Antitumor activity of XR5944, a novel and potent topoisomerase poison

Fragment Localized Molecular Orbitals

We introduce the concept of fragment localized molecular orbitals (FLMOs), which are Hartree-Fock molecular orbitals localized in specific fragments constituting a molecular system. In physical terms, we minimize the local electronic energies of the different fragments, at the cost of maximizing the repulsion between them. To showcase the approach, we rationalize the main interactions occurring in large biological systems in terms of interactions between the fragments of the system. In particular, we study an anticancer drug intercalated within DNA and retinal in anabaena sensory rhodopsin as prototypes of molecular systems embedded in biological matrixes. Finally, the FLMOs are exploited to rationalize the formation of two oligomers, prototypes of amyloid diseases, such as Parkinson and Alzheimer.

Dimeric Drugs

This review intends to summarize the structures of an extensive number of symmetrical-dimeric drugs, having two monomers linked via a bridging entity while emphasizing the large versatility of biologically active substances reported to possess dimeric structures. The largest number of classes of these compounds consist of anticancer agents, antibiotics/antimicrobials, and anti-AIDS drugs. Other symmetrical-dimeric drugs include antidiabetics, antidepressants, analgesics, anti-inflammatories, drugs for the treatment of Alzheimer's disease, anticholesterolemics, estrogenics, antioxidants, enzyme inhibitors, anti-Parkisonians, laxatives, antiallergy compounds, cannabinoids, etc. Most of the articles reviewed do not compare the activity/potency of the dimers to that of their corresponding monomers. Only in limited cases, various suggestions have been made to justify unexpected higher activity of the dimers vs. the corresponding monomers. These suggestions include statistical effects, the presence of dimeric receptors, binding of a dimer to two receptors simultaneously, and others. It is virtually impossible to predict which dimers will be preferable to their respective monomers, or which linking bridges will lead to the most active compounds. It is expected that the extensive number of articles summarized, and the large variety of substances mentioned, which display various biological activities, should be of interest to many academic and industrial medicinal chemists.

PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA

With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand–protein complexes. Besides ligand–protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA or RNA-binding proteins. To date, over 7% of all 3D structures in the Protein Data Bank include DNA or RNA. Therefore, we extended PLIP to encompass these important molecules. We demonstrate the power of this extension with examples of a cancer drug binding to a DNA target, and an RNA–protein complex central to a neurological disease. PLIP is available online at https://plip-tool.biotec.tu-dresden.de and as open source code. So far, the engine has served over a million queries and the source code has been downloaded several thousand times.

Novel DNA Bis-Intercalator XR5944 as a Potent Anticancer Drug-Design and Mechanism of Action

This review is dedicated to Professor William A. Denny’s discovery of XR5944 (also known as MLN944). XR5944 is a DNA-targeted agent with exceptionally potent antitumor activity and a novel DNA binding mode, bis-intercalation and major groove binding, as well as a novel mechanism of action, transcription inhibition. This novel anticancer compound represents a remarkable accomplishment resulting from two decades of drug discovery by Professor Denny and coworkers. Here, we review our work on the structural study of the DNA binding mode of XR5944 and mechanistic study of XR5944 action.

Structures and dynamics of DNA complexes of the desmethyl analog of the cytotoxin MLN944: Insights into activity when a methyl isn't futile

Structure activity relationships for tricyclic-carboxamide topoisomerase II poisons indicate that cytotoxicity is enhanced by the presence of methyl, and other, groups in the position peri to the carboxamide. Linked dimers of phenazine-1-carboxamides are potent cytotoxins and one phenazine dimer, MLN944 (alternatively XR5944), has been in clinical trial. MLN944 is a template inhibitor of transcription, whereas corresponding monomers are not. Nevertheless, its cytotoxic potency is also diminished by removal of its peri methyl groups. Here, we describe NMR and molecular dynamic studies of the interaction of desmethyl MLN944 with d(ATGCAT)₂ , d(TATGCATA)₂ , and d(TACGCGTA)₂ to investigate the influence of the nine-methyl group on the structure of MLN944 complexes. As with MLN944, the carboxamide group hydrogen bonds to the phenazine ring nitrogen, the ligand sandwiches the central GC base pairs in the major groove, and the protonated linker amines hydrogen bond primarily to the O6 atom of the guanines. Molecular dynamics studies reveal that the linker exists in multiple conformations, none of which produce an ideal set of hydrogen bonds. In distinction, however, the carboxamide-to-phenazine ring nitrogen hydrogen bond is weaker, the overall helix winding is less and the NMR resonances are broader in the desmethyl complexes. Exchange between free and complexed DNA, quantified using two-dimensional NOESY spectra, is faster for the desmethyl MLN944 complexes than for MLN944 complexes. Overall, the data suggest that desmethyl MLN944 DNA complexes are "looser" and more unwound at the binding site, leading to faster dissociation rates, which could account for the diminished efficacy of the desmethyl analog.

