2,1-benzisothiazole units are joined by a sulfur bridge. Meisenheimer complex formation, favored by the presence of the 5-nitro substituent on the benzisothiazole ring, was postulated to be a key feature in the formation of these deep-seated rearrangement products. Support for the proposed formation of the pivotal Meisenheimer complexes and their subsequent evolution to the observed products in which the benzisothiazole sulfur atom is either expelled or maintained in the isomeric 2,1-benzisothiazole system was obtained by density function theory calculations.

2-Aminothiazole-4-carboxamides Enhance Readthrough of Premature Termination Codons by Aminoglycosides.

Nonsense mutations introduce a premature termination codon (PTC) and are the underlying cause of multiple rare genetic diseases and cancers. Although certain aminoglycosides bind to eukaryotic ribosomes enabling incorporation of an amino acid at the PTC and formation of full-length protein, they are inefficient and toxic at therapeutic doses. Library screening in assays that measure readthrough at a PTC in the TP53 gene in human HDQ-P1 cells identified six novel 2-aminothiazole-4-carboxamide derivatives that potentiate the PTC readthrough (PTCR) efficiency of G418 when used in combination. The two most potent compounds incorporated a 4-indazole motif on the 2-aminothiazole nitrogen and a hydrophobic aryl substituent on the carboxamide nitrogen. These compounds are valuable tools to further investigate the therapeutic potential of aminoglycoside-induced PTCR.

Development of Novel Monoamine Oxidase-B (MAO-B) Inhibitors with Reduced Blood-Brain Barrier Permeability for the Potential Management of Noncentral Nervous System (CNS) Diseases.

Studies indicate that MAO-B is induced in peripheral inflammatory diseases. To target peripheral tissues using MAO-B inhibitors that do not permeate the blood-brain barrier (BBB) the MAO-B-selective inhibitor deprenyl was remodeled by replacing the terminal acetylene with a CO2H function, and incorporating a para-OCH2Ar motif (compounds 10a-s). Further, in compound 32 the C-2 side chain corresponded to CH2CN. In vitro, 10c, 10j, 10k, and 32 were identified as potent reversible MAO-B inhibitors, and all four compounds were more stable than deprenyl in plasma, liver microsomal, and hepatocyte stability assays. In vivo, they demonstrated greater plasma bioavailability. Assessment of in vitro BBB permeability showed that compound 10k is a P-glycoprotein (P-gp) substrate and 10j displayed mild interaction. Importantly, compounds 10c, 10j, 10k, and 32 displayed significantly reduced BBB permeability after intravenous, subcutaneous, and oral administration. These polar MAO-B inhibitors are pertinent leads for evaluation of efficacy in noncentral nervous system (CNS) inflammatory disease models.

Tribochemical Wear of Diamond-Like Carbon-Coated Atomic Force Microscope Tips.

Nanoscale wear is a critical issue that limits the performance of tip-based nanomanufacturing and nanometrology processes based on atomic force microscopy (AFM). Yet, a full scientific understanding of nanoscale wear processes remains in its infancy. It is therefore important to quantitatively understand the wear behavior of AFM tips. Tip wear is complex to understand due to adhesive forces and contact stresses that change substantially as the contact geometry evolves due to wear. Here, we present systematic characterization of the wear of commercial Si AFM tips coated with thin diamond-like carbon (DLC) coatings. Wear of DLC was measured as a function of external loading and sliding distance. Transmission electron microscopy imaging, AFM-based adhesion measurements, and tip geometry estimation via inverse imaging were used to assess nanoscale wear and the contact conditions over the course of the wear tests. Gradual wear of DLC with sliding was observed in the experiments, and the tips evolved from initial paraboloidal shapes to flattened geometries. The wear rate is observed to increase with the average contact stress, but does not follow the classical wear law of Archard. A wear model based on the transition state theory, which gives an Arrhenius relationship between wear rate and normal stress, fits the experimental data well for low mean contact stresses (<0.3 GPa), yet it fails to describe the wear at higher stresses. The wear behavior over the full range of stresses is well described by a recently proposed multibond wear model that exhibits a change from Archard-like behavior at high stresses to a transition state theory description at lower stresses.

Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication.

