Kinase Domain Mutations in Cancer: Implications for Small Molecule Drug Design Strategies

Copper-mediated [3 + 2] oxidative cyclization of oxime acetate and its utility in the formal synthesis of fentiazac

A new protocol for the direct synthesis of 2-aminothiazole has been developed from oxime acetate and readily available sodium thiocyanate using a copper catalyst. The present transformation has good functional group tolerance. Various thiazoles were smoothly synthesized in good to excellent yields. The applicability of the present method has been extended to the formal synthesis of the non-steroidal and anti-inflammatory drug, fentiazac via the Sandmeyer reaction and Suzuki coupling.

The Essence in Selectivity of Copper-Mediated Intermolecular Nucleophilic Substitution of a meta C-H Bond in 2-Methyl-N-methoxyaniline: A Theoretical Study

The detailed mechanism for NHC-Cu(I)-catalyzed intermolecular nucleophilic substitution of the C-H bonds at aniline (2-methyl-N-methoxyaniline) was studied via DFT methods to reveal the essence of the selectivity. Calculations revealed that the meta C-H functionalization proceeds via two nucleophilic attacks on the aromatic ring rather than a one-step meta C-H substitution to give the experimentally observed major product. The reaction is initiated by activation of the substrate via oxidative addition with an NHC-Cu(I) catalyst, through which an umpolung occurs at the ring. From the activated intermediate, methoxyl group transfer to benzyl forms a resting state, while a nucleophile can attack the ortho position of benzyl to form a more stable intermediate. The nucleophile group can then transfer to the meta position by a 1,2-Wagner-Meerwein rearrangement to form the final product through a proton shuttle. In contrast, other transfer processes affording ortho- or para-substituted products encounter higher activation barriers. This work investigates the relationship of product selectivity with the umpolung of the aromatic ring, as well as the priority of a nucleophilic attack at the ortho position of the aromatic, 1,2-Wagner-Meerwein rearrangement from the ortho-substituted intermediate, and proton shuttle from the meta-substituted intermediate.

Cu(ii)-catalyzed C-N coupling of 2-aminobenzothiazoles with boronic acids at room temperature

A Cu(ii)-catalyzed, effective C-N coupling of 2-aminobenzothiazoles with boronic acids in acetonitrile under open vessel chemistry was achieved. This protocol demonstrates the N-arylation of 2-aminobenzothiazoles with a broad range of differently substituted phenylboronic acids at room temperature and accomplishes moderate to excellent yields of the desired products. Under the optimized condition, phenylboronic acids bearing halogen at the para and meta positions were found to be more fruitful.

New pyrazolopyridine and pyrazolothiazole-based compounds as anti-proliferative agents targeting c-Met kinase inhibition: design, synthesis, biological evaluation, and computational studies

c-Met tyrosine kinase plays a key role in the oncogenic process. Inhibition of the c-Met has emerged as an attractive target for human cancer treatment. This work deals with the design and synthesis of a new set of derivatives bearing pyrazolo[3,4-b]pyridine, pyrazolo[3,4-b]thieno[3,2-e]pyridine, and pyrazolo[3,4-d]thiazole-5-thione scaffolds, 5a,b, 8a-f, and 10a,b, respectively, utilizing 3-methyl-1-tosyl-1H-pyrazol-5(4H)-one (1) as a key starting material. All the new compounds were evaluated as antiproliferative agents against HepG-2, MCF-7, and HCT-116 human cancer cell lines utilizing 5-fluorouracil and erlotinib as two standard drugs. Compounds 5a,b and 10a,b represented the most promising cytotoxic activity of IC₅₀ values ranging from 3.42 ± 1.31 to 17.16 ± 0.37 μM. Both 5a and 5b showed the most cytotoxicity and selectivity toward HepG-2, with IC₅₀ values of 3.42 ± 1.31 μM and 3.56 ± 1.5 μM, respectively. The enzyme assay demonstrated that 5a and 5b had inhibition potency on c-Met with IC₅₀ values in nanomolar range of 4.27 ± 0.31 and 7.95 ± 0.17 nM, respectively in comparison with the reference drug cabozantinib (IC₅₀; 5.38 ± 0.35 nM). The impact of 5a on the cell cycle and apoptosis induction potential in HepG-2 and on the apoptotic parameters; Bax, Bcl-2, p53, and caspase-3 was also investigated. Finally, the molecular docking simulation of the most promising derivatives 5a and 5b was screened against c-Met to investigate the binding patterns of both compounds in the active site of the c-Met enzyme. In silico ADME studies were also performed for 5a and 5b to predict their physicochemical and pharmacokinetic characteristics.

