DNA interaction of the tyrosine protein kinase inhibitor PD153035 and its N-methyl analogue

Intrinsically Fluorescent Anti-Cancer Drugs

At present, about one-third of the total protein targets in the pharmaceutical research sector are kinase-based. While kinases have been attractive targets to combat many diseases, including cancer, selective kinase inhibition has been challenging, because of the high degree of structural homology in the active site where many kinase inhibitors bind. Despite efficacy as cancer drugs, kinase inhibitors can exhibit limited target specificity and rationalizing their target profiles in the context of precise molecular mechanisms or rearrangements is a major challenge for the field. Spectroscopic approaches such as infrared, Raman, NMR and fluorescence have the potential to provide significant insights into drug-target and drug-non-target interactions because of sensitivity to molecular environment. This review places a spotlight on the significance of fluorescence for extracting information related to structural properties, discovery of hidden conformers in solution and in target-bound state, binding properties (e.g., location of binding sites, hydrogen-bonding, hydrophobicity), kinetics as well as dynamics of kinase inhibitors. It is concluded that the information gleaned from an understanding of the intrinsic fluorescence from these classes of drugs may aid in the development of future drugs with improved side-effects and less disease resistance.

A PET imaging approach for determining EGFR mutation status for improved lung cancer patient management

Tumor heterogeneity and changes in epidermal growth factor receptor (EGFR) mutation status over time challenge the design of effective EGFR tyrosine kinase inhibitor (TKI) treatment strategies for non-small cell lung cancer (NSCLC). Therefore, there is an urgent need to develop techniques for comprehensive tumor EGFR profiling in real time, particularly in lung cancer precision medicine trials. We report a positron emission tomography (PET) tracer, N-(3-chloro-4-fluorophenyl)-7-(2-(2-(2-(2-¹⁸F-fluoroethoxy) ethoxy) ethoxy) ethoxy)-6-methoxyquinazolin-4-amine (¹⁸F-MPG), with high specificity to activating EGFR mutant kinase. We evaluate the feasibility of using ¹⁸F-MPG PET for noninvasive imaging and quantification of EGFR-activating mutation status in preclinical models of NSCLC and in patients with primary and metastatic NSCLC tumors. ¹⁸F-MPG PET in NSCLC animal models showed a significant correlation (R² = 0.9050) between ¹⁸F-MPG uptake and activating EGFR mutation status. In clinical studies with NSCLC patients (n = 75), the concordance between the detection of EGFR activation by ¹⁸F-MPG PET/computed tomography (CT) and tissue biopsy reached 84.29%. There was a greater response to EGFR-TKIs (81.58% versus 6.06%) and longer median progression-free survival (348 days versus 183 days) in NSCLC patients when ¹⁸F-MPG PET/CT SUV_max (maximum standard uptake value) was ≥2.23 versus <2.23. Our study demonstrates that ¹⁸F-MPG PET/CT is a powerful method for precise quantification of EGFR-activating mutation status in NSCLC patients, and it is a promising strategy for noninvasively identifying patients sensitive to EGFR-TKIs and for monitoring the efficacy of EGFR-TKI therapy.

Design, synthesis and antitumor evaluation of phenyl N-mustard-quinazoline conjugates

A series of N-mustard-quinazoline conjugates was synthesized and subjected to antitumor studies. The N-mustard pharmacophore was attached at the C-6 of the 4-anilinoquinazolines via a urea linker. To study the structure-activity relationships of these conjugates, various substituents were introduced to the C-4 anilino moiety. The preliminary antitumor studies revealed that these agents exhibited significant antitumor activity in inhibiting various human tumor cell growths in vitro. Compounds 21b, 21g, and 21h were selected for further antitumor activity evaluation against human breast carcinoma MX-1 and prostate PC-3 xenograft in animal model. These agents showed 54-75% tumor suppression with low toxicity (5-7% body-weight changes). We also demonstrate that the newly synthesized compounds are able to induce DNA cross-linking through alkaline agarose gel shift assay and inhibited cell cycle arrest at G2/M phase.