Topoisomerase 1B poisons: Over a half-century of drug leads, clinical candidates, and serendipitous discoveries

Topoisomerases are DNA processing enzymes that relieve supercoiling (torsional strain) in DNA, are necessary for normal cellular division, and act by nicking (and then religating) DNA strands. Type 1B topoisomerase (Top1) is overexpressed in certain tumors, and the enzyme has been extensively investigated as a target for cancer chemotherapy. Various chemical agents can act as "poisons" of the enzyme's religation step, leading to Top1-DNA lesions, DNA breakage, and eventual cellular death. In this review, agents that poison Top1 (and have thus been investigated for their anticancer properties) are surveyed, including natural products (such as camptothecins and indolocarbazoles), semisynthetic camptothecin and luotonin derivatives, and synthetic compounds (such as benzonaphthyridines, aromathecins, and indenoisoquinolines), as well as targeted therapies and conjugates. Top1 has also been investigated as a therapeutic target in certain viral and parasitic infections, as well as autoimmune, inflammatory, and neurological disorders, and a summary of literature describing alternative indications is also provided. This review should provide both a reference for the medicinal chemist and potentially offer clues to aid in the development of new Top1 poisons.

DNA Recognition by a Novel Bis-Intercalator, Potent Anticancer Drug XR5944

XR5944 is a potent anticancer drug with a novel DNA binding mode: DNA bisintercalationg with major groove binding. XR5944 can bind the estrogen response element (ERE) sequence to block ER-ERE binding and inhibit ERα activities, which may be useful for overcoming drug resistance to currently available antiestrogen treatments. This review discusses the progress relating to the structure and function studies of specific DNA recognition of XR5944. The sites of intercalation within a native promoter sequence appear to be different from the ideal binding site and are context- and sequence- dependent. The structural information may provide insights for rational design of improved EREspecific XR5944 derivatives, as well as of DNA bis-intercalators in general.

The solution structure of bis(phenazine-1-carboxamide)-DNA complexes: MLN 944 binding corrected and extended

MLN 944 is a bisintercalating DNA-binding antitumor agent known to be a template inhibitor of transcription. Previous (1) H NMR studies of its d(ATGCAT)2 complex concluded that its phenazine chromophores are protonated. However, we find that this is not so, which has important consequences for the charged state of the ligand, for the orientation of its 1-carboxamide group in the complex, and for the details of the interaction of its protonated interchromophore linker with the DNA base pairs. Here, we report a corrected solution structure of the MLN 944-d(ATGCAT)2 complex, and extend the study to complexes with d(TATGCATA)2 , and d(TACGCGTA)2 , using a variety of (1) H and (31) P NMR methods and molecular dynamics simulations employing the AMBER 12 force field. We find that for all three complexes MLN 944 binds as a dication, in which the chromophores are uncharged, in the DNA major groove spanning the central 2 GC base pairs in a manner that maintains the dyad symmetry of the DNA. The carboxamide group lies in the plane of the chromophore, its NH making hydrogen bonding interactions with the phenazine N10 nitrogen, and the protonated linkers form hydrogen bonds with the O6 atom of guanine. The dynamics simulations reveal extensive solvent interactions involving the linker amines, the carboxamide group, and the DNA bases.

Ruthenium(II) polypyridyl complexes with 1,8-naphthalimide group as DNA binder, photonuclease, and dual inhibitors of topoisomerases I and IIα

Two ruthenium(II) polypyridyl complexes containing 1,8-naphthalimide group as DNA binders, photonucleases, and inhibitors of topoisomerases I and IIα are evaluated. The binding properties of [Ru(phen)₂(pnip)]²⁺ {1; phen=1,10-phenanthroline; pnip=12-[N-(p-phenyl)-1,8-napthalimide]- imidazo[4',5'-f] [1,10]phenanthroline} and [Ru(bpy)₂(pnip)]²⁺ (2; bpy=2,2'-bipyridine) with calf thymus DNA increases with increasing the bulkiness and hydrophobic character of ancillary ligands, although the two complexes possess high affinities for DNA via intercalation. Moreover, photoirradiation (λ=365nm) of the two complexes are found to induce strand cleavage of closed circular pBR322 plasmid DNA via singlet oxygen mechanism, while complex 1 displays more effective photocleavage activity than complex 2 under the same conditions. Topoisomerase inhibition and DNA strand passage assay reflect that complexes 1 and 2 are efficient dual poisons of topoisomerases I and IIα.