Synthesis of 4,5-Dihydro-1H-[1,2]dithiolo[3,4-c]quinoline-1-thione Derivatives and Their Application as Protein Kinase Inhibitors

This study represents the design and synthesis of a new set of hybrid and chimeric derivatives of 4,5-dihydro-4,4-dimethyl-1H-[1,2]dithiolo[3,4-c]quinoline-1-thiones, the structure of which the tricyclic fragment linearly bound or/and condensed with another heterocyclic fragment. Using the PASS Online software, among the previously synthesized and new derivatives of 1,2-dithiolo[3,4-c]quinoline-1-thione we identified 12 substances with pleiotropic activity, including chemoprotective and antitumor activity. All the synthesized derivatives were screened for their inhibitory assessment against a number of kinases. Compounds which exhibited prominent inhibition percentage in cells (>85%) were also examined for their inhibitory efficiency on human kinases via ELISA utilizing sorafenib as a reference standard to estimate their IC50 values. It was revealed that compounds 2a, 2b, 2c, and 2q displayed a significant inhibition JAK3 (IC50 = 0.36 μM, 0.38 μM, 0.41 μM, and 0.46 μM, respectively); moreover, compounds 2a and 2b displayed excellent activities against NPM1-ALK (IC50 = 0.54 μM, 0.25 μM, respectively), against cRAF[Y340D][Y341D], compound 2c showed excellent activity, and compound 2q showed weak activity (IC50 = 0.78 μM, 5.34 μM, respectively) (sorafenib IC50 = 0.78 μM, 0.43 μM, 1.95 μM, respectively). Thus, new promising preferred structures for the creation of drugs for the treatment of cancer and other multifactorial diseases in the future have been found.

General Method of Synthesis of 5-(Het)arylamino-1,2,3-triazoles via Buchwald–Hartwig Reaction of 5-Amino- or 5-Halo-1,2,3-triazoles

An efficient access to the novel 5-(het)arylamino-1,2,3-triazole derivatives has been developed. The method is based on Buchwald–Hartwig cross-coupling reaction of 5-Amino or 5-Halo-1,2,3-triazoles with (het)aryl halides and amines, respectively. As result, it was found that palladium complex [(THP-Dipp)Pd(cinn)Cl] bearing expanded-ring N-heterocyclic carbene ligand is the most active catalyst for the process to afford the target molecules in high yields.

Base-Promoted Cobalt-Catalyzed Regio- and Enantioselective para-Friedel-Crafts Alkylation of Aniline Derivatives

Herein we disclose a highly efficient enantioselective para-C-H alkylation of aniline derivatives promoted by a base/Co/indeno-pybox ligand system. This methodology leads to the efficient construction of a series of enantioenriched aniline derivatives bearing all-carbon quaternary stereocenters. In addition, several special biologically or medicinally active indoles are facilely synthesized by our Co-catalyzed asymmetry synthesis method. Density functional theory calculations and experiment results suggest that the (acac)^- anion of Co(acac)₂ plays a very important role in chiral control during the nucleophilic reaction.