Determining the binding mode and binding affinity constant of tyrosine kinase inhibitor PD153035 to DNA using optical tweezers

Accurately predicting binding affinity constant (K(A)) is highly required to determine the binding energetics of the driving forces in drug-DNA interactions. Recently, PD153035, brominated anilinoquinazoline, has been reported to be not only a highly selective inhibitor of epidermal growth factor receptor but also a DNA intercalator. Here, we use a dual-trap optical tweezers to determining K(A) for PD153035, where K(A) is determined from the changes in B-form contour length (L) of PD153035-DNA complex. Here, L is fitted using a modified wormlike chain model. We found that a noticeable increment in L in 1 mM sodium cacodylate was exhibited. Furthermore, our results showed that K(A)=1.18(±0.09)×10(4) (1/M) at 23±0.5°C and the minimum distance between adjacent bound PD153035≈11 bp. We anticipate that by using this approach we can determine the complete thermodynamic profiles due to the presence of DNA intercalators.

Design, synthesis, and DNA-binding of N-alkyl(anilino)quinazoline derivatives

New N-alkylanilinoquinazoline derivatives 5, 12, 20, and 22 have been prepared from 4-chloro-6,7-dimethoxyquinazoline 3, 4-chloro-6,7-methylenedioxyquinazoline 19, and commercially available anilines. Differents classes of compounds substituted by an aryloxygroup (6a-c, 16a,b, and 17a,b), (aminophenyl)ureas (12a,b and 13a-f), anilines (4a-m, 20a,b), N-alkyl(aniline) (5a-m, 21a,b, 22a,d), and N-aminoalkyl(aniline) (22e-g) have been synthesized. These molecules were evaluated for their cytotoxic activities and as potential DNA intercalating agents. We studied the strength and mode of binding to DNA of these molecules by DNA melting temperature measurements, fluorescence emission, and circular dichroism. The results of various spectral and gel electrophoresis techniques obtained with the different compounds, in particular compounds 5g and 22f, revealed significant DNA interaction. These experiments confirm that the N-aminoalkyl(anilino)-6,7-dimethoxyquinazoline nucleus is an efficient pharmacophore to trigger binding to DNA, via an intercalative binding process.

Nitroimidazole-based bioreductive compounds bearing a quinazoline or a naphthyridine chromophore

In our search for novel bioreductive agents with weak DNA-binding characteristics, we have synthesized two new 2-nitroimidazolyl derivatives tethered to a fused aromatic-ring chromophore with two nitrogen atoms: 4-[3-(2-nitro-1-imidazolyl)-propylamino]-2-methyl-quinazoline hydrochloride (NLQZ-1) and 4-[3-(2-nitro-1-imidazolyl)-propylamino]-1,5-naphthyridine hydrochloride (NLPP-1). DNA binding was evaluated by using the ethidium bromide displacement assay. Cytotoxicity, radiosensitization, and interaction with chemotherapeutic agents were evaluated in V79 and A549 cells by using the clonogenic assay. Both compounds are not DNA intercalators and showed relatively low uptake characteristics in V79 cells. A slightly increasing hypoxic selectivity [HS = IC(50)(A)/IC(50)(H) (IC(50) is the product of a compound's concentration and the time necessary for 50% reduction in clonogenicity under aerobic (A) or hypoxic (H) conditions)] was observed with incubation time in the case of NLPP-1 (12-19 and 15-26 in V79 and A549 cells, respectively, with 1-3 h of incubation). The HS of NLQZ-1 was approximately 14, independently of incubation time. Good radiosensitization of hypoxic V79 cells was obtained with both compounds at nontoxic concentrations [the concentration for a sensitization enhancement ratio of 1.6 (C(1.6)) was 61.4 and 75.0 micromol/l for NLQZ-1 and NLPP-1, respectively]. For NLPP-1, a C(1.6) of 44.1 micromol/l was obtained in A549 cells. Both compounds interacted synergistically with cisplatin or melphalan in V79 cells, under hypoxic preexposure conditions and dose modification factors values of approximately 2.5 were obtained at 10% survival. It is concluded that although compounds that do not bind to DNA are in general less potent hypoxic cytotoxins, they can still show good HS values and interact synergistically with radiation/chemotherapeutic agents. Therefore, a further in-vivo evaluation of NLQZ-1 and NLPP-1 is worthwhile.