We recently identified the 4-pyridinone-benzisothiazole carboxamide compound 1C8 as displaying strong anti-HIV-1 potency against a variety of clinical strains in vitro. Here we show that 1C8 decreases the expression of HIV-1 and alters splicing events involved in the production of HIV-1 mRNAs. Although 1C8 was designed to be a structural mimic of the fused tetracyclic indole compound IDC16 that targets SRSF1, it did not affect the splice site shifting activity of SRSF1. Instead, 1C8 altered splicing regulation mediated by SRSF10. Depleting SRSF10 by RNA interference affected viral splicing and, like 1C8, decreased expression of Tat, Gag and Env. Incubating cells with 1C8 promoted the dephosphorylation of SRSF10 and increased its interaction with hTra2ß, a protein previously implicated in the control of HIV-1 RNA splicing. While 1C8 affects the alternative splicing of cellular transcripts controlled by SRSF10 and hTra2ß, concentrations greater than those needed to inhibit HIV-1 replication were required to elicit significant alterations. Thus, the ability of 1C8 to alter the SRSF10-dependent splicing of HIV-1 transcripts, with minor effects on cellular splicing, supports the view that SRSF10 may be used as a target for the development of new anti-viral agents.

A Parallel Synthesis Approach to the Identification of Novel Diheteroarylamide-Based Compounds Blocking HIV Replication: Potential Inhibitors of HIV-1 Pre-mRNA Alternative Splicing.

A 256-compound library was evaluated in an anti-HIV screen to identify structural "mimics" of the fused tetracyclic indole compound 1 (IDC16) that conserve its anti-HIV activity without associated cytotoxicity. Four diheteroarylamide-type compounds, containing a common 5-nitroisobenzothiazole motif, were identified as active. In subsequent screens, the most potent compound 9 (1C8) was active against wild-type HIV-1IIIB (subtype B, X4-tropic) and HIV-1 97USSN54 (subtype A, R5-tropic) with EC50's of 0.6 and 0.9 µM, respectively. Compound 9 also inhibited HIV strains resistant to drugs targeting HIV reverse transcriptase, protease, integrase, and coreceptor CCR5 with EC50's ranging from 0.9 to 1.5 µM. The CC50 value obtained in a cytotoxicity assay for compound 9 was >100 µM, corresponding to a therapeutic index (CC50/EC50) of approximately 100. Further comparison studies revealed that, whereas the anti-HIV activity for compound 9 and the parent molecule 1 are similar, the cytotoxic effect for compound 9 was, as planned, markedly suppressed.

Simulated adhesion between realistic hydrocarbon materials: effects of composition, roughness, and contact point.

The work of adhesion is an interfacial materials property that is often extracted from atomic force microscope (AFM) measurements of the pull-off force for tips in contact with flat substrates. Such measurements rely on the use of continuum contact mechanics models, which ignore the atomic structure and contain other assumptions that can be challenging to justify from experiments alone. In this work, molecular dynamics is used to examine work of adhesion values obtained from simulations that mimic such AFM experiments and to examine variables that influence the calculated work of adhesion. Ultrastrong carbon-based materials, which are relevant to high-performance AFM and nano- and micromanufacturing applications, are considered. The three tips used in the simulations were composed of amorphous carbon terminated with hydrogen (a-C-H), and ultrananocrystalline diamond with and without hydrogen (UNCD-H and UNCD, respectively). The model substrate materials used were amorphous carbon with hydrogen termination (a-C-H) and without hydrogen (a-C); ultrananocrystalline diamond with (UNCD-H) and without hydrogen (UNCD); and the (111) face of single crystal diamond with (C(111)-H) and without a monolayer of hydrogen (C(111)). The a-C-H tip was found to have the lowest work of adhesion on all substrates examined, followed by the UNCD-H and then the UNCD tips. This trend is attributable to a combination of roughness on both the tip and sample, the degree of alignment of tip and substrate atoms, and the surface termination. Continuum estimates of the pull-off forces were approximately 2-5 times larger than the MD value for all but one tip-sample pair.

Mechanics of interaction and atomic-scale wear of amplitude modulation atomic force microscopy probes.

Wear is one of the main factors that hinders the performance of probes for atomic force microscopy (AFM), including for the widely used amplitude modulation (AM-AFM) mode. Unfortunately, a comprehensive scientific understanding of nanoscale wear is lacking. We have developed a protocol for conducting consistent and quantitative AM-AFM wear experiments. The protocol involves controlling the tip-sample interaction regime during AM-AFM scanning, determining the tip-sample contact geometry, calculating the peak repulsive force and normal stress over the course of the wear test, and quantifying the wear volume using high-resolution transmission electron microscopy imaging. The peak repulsive tip-sample interaction force is estimated from a closed-form equation accompanied by an effective tip radius measurement procedure, which combines transmission electron microscopy and blind tip reconstruction. The contact stress is estimated by applying Derjaguin-Müller-Toporov contact mechanics model and also numerically solving a general contact mechanics model recently developed for the adhesive contact of arbitrary axisymmetric punch shapes. We discuss the important role that the assumed tip shape geometry plays in calculating both the interaction forces and the contact stresses. Contact stresses are significantly affected by the tip geometry while the peak repulsive force is mainly determined by experimentally controlled parameters, specifically, the free oscillation amplitude and amplitude ratio. The applicability of this protocol is demonstrated experimentally by assessing the performance of diamond-like carbon-coated and silicon-nitride-coated silicon probes scanned over ultrananocrystalline diamond substrates in repulsive mode AM-AFM. There is no sign of fracture or plastic deformation in the case of diamond-like carbon; wear could be characterized as a gradual atom-by-atom process. In contrast, silicon nitride wears through removal of the cluster of atoms and plastic deformation.