Dual inhibition of topoisomerases I and IIα by ruthenium(II) complexes containing asymmetric tridentate ligands

Five novel ruthenium(II) complexes, [Ru(dtzp)(dppt)](2+) (1), [Ru(dtzp)(pti)](2+) (2), [Ru(dtzp)(ptn)](2+) (3), [Ru(dtzp)(pta)](2+) (4) and [Ru(dtzp)(ptp)](2+) (5) (where dtzp = 2,6-di(thiazol-2-yl)pyridine, dppt = 3-(1,10-phenanthroline-2-yl)-5,6-diphenyl-as-triazine), pti = 3-(1,10-phenanthroline-2-yl)-as-triazino-[5,6-f]isatin, ptn = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]naphthalene, pta = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]acenaphthylene, and ptp = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]-phenanthrene), were synthesised and characterised. The structures of complexes 3-5 were determined by X-ray diffraction. The DNA binding behaviours of the complexes were studied by spectroscopic and viscosity measurements. The results suggested that the Ru(II) complexes, except for complex 1, bind to DNA in an intercalative mode. Topoisomerase inhibition and DNA strand passage assay confirmed that Ru(II) complexes 3, 4, and 5 acted as efficient dual inhibitors of topoisomerases I and IIα. In vitro cytotoxicity assays indicated that these complexes exhibited anticancer activity against various cancer cell lines. Ruthenium(ii) complexes were confirmed to preferentially accumulate in the nucleus of cancer cells and induced DNA damage. Flow cytometric analysis and AO/EB staining assays indicated that these complexes induced cell apoptosis. With the loss of the mitochondrial membrane potential, the Ru(ii) complexes induce apoptosis via the mitochondrial pathway.

Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator

XR5944, a deoxyribonucleic acid (DNA) bis-intercalator with potent anticancer activity, can bind the estrogen response element (ERE) sequence to inhibit estrogen receptor-α activities. This novel mechanism of action may be useful for overcoming drug resistance to currently available antiestrogen treatments, all of which target the hormone-receptor complex. Here we report the nuclear magnetic resonance solution structure of the 2:1 complex of XR5944 with the naturally occurring TFF1-ERE, which exhibits important and unexpected features. In both drug–DNA complexes, XR5944 binds strongly at one intercalation site but weakly at the second site. The sites of intercalation within a native promoter sequence appear to be context and sequence dependent. The binding of one drug molecule influences the binding site of the second. Our structures underscore the fact that the DNA binding of a bis-intercalator is directional and different from the simple addition of two single intercalation sites. Our study suggests that improved XR5944 bis-intercalators targeting ERE may be designed through optimization of aminoalkyl linker and intercalation moieties at the weak binding sites.

Small and Innovative Molecules as New Strategy to Revert MDR

Multidrug resistance (MDR) is a complex phenomenon principally due to the overexpression of some transmembrane proteins belonging to the ATP binding cassette (ABC) transporter family. Among these transporters, P-glycoprotein (P-gp) is mostly involved in MDR and its overexpression is the major cause of cancer therapy failure. The classical approach used to overcome MDR is the co-administration of a P-gp inhibitor and the classic antineoplastic drugs, although the results were often unsatisfactory. Different classes of P-gp ligands have been developed and, among them, Tariquidar has been extensively studied both in vitro and in vivo. Although Tariquidar has been considered for several years as the lead compound for the development of P-gp inhibitors, recent studies demonstrated it to be a substrate and inhibitor, in a dose-dependent manner. Moreover, Tariquidar structure-activity relationship studies were difficult to carry out because of the complexity of the structure that does not allow establishing the role of each moiety for P-gp activity. For this purpose, SMALL molecules bearing different scaffolds such as tetralin, biphenyl, arylthiazole, furoxane, furazan have been developed. Many of these ligands have been tested both in in vitro assays and in in vivo PET studies. These preliminary evaluations lead to obtain a library of P-gp interacting agents useful to conjugate chemotherapeutic agents displaying reduced pharmacological activity and appropriate small molecules. These molecules could get over the limits due to the antineoplastic-P-gp inhibitor co-administration since pharmacokinetic and pharmacodynamic profiles are related to a dual innovative drug.

New class of highly stable nonaromatic tautomers

A new and efficient one-pot synthesis of highly stable bridged-bisphenazine-type molecules with loss of their aromaticity in the ground state in favor of a quinoid-type structure is described (either in solution or in solid-state).

Effect of phenazine compounds XR11576 and XR5944 on DNA topoisomerases

PURPOSE

Previous in vitro cleavage data showed that XR11576 and XR5944 stabilised topoisomerase I and topoisomerase II complexes on DNA in a dose-dependent fashion. However, some studies indicated a possible topoisomerase-independent mechanism of action for these drugs.

METHODS

Three methods, the TARDIS assay, immunoband depletion and the K(+)/SDS assay have been used to assess topoisomerase complex formation induced by XR11576 or XR5944 in human leukaemic K562 cells.