The DNA-binding epidermal growth factor-receptor inhibitor PD153035 and other DNA-intercalating cytotoxic drugs reactivate the expression of the retinoic acid receptor-β tumor-suppressor gene in breast cancer cells

We have previously shown that the epidermal growth factor-receptor (EGFR) tyrosine kinase inhibitor PD153035 induces retinoic acid receptor-beta (RAR-beta) expression in malignant cells by mechanisms that are independent of its blocking activity on EGFR (ErbB1) or on any other ErbB receptor (ErbB2, ErbB3, ErbB4). RAR-beta2, one of three human RAR-beta isoforms (RAR-beta1, RAR-beta2, RAR-beta4), is silenced in many tumors and acts as a tumor suppressor. Forced expression of RAR-beta2 reverts the malignant phenotype of RAR-beta2-negative breast cancer cells and reconstitutes retinoid sensitivity in these cells. Here, we demonstrate that the EGFR inhibitor PD153035 specifically induces RAR-beta2, but not the other two isoforms (RAR-beta1, RAR-beta4) in MDA-MB-468 and MDA-MB-453 human breast cancer cells. Induction was seen at the mRNA (reverse transcription-polymerase chain reaction) and protein level (Western analysis). PD153035-mediated induction of RAR-beta2 was associated with synergistic growth inhibition in cells co-treated with PD153035 and all-trans retinoic acid (tRA). Most importantly, PD153035 restored retinoic acid sensitivity in retinoic acid-resistant cells. Our previous work also revealed that PD153035 directly intercalates into the DNA suggesting that changes in the chromatin structure contribute to the RAR-beta2-inducing effect of PD153035. This prompted us to examine the effect of DNA intercalating chemotherapeutic drugs such as doxorubicin, amsacrine, and mitoxantrone on the expression of RAR-beta. Vincristine was used for comparative reasons, because this drug does not target DNA. All four compounds caused dose-dependent growth inhibition in MDA-MB-468 and MDA-MB-453 cells. Interestingly, compounds that directly interact with the DNA (doxorubicin, amsacrine, mitoxantrone) caused a time-dependent up-regulation of the RAR-beta expression in all cell lines examined, whereas the negative control drug vincristine, which causes disruption of microtubule structures, did not stimulate RAR-beta expression. These data further support the notion that induction of the RAR-beta tumor-suppressor gene in cancer cells by PD153035 is mediated at least in part by its DNA intercalating activity.

Upregulation of retinoic acid receptor-β by the epidermal growth factor-receptor inhibitor PD153035 is not mediated by blockade of ErbB pathways