Design and synthesis of novel N-[3-(benzimidazol-2-ylamino)phenyl]amine and N-[3-(benzoxazol-2-ylamino)phenyl]amine derivatives as potential anticancer agents

In this contribution, we report the design, synthesis and cytotoxicity studies of a series of N-[3-(benzimidazol-2-yl-amino)phenyl]amine and N-[3-(benzoxazol-2-ylamino)phenyl]amine derivatives. In vitro cytotoxicity assay of 26 selected compounds was carried out at National Cancer Institute (NCI), USA. Out of them, compounds 10e (NSC D-762842/1) and 11s (NSC D-764942/1) have shown remarkable cytotoxicity with GI₅₀ values ranging between "0.589-14.3 µM" and "0.276-12.3 µM," respectively, in the representative nine subpanels of human tumor cell lines. Further, flow cytometry analysis demonstrated that compound 10e exerted cell cycle arrest at G2/M phase and showed dose-dependent enhancement in apoptosis in K-562 leukemia cancer cells.

Synthesis and Anti-Proliferation Activity Evaluation of Novel 2-Chloroquinazoline as Potential EGFR-TK Inhibitors

A novel series of 2-chloroquinazoline derivatives had been synthesized and their anti-proliferation activities against the four EGFR high-expressing cells A549, NCI-H1975, AGS and HepG2 cell lines were evaluated. The preliminary SAR study of the scaffold of new compounds showed that the compounds with a chlorine substituent on R³ had a better anti-proliferation activity than those substituted by hydrogen atom or vinyl group. Among them, 2-chloro-N-[2-chloro-4-(3-chloro-4-fluoroanilino)quinazolin-6-yl]acetamide (10b) had the best activity, and the corresponding IC₅₀ were 3.68, 10.06, 1.73 and 2.04 μM, respectively. And compound 10b had better or equivalent activity against four cell lines than Gefitinib. The activity of the compound 10b on the EGFR enzyme was subsequently tested. The Wound Healing of A549, AGS and HepG2 cells by this compound showed that the compound can inhibit the migration of cancer cells. Finally, the action channel of the compound 10b was supported by western blotting experiments. It provides useful information for the design of EGFR-TK inhibitors.

Metal-Free Twofold Electrochemical C-H Amination of Activated Arenes: Application to Medicinally Relevant Precursor Synthesis

The efficient production of many medicinally or synthetically important starting materials suffers from wasteful or toxic precursors for the synthesis. In particular, the aromatic non-protected primary amine function represents a versatile synthetic precursor, but its synthesis typically requires toxic oxidizing agents and transition metal catalysts. The twofold electrochemical amination of activated benzene derivatives via Zincke intermediates provides an alternative sustainable strategy for the formation of new C-N bonds of high synthetic value. As a proof of concept, we use our approach to generate a benzoxazinone scaffold that gained attention as a starting structure against castrate-resistant prostate cancer. Further improvement of the structure led to significantly increased cancer cell line toxicity. Thus, exploiting environmentally benign electrooxidation, we present a new versatile and powerful method based on direct C-H activation that is applicable for example the production of medicinally relevant compounds.

Mechanistic Study of Domino Rearrangement-Promoted Meta C-H Activation in 2-Methyl-N-methoxyaniline via Cu(NHC)+: Motivation and Selectivity

Here we report a detailed theoretical study of the mechanism of Cu⁺-catalyzed domino rearrangement of 2-methyl-N-methoxyaniline with a deep understanding of the unique motivation and selectivity of these migrations. We find that the Cu⁺ catalyst accelerates the [1,3]-methoxy migration to the methyl-bound ortho position of umpolung phenyl. The following domino transfer prefers methyl [1,2]-migration, and the rate-determining step for the whole reaction is the transfer of a proton from the phenyl ring to amine to finish the catalytic cycle.

Design, synthesis and antitumor evaluation of novel 5-methylpyrazolo[1,5-a]pyrimidine derivatives as potential c-Met inhibitors