"Soft Si": effective stiffness of supported crystalline nanomembranes.

We investigate the effective mechanical response of a layered system consisting of a thin crystalline sheet (nanomembrane) on a bulk substrate, with a high elastic mismatch (in the range of 5 to 9 orders of magnitude) between the stiff sheet and the compliant substrate. Using finite-element mechanics models and indentation experiments ranging from micro to nano, we show that the mismatch between the sheet and substrate elastic moduli, the length scale of deformation, and the sheet thickness all play a significant role in defining the effective stiffness of the layered system. For a wide range of indenter sizes, the mechanical response of the composite system is indistinguishable from that of the compliant substrate. In particular, at large indenter sizes, the mechanical response of the layered system is dominated by that of the compliant substrate. For decreasing indenter sizes, the effective stiffness of the layered structure reaches a finite value different from either the one expected for the compliant substrate or for a bulk crystal of the same material as the stiff top membrane.

Targeting the cell cycle and the PI3K pathway: a possible universal strategy to reactivate innate tumor suppressor programmes in cancer cells.

Corruption of the Rb and p53 pathways occurs in virtually all human cancers. This could be because it lends oncogene-bearing cells a surfeit of Cdk activity and growth, enabling them to elaborate strategies to evade tumor-suppressive mechanisms and divide inappropriately. Targeting both Cdk activities and the PI3K pathway might be therefore a potentially universal means to palliate their deficiency in cancer cells. We showed that the killing efficacy of roscovitine and 16 other purines and potentiation of roscovitine-induced apoptosis by the PI3K inhibitor, LY294002, decreased with increasing corruption of the Rb and p53 pathways. Further, we showed that purines differing by a single substitution, which exerted little lethal effect on distant cell types in rich medium, could display widely-differing cytotoxicity profiles toward the same cell types in poor medium. Thus, closely-related compounds targeting similar Cdks may interact with different targets that could compete for their interaction with therapeutically-relevant Cdk targets. In the perspective of clinical development in association with the PI3K pathway inhibitors, it might thus be advisable to select tumor cell type-specific Cdk inhibitors on the basis of their toxicity in cell-culture-based assays performed at a limiting serum concentration sufficient to suppress their interaction with undesirable crossreacting targets whose range and concentration would depend on the cell genotype.

Synthesis and biological evaluation of C-5 methyl substituted 4-arylthio and 4-aryloxy-3-Iodopyridin-2(1H)-one type anti-HIV agents.

A series of C-5 methyl substituted 4-arylthio- and 4-aryloxy-3-iodopyridin-2(1H)-ones has been synthesized as new pyridinone analogues for their evaluation as anti-HIV inhibitors. The optimization at the 5-position was developed through an efficient use of the key intermediates 5-ethoxycarbonyl- and 5-cyano-pyridin-2(1H)-ones (14 and 15). Biological studies revealed that several compounds show potent HIV-1 reverse transcriptase inhibitory properties, for example, compounds 93 and 99 are active at 0.6-50 nM against wild type HIV-1 and a panel of major simple/double HIV mutant strains.

Identification of allosteric inhibitors blocking the hepatitis C virus polymerase NS5B in the RNA synthesis initiation step.

Hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B constitutes a target of choice for the development of anti-HCV drugs. Although many small molecules have been identified as allosteric inhibitors of NS5B, very few are active in clinical applications. We have screened 17,000 compounds in an enzymatic assay involving the purified NS5B in order to increase the therapeutic arsenal. We hoped to shed some light on the precise mechanism of RNA synthesis. We succeeded in isolating a series of 21 original inhibitors of the RNA synthesis by NS5B. Four of these non-nucleoside inhibitors (NNIs) could be mapped to the known binding site called 'B' as judged by the decrease in their inhibition potency when assayed with a 'B' site mutant, M423T NS5B. Incidentally, our in silico model pointed to Y477 as a key residue for inhibitor binding. In vitro, Y477F mutant loses its sensitivity to the newly discovered inhibitors but is unable to extend primers during the elongation phase. Our results demonstrate that elements of the 'B' site are involved in the conformational changes required in the switch between the different RNA synthesis steps and that compounds targeting this site could lock the enzyme in its initiation phase.

Benzo[e]pyridoindoles, novel inhibitors of the aurora kinases.