RESULTS

TARDIS and immunoband depletion assays demonstrated that XR11576 and XR5944 induced complex formation for both topoisomerase I and topoisomerase II (alpha and beta) in a dose- and time-dependent manner, following exposure times of 24 and 48 h at concentrations of 1 or 10 microM. The K(+)/SDS assay showed the formation of protein/DNA complexes after a 1 h exposure to 1 or 10 muM XR11576.

CONCLUSION

Our data confirm that XR11576 or XR5944 can form topoisomerase complexes, after long periods of exposure.

First-into-man phase I and pharmacokinetic study of XR5944.14, a novel agent with a unique mechanism of action

The bis-phenazine XR5944.14 is a novel cytotoxic agent which intercalates into DNA and inhibits transcription. The objectives of this study were to determine the dose-limiting toxicity (DLT), the maximum tolerated dose (MTD) and to describe the pharmacokinetics (PKs) of XR5944.14 when given at doses ranging from 3.6 to 36 mg m⁻² every 3 weeks to patients with advanced tumours. Twenty-seven patients were treated with a total of 77 cycles. Dose-limiting toxicities occurred at doses ⩾24 mg m⁻². Oral mucositis was the most common DLT. Two patients developed acute renal failure possibly related to the study drug. Other less-severe toxicities were diarrhoea, nausea, vomiting and fatigue. Haematological toxicity was mild. One patient showed an objective partial response. Pharmacokinetic analysis was performed during the first cycle of treatment and plasma was assayed for XR5944.14 using a validated liquid chromatography tandem mass spectrometry. The systemic exposure of XR5944.14 increased more than proportionally with increasing dose, with inter-patient variability increasing from dose level 24 mg m⁻² onwards. The lack of correlation between toxicity and PK values makes it difficult to recommend a dose for further study in phase 2 trials. More work is needed to explain the inter- and intra-individual variation in PKs and pharmacodynamics.

Mode of action of the novel phenazine anticancer agents XR11576 and XR5944

The substituted phenazines XR11576 and XR5944 were originally described as dual topoisomerase-I/II poisons. Subsequent reports, however, indicated that the association of their cytotoxicity with cellular topoisomerases was not clear. We set out to study this further using human tumour cell lines, PEO1 ovarian cancer, MDA-MB-231 breast cancer and variants with acquired resistance to VP-16 and XR11576: PEO1VPR, MB-231VPR, MB-231-11576R and camptothecin: PEO1CamR. Cytotoxicity testing [3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl tetrazolium bromide assay], DNA-protein crosslink formation, cell cycle analysis (flow cytometry) for DNA content, apoptosis (flow cytometry) for Annexin V and Western blotting for apoptotic factors. Cytotoxicity testing showed potent cytotoxicity with no cross-resistance to XR11576 or XR5944 in VP-16 or camptothecin-resistant lines. Importantly, we have shown for the first time that the activities of XR5944 and XR11576 are similar as MB-231-11576R cells were resistant to both agents and to a similar extent. XR5944 showed the greatest, albeit slower, interaction with DNA with high levels of DNA-protein crosslinks. Levels of apoptosis in XR5944-treated cells were significantly less than those in VP-16 or XR11576 treatments, suggestive of a more cytostatic rather than cytotoxic mode of action. Interestingly, XR5944 failed to give rise to a G2/M blockade, in contrast to VP-16 or XR11576. XR5944 and XR11576, in line with a dual topoisomerase-I/II-directed mechanism of action, retain potent activity in tumour cells with acquired resistance to VP-16 and camptothecin. Although these agents appear to behave differently from each other according to experimental conditions, this study suggests a substantial overlap in their mechanism(s) of action.

XR5944: A potent inhibitor of estrogen receptors

The anticancer drug XR5944 was originally developed as a topoisomerase inhibitor and was subsequently shown to be a transcription inhibitor. It has shown exceptional anticancer activity both in vitro and in vivo and was significantly more potent than traditional topoisomerase inhibitors. The solution structure of the XR5944/DNA complex recently obtained in our laboratory indicates that XR5944 bis-intercalates at the 5'-(TpG):(CpA) site of duplex DNA, which is found in the consensus DNA-binding site of estrogen receptor (ER). Thus, we tested the ability of XR5944 to inhibit ER activity both in vitro and in cultured cells. In electrophoretic mobility shift assays, it is seen that the DNA binding of recombinant ERalpha protein, as well as ER from nuclear extracts, is inhibited by XR5944 in a dose-dependent manner. In luciferase reporter assays, XR5944 inhibited the reporter gene expression from an estrogen response element-containing promoter but not from a basal promoter sequence that lacks any cis-acting elements. In contrast, the RNA polymerase inhibitor actinomycin D inhibits the transcription from both the above-mentioned promoters. The specificity of XR5944 activity is displayed by a separate reporter assay in which the transactivation of reporter gene expression by Sp1 proteins was not inhibited by XR5944. Collectively, these data suggest that XR5944 is capable of specifically inhibiting the binding of ER to its consensus DNA sequence and its subsequent activity. This represents a novel mechanism of ER inhibition, which may allow the development of agents capable of overcoming resistance to current antiestrogens.