A series of novel 5-methylpyrazolo[1,5-a]pyrimidine derivatives (10a-10x) were designed, synthesized, and evaluated for their in vitro inhibitory activities against c-Met kinase and antiproliferative activities against the SH-SY5Y, MDA-MB-231, A549, and HepG2 cell lines. Most of the compounds remarkably inhibited c-Met kinase and showed moderate to good cytotoxicity and selectivity toward the four cancer cell lines. Among them, compounds 10b and 10f were the two most potent selective c-Met inhibitors with half-maximal inhibitory concentration (IC₅₀) values of 5.17 ± 0.48 nM and 5.62 ± 0.78 nM, respectively, and suppression abilities comparable with the positive control cabozantinib. Cell proliferation assay further demonstrated that the two most promising compounds 10a and 10b also showed good cytotoxicity and selectivity toward MDA-MB-231 cells, with IC₅₀ values of 26.67 ± 2.56 μM and 26.83 ± 2.41 μM, respectively. Compounds 10f and 10g showed cytotoxicity and selectivity toward A549 cells, with IC₅₀ values of 20.20 ± 2.04 μM and 21.65 ± 1.58 μM, respectively. All antiproliferative activities were within the range of those of cabozantinib. Notably, these compounds presented relatively low hepatotoxicity compared with reference drugs. Moreover, the preliminary structure-activity relationship and docking studies revealed that replacement of a nitrogen-containing heterocycle on the R₂ (block A) group might improve the c-Met kinase inhibitory and antiproliferative effects in MDA-MB-231 cells, whereas displacement by a substituted benzene ring, especially for the p-fluorophenyl or 4-fluoro-3-methoxyphenyl moiety, on the R₂ group enhanced cytotoxicity toward A549 cells. Together, these results suggest that 10b and 10f are promising compounds and provide a basis for their development as new antitumor agents.

Potent dual EGFR/Her4 tyrosine kinase inhibitors containing novel (1,2-dithiolan-4-yl)acetamides

Modifications at C₆ and C₇ positions of 3-cyanoquinolines 6 and 7 led to potent inhibitors of the ErbB family of kinases particularly against EGFR^WT and Her4 enzymes in the radioisotope filter binding assay. The lead (4, SAB402) displayed potent dual biochemical activities with EGFR^WT/Her4 IC₅₀ ratio of 80 due to its potent inhibition of Her4 activity (IC₅₀ 0.03 nM), however, the selectivity towards activating mutations (EGFR^L858R, EGFR^ex19del) was decreased. Inhibitor 4 also exhibited excellent growth inhibition in seven different cancer types and reduced cell viability in female NMRI nude mice in the intraperitoneally implanted hollow fibers which have been loaded with MOLT-4 (leukemia) and NCI-H460 (NSCLC) cells in a statistically significant manner.

A one-pot synthesis of 2-aminothiazoles via the coupling of ketones and thiourea using I2/dimethyl sulfoxide as a catalytic oxidative system

A series of 2-aminothiazoles is prepared in moderate-to-good yields by the direct coupling of ketones and thiourea using I2/dimethyl sulfoxide as a catalytic oxidative system. This method avoids the preparation of lachrymatory and toxic α-haloketones and the use of an acid-binding agent, thus providing a more convenient approach to 2-aminothiazoles compared to the Hantzsch reaction.

Design, synthesis, and evaluations of the antiproliferative activity and aqueous solubility of novel carbazole sulfonamide derivatives as antitumor agents

Optimization of IG-105 (1) on the carbazole ring provided five series of new carbazole sulfonamides derivatives, 7a-e, 8a-g, 9a-g, 10a-e, and 11a-g. All of the compounds were evaluated against HepG2, MCF-7, MIA PaCa-2, and Bel-7402 cells for antiproliferative activity. Each series of compounds was 2-5 times more active against HepG2 cells (IC₅₀: 1.00-10.0 μM) than the other three tumor cell lines. Several representative compounds, selected from each series, showed aqueous solubility (13.4-176.5 µg/mL at pH 7.4 and 2.0) better than 1, with the aqueous solubility of corresponding salts > 30 mg/mL. From the results of evaluating the effects of the compounds 7b, 8c, 9c, 10c and 11c on tubulin in vitro, we speculated that their targets were different from those of 1 and CA-4P. We tested the antitumor activity of the representative compound 7b·HCl (10 mg/kg) in an in vivo study and found that its tumor growth inhibition rate was 41.1%. The tumor growth inhibition rate of 7b·HCl (20 mg/kg) was 54.6%, whereas the tumor growth inhibition rate of CA-4P (50 mg/kg) was 48.3%. And in another batch of in vivo antitumor activity testing, 9c·HCl and 11c·HCl at doses of 10 mg/kg resulted in 61.1% and 50.0% inhibition, respectively. These promising results warrant further development of the derivatives, which may use a novel mechanism and show potential potency as antitumor drug candidates.