Inhibiting epidermal growth factor-receptor (ErbB-1) represents a powerful anticancer strategy. Activation of retinoid pathways is also in development for cancer treatment. Retinoic acid receptor-beta-the tumor suppressor and main retinoid mediator--is silenced in many tumors. The ErbB-1 inhibitor PD153035 cooperates with retinoic acid during growth inhibition and induces retinoic acid receptor-beta suggesting that ErbB-1 controls retinoic acid receptor-beta. However, here we demonstrate that ErbB pathways are not involved in PD153035-mediated retinoic acid receptor-beta-upregulation. PD153035 inhibits ErbB-1-phosphorylation, whereas its derivative EBE-A22 is inactive. Yet both inhibit cell growth and upregulate retinoic acid receptor-beta in ErbB-1-overexpressing (MDA-MB-468), moderately expressing (OVCAR-3), ErbB-1-negative (MDA-MB-453) or ErbB-negative cells (CEM, Jurkat). Both bind DNA, whereas the closely related ErbB-1 inhibitors AG1478 and ZD1839, which are inactive on retinoic acid receptor-beta, do not significantly bind DNA. None of the other ErbB-1/ErbB-2 inhibitors tested (RG-14620, LFM-A12, AG879, AG825) affect retinoic acid receptor-beta. PD153035 decreases methylation of the retinoic acid receptor-beta2 promoter. In OVCAR-3, it stimulates dislodgement of histone deacetylase 1 from the promoter and acetylation of histones H3 and H4. Consequently, PD153035 facilitates recruitment of RNA polymerase II to the promoter and stimulates transcriptional activity. Moreover, PD153035 increases the retinoic acid receptor-beta mRNA half-life. No other retinoid receptor, nor estrogen receptor-alpha, nor RASSF1A is upregulated by PD153035. Thus PD153035 induces retinoic acid receptor-beta by ErbB-independent transcriptional and post-transcriptional mechanisms. This report highlights a triple action for an ErbB-1 inhibitor (ErbB-1 inhibition, DNA intercalation, retinoic acid receptor-beta-induction). Such multitargeting drugs bear great potential for cancer treatment.

Synthesis and anticancer activity of new pyrrolocarbazoles and pyrrolo-β-carbolines

'Bended' 1, 3 or 'linear' 2 pyrrolidino-fused (aza)carbazoles were prepared and screened towards a few cancer-related targets. Whereas 'bended' derivatives 1 and 3 proved to be weakly toxic, several members of the 'linear' family strongly interact with DNA, especially derivative 28a.

Selective Inhibition of Topoisomerase I and Various Steps of Spliceosome Assembly by Diospyrin Derivatives

Pre-mRNA splicing is an essential step of the expression of most metazoan protein-coding genes, which is often regulated in a cell type-specific or developmental manner. We have demonstrated previously that human DNA topoisomerase I, an extensively studied target for anticancer drugs, also has an intrinsic protein kinase activity that specifically phosphorylates proteins involved in splice site selection. Therefore, DNA topoisomerase I was recently shown to play a critical role in alternative splicing. Here, we have exploited these novel properties of DNA topoisomerase I to develop entirely novel diospyrin derivatives targeting its protein kinase activity and thereby modulating pre-mRNA splicing. Although some derivatives indeed inhibit kinase activity of topoisomerase I, they did not block reactions of topoisomerase I on DNA. However, these drugs interfere with camptothecin-dependent topoisomerase I-mediated DNA cleavage, implying that diospyrin derivatives mediate a conformational change of topoisomerase I. It is note-worthy that in vitro splicing reactions revealed that diospyrin derivatives alter various steps of splicing. Some diospyrin derivatives inhibit either the first or the second catalytic step of splicing but not spliceosome assembly, whereas diospyrin itself prevents the formation of full spliceosome. Our data revealed for the first time that diospyrin derivatives are able to stall the dynamic assembly of the spliceosome and open the exciting possibility of using these derivatives to correct aberrant splicing in human genetic diseases.

Synthesis of condensed quinolines and quinazolines as DNA ligands

Among new condensed quinolines and quinazolines the design of which were inspired by anti-cancer DNA-binding alkaloids such as camptothecin and batracyclin, DNA binding tests identify the 8-methoxy-7-piperazinylpropoxyindeno[1,2-b]quinolin-11-one tetracyclic system as a new motif for DNA recognition.