C-(2-chloroquinoline-3-yl)-N-phenyl nitrone: new synthetic antioxidant inhibits proliferation and induces apoptosis of breast carcinoma MCF-7 cells

In this work, a new quinoline nitrone derivative, C-(2-chloroquinoline-3-yl)-N-phenyl nitrone (CQPN) was successfully prepared and proved by spectral analysis. The antioxidant activity of CQPN against various radicals was investigated and its anti-cancer properties against different human tumor cell lines including the solid tumor cell lines hepatocarcinoma (Hep-G2) and breast carcinoma (MCF-7); the hematopoietic tumor cell line lymphoblastic leukemia (1301) was also explored. CQPN activities were compared to that of the known nitrone C-phenyl-N-tert-butyl nitrone (PBN). Our results showed that although PBN was the stronger antioxidant than CQPN, the latter was an effective scavenger of different non-physiological (1,1-diphenyl-2-picrylhyrazyl) and physiological (peroxyl and hydroxyl) radicals. Both of CQPN and PBN possess a significant inhibitory property against LPS-stimulated NO production in macrophage. CQPN and PBN treatment resulted in a growth inhibition in Hep-G2 cells (IC50 31.42 microM and 18.6 microM, respectively). Unlike PBN, CQPN strongly inhibited the growth of MCF-7 cells (IC50 14.01 microM) in a dose-dependent manner. On contrary, CQPN and PBN exhibited a proliferative stimulatory activity of the immune cells including macrophages and lymphocytes. Exploring the cytotoxic effect of CQPN against MCF-7 cells indicated that CQPN led to a major time-dependent disturbance in the cell-cycle phases including progressive arrest in both S- and G2/M-phases. This disturbance was found to be associated with a kinetic induction of apoptosis. The novel nitrone derivative CQPN is a strong antioxidant, though less than PBN, and it may be an effective anti-proliferative compound against breast carcinoma.

The antiproliferative agent MLN944 preferentially inhibits transcription

MLN944 is a novel compound currently being codeveloped by Millennium Pharmaceuticals and Xenova Ltd. as a cancer therapeutic and is in a phase I clinical trial for solid tumors. Although MLN944 was originally proposed to function as a topoisomerase I and II inhibitor, more recent data has shown that it is a DNA-intercalating agent that does not inhibit the catalytic activity of topoisomerase I or II. We show here that MLN944 inhibits incorporation of radiolabeled precursors into RNA preferentially over incorporation into DNA and protein in HCT116 and H460 cells. To determine if MLN944 inhibits transcription, a human RNA polymerase II in vitro transcription system was used. MLN944 inhibited initiation when added before or after the formation of preinitiation complexes and inhibited elongation at higher concentrations. The preferential inhibition of initiation differentiates MLN944 from actinomycin D, which more strongly inhibits elongation. Transcription of all RNA polymerases was inhibited in nuclei isolated from HeLa cells treated with low concentrations of MLN944. Our data are consistent with transcription as the target of the potent cytotoxic effects of MLN944.

Interaction of phenazine with water and DNA bases

The fluorescence spectrum of aqueous phenazine (PZ), an N-heterocyclic compound, shows some interesting features that indicate the formation of PZ-water complex in the excited state. Two types of complexes are postulated; Type I, formed by the association of water molecule with one of the nitrogen of PZ and Type II, formed by the association of water molecules with both the nitrogen of PZ. In addition, PZ also interacts with the DNA bases, adenine and thymine and the corresponding nucleosides, adenosine and thymidine. Fluorescence and laser flash photolysis studies indicate that the mode of interaction may be photoinduced electron transfer.