In Silico Reoptimization of Binding Affinity and Drug-Resistance Circumvention Ability in Kinase Inhibitors: A Case Study with RL-45 and Src Kinase

A major bottleneck in the development of kinase inhibitors has been the onset of drug resistance around the gatekeeper residues of Src kinase. Although recent times have seen the reports of certain second-generation kinase inhibitors which are capable of bypassing the drug resistance by circumventing kinase mutation, their kinase-binding efficacy has remained considerably weaker than that of the classical adenosine 5'-triphosphate-competitive kinase inhibitors. Using a recently synthesized second-generation kinase inhibitor RL-45 as a template, the current work integrates fragment-based drug discovery and quantitative structure-activity relationship study with enhanced molecular dynamics simulation approaches, namely, metadynamics and replica exchange free-energy perturbation, and demonstrates how one can optimally redesign and assess novel Src kinase inhibitors, by minimal introduction of new functional moieties around template kinase inhibitor. Interestingly, unlike many synthetic kinase inhibitors, these in silico optimized small-molecule derivatives of RL-45 are found to be potentially capable of serving dual purposes, crucial for efficacy of an ideal kinase inhibitor: (a) circumventing gatekeeper residue mutation-related drug resistance in Src kinase, unlike many commercial kinase inhibitors and (b) manifesting superior resilience against unbinding from the kinase active site. The computer simulation, boosted by enhanced sampling techniques, further reveals that these designed inhibitors bring about key interactions in the form of significantly long-standing hydrogen bonds and hydrophobic pocket otherwise weak in the template bioactive kinase inhibitor, which enhance the binding efficacy of these newly designed ligands in the kinase-binding pocket.

Selective Proteolysis to Study the Global Conformation and Regulatory Mechanisms of c-Src Kinase

Protein kinase pathways are traditionally mapped by monitoring downstream phosphorylation. Meanwhile, the noncatalytic functions of protein kinases remain under-appreciated as critical components of kinase signaling. c-Src is a protein kinase known to have noncatalytic signaling function important in healthy and disease cell signaling. Large conformational changes in the regulatory domains regulate c-Src's noncatalytic functions. Herein, we demonstrate that changes in the global conformation of c-Src can be monitored using a selective proteolysis methodology. Further, we use this methodology to investigate changes in the global conformation of several clinical and nonclinical mutations of c-Src. Significantly, we identify a novel activating mutation observed clinically, W121R, that can escape down-regulation mechanisms. Our methodology can be expanded to monitor the global conformation of other tyrosine kinases, including c-Abl, and represents an important tool toward the elucidation of the noncatalytic functions of protein kinases.

Direct Amination of Arenes with Azodicarboxylates Catalyzed by Bisulfate Salt/HFIP Association

A mild and efficient amination of arenes with azodicarboxylates using potassium bisulfate (KHSO4) as the catalyst in 1,1,1,3,3,3-hexafluoro-2-propanol has been developed. This protocol allowed the amination of a broad range of arenes leading to corresponding hydrazides in good to excellent yields.

Electrochemical Arylation Reaction

Arylated products are found in various fields of chemistry and represent essential entities for many applications. Therefore, the formation of this structural feature represents a central issue of contemporary organic synthesis. By the action of electricity the necessity of leaving groups, metal catalysts, stoichiometric oxidizers, or reducing agents can be omitted in part or even completely. The replacement of conventional reagents by sustainable electricity not only will be environmentally benign but also allows significant short cuts in electrochemical synthesis. In addition, this methodology can be considered as inherently safe. The current survey is organized in cathodic and anodic conversions as well as by the number of leaving groups being involved. In some electroconversions the reagents used are regenerated at the electrode, whereas in other electrotransformations free radical sequences are exploited to afford a highly sustainable process. The electrochemical formation of the aryl-substrate bond is discussed for aromatic substrates, heterocycles, other multiple bond systems, and even at saturated carbon substrates. This survey covers most of the seminal work and the advances of the past two decades in this area.