Synthesis of Mono- and Bisdihydrodipyridopyrazines and Assessment of Their DNA Binding and Cytotoxic Properties

Aminoalkyl-substituted monomeric and dimeric dihydrodipyridopyrazines have been synthesized and evaluated as antitumor agents. Potent cytotoxic compounds were identified in both series. Biochemical and biophysical studies indicated that all these compounds strongly stabilized the duplex structure of DNA and some of them elicited a selectivity for GC-rich sequences. Sequence recognition by of the dimeric dihydrodipyridopyrazines is reminiscent of that of certain antitumor bisnaphthalimides. Compared to monomers, corresponding dimeric derivatives showed higher affinity for DNA. This property was attributed to a bisintercalative binding to DNA. This assumption was indirectly probed by electric linear dichroism and DNA relaxation experiments. DNA provides a bioreceptor for these dihydrodipyridopyrazine derivatives, but no poisoning of human topoisomerases I or II was detected. Most of the compounds efficiently inhibited the growth of L1210 murine leukemia cells and perturbed the cell cycle progression (with a G2/M block in most cases). A weak but noticeable in vivo antitumor activity was observed with one of the dimeric compounds. This studies identifies monomeric and dimeric dihydrodipyridopyrazines as a new class of DNA-targeted antitumor agents.

Synergistic antiproliferative and apoptotic effects induced by epidermal growth factor receptor and protein kinase a inhibitors in human prostatic cancer cell lines

Our results revealed that the blockade of epidermal growth factor receptor (EGFR) tyrosine kinase and protein kinase A (PKA) signaling pathways by specific inhibitors (PD153035 and Rp-cAMPs) leads to a synergistic inhibition of EGF- and serum-stimulated growth of human prostatic cancer cells (LNCaP, DU145 and PC3) concomitant with an arrest in the G1 phase of cellular cycle. Of particular interest, the combination of PD153035 and Rp-cAMPs also caused a more substantial apoptotic/necrotic death of these prostatic cancer cells as compared to drugs alone. Moreover, we observed that the inhibition of acidic sphingomyelinase and caspase cascades results in a marked reduction of DNA fragmentation and apoptotic death induced by PD153035, alone or in combination with Rp-cAMPs, in EGF stimulated PC3 cells. This suggests that these agents might mediate their cytotoxic effects at least in part via the ceramide generation and activation of caspase signaling pathways. N-oleoylethanolamine (OE), an inhibitor of acidic ceramidase, consistently potentiated the apoptotic effects of PD153035 in all the prostatic cancer cell lines tested. Additionally, the cellular ceramide content estimated for PC3 cells was increased after treatment with PD153035, alone or in combination, at a lower dose with OE and Rp-cAMPs. The synergistic apoptotic effect of PD153035 plus Rp-cAMPs induced in PC3 was also accompanied by a significant rate of mitochondrial membrane depolarization and release of cytochrome c into cytosol as compared to drugs alone. Combined, the results indicated that the simultaneous inhibition of EGFR and PKA signaling cascades might lead to a more massive apoptotic death of metastatic prostatic cancer cells by increasing ceramide accumulation and activating of caspase cascade of a mitochondrial dependent manner.

Indolizino[1,2-b]quinolines derived from A-D rings of camptothecin: synthesis and DNA interaction

Camptothecin consists of a lactone E-ring adjacent to a tetracyclic A-D ring planar chromophore which are essential for topoisomerase I inhibition and DNA interaction, respectively. The A-D ring system can be exploited to develop DNA-binding molecules. Indolizino[1,2-b]quinoline derivatives substituted with a piperidinoethyloxy side chain on the A-ring and an aminomethyl function on the D one were synthesized and their DNA-binding properties and in vitro cytotoxicity investigated.

Highly cytotoxic benzo[c]pyrido[2,3,4-kl]acridines

Several benzo[c]pyrido[2,3,4-kl]acridines bearing different substituents on the A and E rings were synthesized and evaluated for their capacity to bind to DNA and to inhibit DNA topoisomerases. Potent cytotoxic compounds were discovered but no strict correlation with their DNA binding affinity and effects on topoisomerases were observed. DNA is one but not the unique target of these compounds.