Preclinical anti-tumor activity of XR5944 in combination with carboplatin or doxorubicin in non-small-cell lung carcinoma

XR5944 (MLN944) is a novel bis-phenazine currently in phase I clinical trials that has demonstrated potent cytotoxic activity against a variety of tumor models. The combinations of XR5944 with carboplatin or doxorubicin were investigated in COR-L23/P human non-small-cell lung carcinoma (NSCLC) cells in vitro and the corresponding xenografts in vivo. In vitro cytotoxicity was evaluated by the sulforhodamine B assay and the drug interactions following simultaneous or sequential exposure were determined using median-effect analysis to calculate combination indices (CIs). XR5944 demonstrated potent cytotoxicity compared to either carboplatin or doxorubicin in COR-L23/P cells. Simultaneous or sequential exposure of XR5944 followed by carboplatin led to a synergistic response (CI<1), whereas the reverse order of addition showed an additive or antagonistic response (CI< or =1). Sequential administration of doxorubicin followed by XR5944 demonstrated marginally improved cytotoxicity (CI=1.31-0.77) than other schedules (CI=1.50-1.22) relative to individual drugs. Anti-tumor activity against COR-L23/P xenografts in nude mice was enhanced by administration of XR5944 (2 or 5 mg/kg) immediately before carboplatin (50 mg/kg) compared to single-agent treatment at the same doses. Improved efficacy was also observed by sequential administration of 7 mg/kg doxorubicin 48 h before 2.5 or 5 mg/kg XR5944. No additional toxicity was observed with combinations compared to single-agent treatment alone as determined by body weights. These data suggest that combinations of XR5944 with carboplatin or doxorubicin are of significant interest for clinical use, and that the schedule of administration may be important for achieving clinical efficacy over single-agent therapy.

Ex vivo characterization of XR11576 (MLN576) against ovarian cancer and other solid tumors

XR11576 (MLN576) is a novel monophenazine with a mechanism of action that includes interaction with both topoisomerase (Topo) I and II. The aim of this study was to evaluate its cytotoxicity against fresh tumor cells taken from patients with a variety of solid tumors. Cells were obtained from 89 patients and exposed for 6 days to XR11576 alone, or in combination with doxorubicin, cisplatin, treosulfan, paclitaxel or vinorelbine. Cell survival was measured using the ATP-Tumor Chemosensitivity Assay (ATP-TCA). Immunohistochemical staining of Topo I, Topo IIalpha and MDR1 was performed on paraffin-embedded blocks in those tumors for which tissue was available (n = 49). Overall, the median IC90 and IC50 values of XR11576 in tumor-derived cells were 242 and 110 nM, respectively. In all samples XR11576 was more potent than the other cytotoxics tested. Breast and gynecological malignancies were most sensitive to XR11576, while the potency of this compound was slightly attenuated in gastrointestinal tumors, in which the median IC90 and IC50 values were 308 and 212 nM, respectively. Cases of synergism were identified when combining XR11576 with vinorelbine (nine of 30 samples) and doxorubicin (12 of 38 samples), while the addition of paclitaxel resulted in an antagonistic effect (CI50>1.2) in 38 of 42 tumors. A very modest correlation by linear regression analysis was found between the intensity of MDR1 staining and the IC50 of XR11576 (r = 0.311, p = 0.0312), but not with the IC90 (r = 0.247, NS). These data support the rapid introduction of XR11576 to clinical trials and suggest that it may be effective against a broad spectrum of tumor types.

Antitumour activity of XR5944 in vitro and in vivo in combination with 5-fluorouracil and irinotecan in colon cancer cell lines

XR5944 (MLN944), a novel bis-phenazine, has demonstrated potent cytotoxic activity against a variety of murine and human tumour models. In the present study, the antitumour activity of XR5944 was investigated in combination with 5-fluorouracil (5-FU) or irinotecan in human colon carcinoma cell lines and xenografts. In vitro cytotoxicity of the combinations following exposure to the drugs sequentially or simultaneously was evaluated by the sulphorhodamine-B assay and interactions were determined using median-effect analysis. Antagonism was observed (CI>1) following exposure of HT29 cells simultaneously to XR5944 and 5-FU or SN38 (active metabolite of irinotecan). In contrast, sequential exposure of either combination in either order demonstrated at least an additive response (CI⩽1). At least an additive response was also observed with these combinations in HCT116 cells regardless of schedule. Antitumour activity in HT29 xenografts in nude mice was enhanced by sequential administration of 5-FU (65 mg kg⁻¹) or irinotecan (CPT-11) (35 mg kg⁻¹) 48 h before XR5944 (5, 10, or 15 mg kg⁻¹) compared to single agent treatment at the same or higher doses. Administration of irinotecan (35 mg kg⁻¹) and XR5944 (15 mg kg⁻¹) just 30 min apart yielded similar efficacy to sequential administration 48 h apart. All combinations were well tolerated. These data suggest that combinations of XR5944 with irinotecan or 5-FU are of significant interest in the treatment of colon cancer.