Electrifying Organic Synthesis

The direct synthetic organic use of electricity is currently experiencing a renaissance. More synthetically oriented laboratories working in this area are exploiting both novel and more traditional concepts, paving the way to broader applications of this niche technology. As only electrons serve as reagents, the generation of reagent waste is efficiently avoided. Moreover, stoichiometric reagents can be regenerated and allow a transformation to be conducted in an electrocatalytic fashion. However, the application of electroorganic transformations is more than minimizing the waste footprint, it rather gives rise to inherently safe processes, reduces the number of steps of many syntheses, allows for milder reaction conditions, provides alternative means to access desired structural entities, and creates intellectual property (IP) space. When the electricity originates from renewable resources, this surplus might be directly employed as a terminal oxidizing or reducing agent, providing an ultra-sustainable and therefore highly attractive technique. This Review surveys recent developments in electrochemical synthesis that will influence the future of this area.

Synthesis and structure-activity relationship study of diaryl[d,f][1,3]diazepines as potential anti-cancer agents

We herein report the synthesis, biological activity and preliminary structure-activity relationships of a series of diaryl[1,3]diazepines. These compounds were able to inhibit the proliferation of many cancer cell lines, such as HeLa, MCF-7, SGC7901 and A549. When HeLa cells were treated with lead compounds 7j and 7k at 3 [Formula: see text] concentration, cell arrest was observed in the G2/M phase.

Evaluation of Three Small Molecular Drugs for Targeted Therapy to Treat Nonsmall Cell Lung Cancer

OBJECTIVE

To guide the optimal selection among first-generation epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) in clinical practice. This review attempted to provide a thorough comparison among three first-generation EGFR-TKIs, namely icotinib, erlotinib, and gefitinib, with regard to their molecular structure, pharmacokinetic parameters, clinical data, adverse reactions, and contraindications.

DATA SOURCES

An electronic literature search of the PubMed database and Google Scholar for all the available articles regarding gefitinib, icotinib, and erlotinib in the English language from January 2005 to December 2014 was used.

STUDY SELECTION

The search terms or keywords included but not limited to "lung cancer", "nonsmall cell lung cancer (NSCLC)", "epidemiology", "EGFR", "TKIs", and "optimal selection ".

RESULTS

As suggested by this review, even though the three first-generation EGFR-TKIs share the quinazoline structure, erlotinib had the strongest apoptosis induction activity because of its use of a different side-chain. The pharmacokinetic parameters indicated that both erlotinib and icotinib are affected by food. The therapeutic window of erlotinib is narrow, and the recommended dosage is close to the maximum tolerable dosage. Icotinib enjoys a wider therapeutic window, and its concentration in the blood is within a safe dosage range even if it is administered with food. Based on multiple large-scale clinical trials, erlotinib is universally applied as the first-line treatment. In marked contrast, icotinib is available only in China as the second- or third-line therapeutic approach for treating advanced lung cancer. In addition, it exhibits a similar efficacy but better safety profile than gefitinib.

CONCLUSIONS

Although there is a paucity of literature regarding whether icotinib is superior to erlotinib, its superior toxicity profile, noninferior efficacy, and lower cost indicate that it is a better alternative for Chinese patients living with advanced NSCLC.

The opening/closure of the P-loop and hinge of BCR-ABL1 decodes the low/high bioactivities of dasatinib and axitinib

The open/closed conformations reveal the low/high bioactivities of the ligands.

Copper(ii)-catalyzed Chan–Lam cross-coupling: chemoselective N-arylation of aminophenols

Copper(ii)-catalyzed boronic acid promoted chemoselective N-arylation of unprotected aminophenols has been developed.

Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles

Protein kinases are attractive therapeutic targets because their dysregulation underlies many diseases, including cancer. The high conservation of the kinase domain and the evolution of drug resistance, however, pose major challenges to the development of specific kinase inhibitors. We recently discovered selective Src kinase inhibitors from a DNA-templated macrocycle library. Here, we reveal the structural basis for how these inhibitors retain activity against a disease-relevant, drug-resistant kinase mutant, while maintaining Src specificity. We find that these macrocycles display a degree of modularity: two of their three variable groups interact with sites on the kinase that confer selectivity, while the third group interacts with the universally conserved catalytic lysine and thereby retains the ability to inhibit the "gatekeeper" kinase mutant. We also show that these macrocycles inhibit migration of MDA-MB-231 breast tumor cells. Our findings establish intracellular kinase inhibition by peptidic macrocycles, and inform the development of potent and specific kinase inhibitors.

Structure-guided selection of specificity determining positions in the human Kinome

Background

The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. This is also the case for inhibitors of many other protein families. The increased availability of protein 3D structures has provided much information on the structural variation within a given protein family. However, the relationship between structural variations and binding specificity is complex and incompletely understood. We have developed a structural bioinformatics approach which provides an analysis of key determinants of binding selectivity as a tool to enhance the rational design of drugs with a specific selectivity profile.

Results

We propose a greedy algorithm that computes a subset of residue positions in a multiple sequence alignment such that structural and chemical variation in those positions helps explain known binding affinities. By providing this information, the main purpose of the algorithm is to provide experimentalists with possible insights into how the selectivity profile of certain inhibitors is achieved, which is useful for lead optimization. In addition, the algorithm can also be used to predict binding affinities for structures whose affinity for a given inhibitor is unknown. The algorithm’s performance is demonstrated using an extensive dataset for the human kinome.

Conclusion

We show that the binding affinity of 38 different kinase inhibitors can be explained with consistently high precision and accuracy using the variation of at most six residue positions in the kinome binding site. We show for several inhibitors that we are able to identify residues that are known to be functionally important.

Facile and efficient synthesis and biological evaluation of 4-anilinoquinazoline derivatives as EGFR inhibitors

Series of 4-anilinoquinazoline derivatives were conveniently and efficiently synthesized and their antitumor activities were evaluated by MTT assay in three human cancer cell lines: H1975, HepG2 and SMMC-7721. New compounds 19a-19h were designed and synthesized to seek for powerful EGFR inhibitors and to explore whether methyl group at C-2 position of quinazoline ring has a positive effect on EGFR inhibition. All the compounds of 19a-19h were found potent against all three cell lines and five compounds (19c, 19d, and 19f-19h) were found more potent against H1975 than gefitinib. SAR studies revealed that methyl group at C-2 position of quinazoline ring could significantly improve the antitumor potency of 4-anilinoquinazolines. The same conclusion was also drawn according to the results of Western blotting analysis. Among all the tested compounds, 19g exhibited extremely potent against H1975 with an IC50 value of 0.11μM, remarkably lower than that of gefitinib (1.23μM). The results of western blotting analysis showed that compounds 19c and 19g could notably inhibit the expression of phosphorylated EGFR, especially 19g, almost inhibited completely.

Discovery of a small molecule targeting SET-PP2A interaction to overcome BCR-ABLT315I mutation of chronic myeloid leukemia

Despite the great success in using tyrosine kinase inhibitors (TKIs) to treat chronic myeloid leukemia (CML), the frequent development of multi-drug resistance, particularly the T315I mutation of BCR-ABL, remains a challenging issue. Enhancement of protein phosphatase 2A (PP2A) activity by dissociating its endogenous inhibitor SET is an effective approach to combat TKI-based resistance. Here, we report the identification of a novel 2-phenyloxypyrimidine compound TGI1002 to specifically disrupt SET-PP2A interaction. By binding to SET, TGI1002 inhibits SET-PP2A interaction and increases PP2A activity. In addition, knocking-down SET expression decreases tumor cell sensitivity to TGI1002. TGI1002 treatments also markedly increase dephosphorylation of BCR-ABL. Moreover, TGI1002 significantly inhibits tumor growth and prolongs survival of xenografted mice implanted with BaF3-p210^T315I cells. These findings demonstrate that TGI1002 is a novel SET inhibitor with important therapeutic potential for the treatment of drug-resistant CML.