Aurora kinases are serine/threonine protein kinases that are involved in cancer development and are important targets for cancer therapy. By high throughput screening of a chemical library we found that benzo[e]pyridoindole derivatives inhibited Aurora kinase. The most potent compound (compound 1) was found to be an ATP competitive inhibitor, which inhibited in vitro Aurora kinases at the nanomolar range. It prevented, ex vivo, the phosphorylation of Histone H3, induced mitosis exit without chromosome segregation, known phenomena observed upon Aurora B inactivation. This compound was also shown to affect the localization of Aurora B, since in the presence of the inhibitor the enzyme was delocalized on the whole chromosomes and remained associated with the chromatin of newly formed nuclei. In addition, compound 1 inhibited the growth of different cell lines derived from different carcinoma. Its IC(50) for H358 NSCLC (Non Small Cancer Lung Cells), the most sensitive cell line, was 145 nM. Furthermore compound 1 was found to be efficient towards multicellular tumor spheroid growth. It exhibited minimal toxicity in mice while it had some potency towards aggressive NSCLC tumors. Benzo[e]pyridoindoles represent thus a potential new lead for the development of Aurora kinase inhibitors.

5-Substituted pyrido[2,3-d]pyrimidine, an inhibitor against three receptor tyrosine kinases.

NP506, the 3-{2,4-dimethyl-5-[2-oxo-5-(N'-phenylhydrazinocarbonyl)-1,2-dihydro-indol-3-ylidenemethyl]-1H-pyrrol-3-yl}-propionic acid, was designed as FGF receptor 1 inhibitor by computational study and found to be more active against endothelial proliferation of HUVEC after the rhFGF-2 stimulation than SU6668 with minimum effective dose of 10 microM. NP506 inhibited the tyrosine phosphorylation in FGF, VEGF, and PDGF receptors and the activation of extracellular signal-regulated kinase (ERK), c-Jun-N-terminal-kinase (JNK) and AKT after the rhFGF-2 stimulation. The introduction of the phenyl hydrazide motif to the position 5 of the pyrido[2,3-d]pyrimidine scaffold led to the inhibitory effect in two signaling pathways: inhibition of AKT activation in the phosphatidyl inositol 3'-kinase (PI13K)/AKT signaling pathway and the inhibition of ERK and JNK activation in MAPK pathway.

Stereoselective direct copper-catalyzed alkenylation of oxazoles with bromoalkenes.

A copper-catalyzed direct alkenylation of oxazoles with bromoalkenes has been developed. The method is both regio- and stereoselective and tolerates a variety of functional groups. A wide range of 2-E-vinyl-substituted oxazoles were obtained in high yields including the highly fluorescent alkaloid annuloline.

Ligandless microwave-assisted Pd/Cu-catalyzed direct arylation of oxazoles.

An efficient microwave-assisted palladium/copper co-mediated direct arylation of oxazoles with aryl bromides under ligandless conditions has been developed. The method is functional group tolerant and provides rapid access to medicinally relevant compounds in good yields. Coupled to the van Leusen oxazole ring synthesis, this methodology is illustrated by an expedient two-step synthesis of the four 2,5-diaryloxazole alkaloids texamine, texaline, balsoxin, and O-Me-halfordinol from commercially available starting materials.

Retrograde delivery of photosensitizer (TPPp-O-beta-GluOH)3 selectively potentiates its photodynamic activity.

Photodynamic therapy involves administration of a photosensitizing drug and its subsequent activation by visible light of the appropriate wavelength. Several approaches to increasing the specificity of photosensitizers for cancerous tissues and, in particular, through their conjugation to ligands that are directed against tumor-associated antigens have been investigated. Here, we have studied the delivery of the photocytotoxic porphyrin compound TPP(p-O-beta-D-GluOH)3 into tumor cells that overexpress the glycosphingolipid Gb3, using the Gb3-binding nontoxic B-subunit of Shiga toxin (STxB) as a vector. To allow for site-directed chemical coupling, an STxB variant carrying a free sulfhydryl moiety at its C-terminal end has been used. Binding affinity, cellular uptake, singlet oxygen quantum yield, and phototoxicity of the conjugate have been examined. Despite some effect of coupling on both the photophysical properties of TPP(p-O-beta-D-GluOH)3 and the affinity of STxB for its receptor, the conjugate exhibited a higher photocytotoxic activity than the photosensitizer alone and was exquisitely selective for Gb3-expressing tumor cells. Furthermore, our data strongly suggest that STxB-mediated retrograde delivery of the photosensitizer to the biosynthetic/secretory pathway is critical for optimal cytotoxic activity. In conclusion, a strong rationale for using retrograde delivery tools such as STxB in combination with photosensitizing agents for the photodynamic therapy of tumors is presented.