The ex vivo characterization of XR5944 (MLN944) against a panel of human clinical tumor samples

XR5944 (MLN944) is a novel DNA targeting agent with potent antitumor activity, both in vitro and in vivo, against several murine and human tumor models. We have used an ATP-tumor chemosensitivity assay to assess the ex vivo sensitivity of a variety of solid tumors (n = 90) and a CCRF-CEM leukemia cell line selected with XR5944. Differences in gene expression between the parental CCRF-CEM and the resistant subline were investigated by quantitative reverse transcription-PCR. Immunohistochemistry for topoisomerases I and IIα and multidrug resistance (MDR1) protein was done on those tumors for which tissue was available (n = 32). The CCRF-CEM XR5944 line showed increased mRNA levels of MDR1, major vault protein, and MDR-associated protein 1 compared with the parental line, whereas the expression of topoisomerases I, IIα, and IIβ was essentially unchanged, suggesting that XR5944 is susceptible to MDR mechanisms. The median IC90 and IC50 values for XR5944 in tumor-derived cells were 68 and 26 nmol/L, respectively, 6-fold greater than in resistant cell lines. XR5944 was 40- to 300-fold more potent than the other cytotoxics tested, such as doxorubicin, topotecan, and paclitaxel. Breast and gynecologic malignancies were most sensitive to XR5944, whereas gastrointestinal tumors showed greater resistance. A positive correlation (r = 0.68; P &lt; 0.0001) was found between the IC50 values of XR5944 and P-glycoprotein/MDR1 staining but not with either topoisomerase I or IIα immunohistochemistry index. These data support the rapid introduction of XR5944 to clinical trials and suggest that it may be effective against a broad spectrum of tumor types, especially ovarian and breast cancer.

Novel DNA bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug

The new bisphenazine anticancer drug MLN944 is a novel cytotoxic agent with exceptional anti-tumor activity against a range of human and murine tumor models both in vitro and in vivo. MLN944 has recently entered Phase I clinical trials. Despite the structural similarity with its parent monophenazine carboxamide and acridine carboxamide anticancer compounds, MLN944 appears to work by a distinct mechanism of inhibiting DNA transcription rather than the expected mechanism of topoisomerase I and II inhibition. Here we present the first NMR structure of MLN944 complexed with d(ATGCAT)(2) DNA duplex, demonstrating a novel binding mode in which the two phenazine rings bis-intercalate at the 5'-TpG site, with the carboxamide amino linker lying in the major groove of DNA. The MLN944 molecule adopts a significantly unexpected conformation and side chain orientation in the DNA complex, with the N10 on the phenazine ring protonated at pH 7. The phenazine chromophore of MLN944 is very well stacked with the flanking DNA base pairs using the parallel base-stacking intercalation binding mode. The DNA sequence specificity and the groove recognition of MLN944 binding is determined by several site-specific hydrogen bond interactions with the central G:C base pair as well as the favorable stacking interactions with the 5'-flanking thymine. The specific binding site of MLN944 is known to be recognized by a number of important transcription factors. Our electrophoretic gel mobility shift assay results demonstrated that the c-Jun DNA binding to the AP-1 site is significantly inhibited by MLN944 in a dose-dependent manner. Thus, the exceptional biological activity of MLN944 may be due to its novel DNA binding mode leading to a unique mechanism of action.

Biological characterization of MLN944: A potent DNA binding agent

MLN944 (XR5944) is a novel bis-phenazine that has demonstrated exceptional efficacy against a number of murine and human tumor models. The drug was reported originally as a dual topoisomerase I/II poison, but a precise mechanism of action for this compound remains to be determined. Several lines of evidence, including the marginal ability of MLN944 to stabilize topoisomerase-dependent cleavage, and the sustained potency of MLN944 in mammalian cells with reduced levels of both topoisomerases, suggest that other activities of the drug exist. In this study, we show that MLN944 intercalates into DNA, but has no effect on the catalytic activity of either topoisomerase I or II. MLN944 displays no significant ability to stimulate DNA scission mediated by either topoisomerase I or II compared with camptothecin or etoposide, respectively. In addition, yeast genetic models also point toward a topoisomerase-independent mechanism of action. To examine cell cycle effects, synchronized human HCT116 cells were treated with MLN944, doxorubicin, camptothecin, or a combination of the latter two to mimic a dual topoisomerase poison. MLN944 treatment was found to induce a G1 and G2 arrest in cells that is unlike the typical G2-M arrest noted with known topoisomerase poisons. Finally, transcriptional profiling analysis of xenograft tumors treated with MLN944 revealed clusters of regulated genes distinct from those observed in irinotecan hydrochloride (CPT-11)-treated tumors. Taken together, these findings suggest that the primary mechanism of action of MLN944 likely involves DNA binding and intercalation, but does not appear to involve topoisomerase inhibition.

Multidrug resistance proteins and topoisomerase IIalpha expression in colon cancer: association with metastatic potential

AIMS

To investigate the role of multidrug resistance proteins and topoisomerase IIalpha in colon cancer.

METHODS

Tissue sections from 89 Dukes' stage B-D colon cancer patients were selected. The expression of multidrug resistance proteins and topoisomerase IIalpha in primary tumour cells was assessed by standard immunohistochemistry. The extent of their expression was measured by image analysis and was correlated with clinicopathological features of the patients.

RESULTS

P-glycoprotein was associated with the presence of lymph node metastasis (P=0.005), vessel invasion (P=0.0001) and perineural invasion (P=0.020).

CONCLUSIONS

P-glycoprotein is probably involved in the processes of local invasion and metastatic dissemination.

Homocamptothecins: potent topoisomerase I inhibitors and promising anticancer drugs

Homocamptothecins (hCPTs) represent a new generation of antitumor agents targeting DNA topoisomerase I. The expanded seven-membered lactone E-ring that characterizes hCPTs enhances the plasma stability of the drug and reinforces the inhibition of topoisomerase I compared with conventional six-membered CPTs. hCPTs are more efficient than the CPTs at promoting cleavage at T/G sites and induce additional cleavage at C/G sites. Compound BN80765 and its difluoro analogue diflomotecan (DN80915) are potent cytotoxic agents and efficiently induce apoptosis in tumor cells. They display strong antiproliferative activities against specific tumor types. Diflomotecan is remarkably efficient at inhibiting the growth of human colon cancer cells in vivo and, administered orally, it also shows superior activities against human prostate cancers compared with the benchmark products topotecan (TPT) and irinotecan (IRT). Diflomotecan has entered phase I clinical testing and antitumor activity has been observed in patients. This 9,10-difluoro-hCPTs derivative is one of the most promising new members of the 'tecan' family. This review summarizes the recent discoveries in the topoisomerase I field and presents the different camptothecin (CPT) analogues currently evaluated as anticancer agents. The specific properties of hCPTs are highlighted.

Structural characterisation of bisintercalation in higher-order DNA at a junction-like quadruplex

We report the single-crystal X-ray structure for the complex of the bisacridine bis-(9-aminooctyl(2-(dimethylaminoethyl)acridine-4-carboxamide)) with the oligonucleotide d(CGTACG)(2) to a resolution of 2.4A. Solution studies with closed circular DNA show this compound to be a bisintercalating threading agent, but so far we have no crystallographic or NMR structural data conforming to the model of contiguous intercalation within the same duplex. Here, with the hexameric duplex d(CGTACG), the DNA is observed to undergo a terminal cytosine base exchange to yield an unusual guanine quadruplex intercalation site through which the bisacridine threads its octamethylene linker to fuse two DNA duplexes. The 4-carboxamide side-chains form anchoring hydrogen-bonding interactions with guanine O6 atoms on each side of the quadruplex. This higher-order DNA structure provides insight into an unexpected property of bisintercalating threading agents, and suggests the idea of targeting such compounds specifically at four-way DNA junctions.

Kinetic studies of the binding of acridinecarboxamide topoisomerase poisons to DNA: implications for mode of binding of ligands with uncharged chromophores

We have used stopped-flow spectrophotometry and the sodium dodecyl sulfate sequestration technique to study the kinetics of dissociation of DNA complexes of the mixed topoisomerase I/II poison N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (termed DACA) and a range of related linear tricyclic carboxamides with neutral chromophores. Complexes of DACA and related acridine and phenazinecarboxamides bearing an N,N-dimethylaminoethyl side chain dissociate from calf thymus DNA by a kinetic pathway involving four discernible steps in a manner similar to complexes of N-[(2-dimethylamino)ethyl]-9-aminoacridine-4-carboxamide (termed 9-amino-DACA). We infer from these findings that the side chains of DACA, its phenazine homologue, and 9-amino-DACA make comparable interactions with the DNA base pairs. In the case of 9-amino-DACA, a selective topoisomerase II poison, these are known, by crystallographic analysis, to involve hydrogen-bonding interactions between the protonated dimethylammonium group of the side chain and the O6/N7 atoms of guanine and to include a bridging water molecule hydrogen bonded to the carboxamide group and a phosphate oxygen. By contrast, we find that other linear tricyclic carboxamides with neutral chromophores which lack a peri nitrogen atom and are biologically inactive dissociate from DNA by a different mechanism in which it appears their side chains fail to interact with guanine. We conclude that the ability of the carboxamide group to lie preferentially in the plane of the chromophore, so facilitating the dimethylammonium-guanine hydrogen bond and ensuring maintenance of the water-bridged carboxamide-phosphate interaction, is a critical requirement for antitumor activity among ligands of the linear tricyclic carboxamide class. However, unlike the situation for 9-amino-DACA, for ligands with uncharged chromophores containing peri nitrogen atoms such as DACA, this outcome is possible with the 4-carboxamide group rotated cis or trans with respect to the ring nitrogen. This difference may have relevance to the ability of DACA to be a dual poison of both topoisomerases I and II.