DNA Minor Groove-binding Agent Research Articles

Quinoline-3-Carboxylic Acids "DNA Minor Groove-Binding Agent".

The lead compounds from the series of 2, 4-disubstituted quinoline-3-carboxylic acid derivatives were selected for the in-silico mechanistic study. The compounds were found selective and potent for the cancer cell. Moreover, the relevant ADME in-silico data also support the safety of lead. The objective of the study is to correlate the interaction of DNA and quinoline derivative, which was reported with the fluorescence microscopy images of cells in-vitro data in the recently published data. The detailed interaction study with the DNA dodecanucleotide sequenced d(CGCGAATTCGCG) shows the present lead bounds with the A/T minor groove region of a B-DNA duplex through the important major and minor hydrogen bonds. The present in-silico study supports the interactions of the drug with DNA with sufficient binding interactions and energy. The present study also gives vital information related to the mechanism of drug action, which was initially declared as a DNA targeting molecule through a fluorescence-based target study. The substitution at 2nd position (the carbonyl group) of the lead revealed as a hydrogen bond donor/acceptor for adenine and guanine nucleic acid-base pair. The in-silico prediction also confirmed the interaction pattern of the lead with the DNA, which will be further utilized for drug development.

A Novel Antibody-Drug Conjugate (ADC) Delivering a DNA Mono-Alkylating Payload to Chondroitin Sulfate Proteoglycan (CSPG4)-Expressing Melanoma.

Despite emerging targeted and immunotherapy treatments, no monoclonal antibodies or antibody-drug conjugates (ADCs) directly targeting tumor cells are currently approved for melanoma therapy. The tumor-associated antigen chondroitin sulphate proteoglycan 4 (CSPG4), a neural crest glycoprotein over-expressed on 70% of melanomas, contributes to proliferative signaling pathways, but despite highly tumor-selective expression it has not yet been targeted using ADCs. We developed a novel ADC comprising an anti-CSPG4 antibody linked to a DNA minor groove-binding agent belonging to the novel pyrridinobenzodiazepine (PDD) class. Unlike conventional DNA-interactive pyrrolobenzodiazepine (PBD) dimer payloads that cross-link DNA, PDD-based payloads are mono-alkylating agents but have similar efficacy and substantially enhanced tolerability profiles compared to PBD-based cross-linkers. We investigated the anti-tumor activity and safety of the anti-CSPG4-(PDD) ADC in vitro and in human melanoma xenografts. Anti-CSPG4-(PDD) inhibited CSPG4-expressing melanoma cell growth and colony formation and triggered apoptosis in vitro at low nanomolar to picomolar concentrations without off-target Fab-mediated or Fc-mediated toxicity. Anti-CSPG4-(PDD) restricted xenograft growth in vivo at 2 mg/kg doses. One 5 mg/kg injection triggered tumor regression in the absence of overt toxic effects or of acquired residual tumor cell resistance. This anti-CSPG4-(PDD) can deliver a highly cytotoxic DNA mono-alkylating payload to CSPG4-expressing tumors at doses tolerated in vivo.

Isatin derivatives as DNA minor groove-binding agents: a structural and theoretical study

Cervical cancer is the fourth most frequently occurring malignancy in women worldwide. It is of vital importance to find new alternatives for the treatment of this disease. Isatin is a natural compound with a molecular versatile architecture, which allows its use in a wide range of fields in medicinal chemistry. Many of these compounds have been evaluated as anticancer agents in many cell lines; however, their action mechanism remains uncertain. In this work, we investigated 55 isatin derivatives with reported cytotoxic activity against the human cervical cancer cell line (HeLa), to propose their action mechanism. As a first step, to unravel the key structural features of these compounds that result in anticancer activity over the HeLa line, a QSAR study was done. Our QSAR model revealed that the positive ionizable groups, planar molecular shape and hydrophobic character define the potency of the compounds. The statistical parameters values of our QSAR model were Q2 = 87.5, R2 = 91.24, s = 0.165 and F = 52.08; additionally, the QUIK, redundancy and overfitting rules were applied. The predictive ability of the model was evaluated using 30% of the compounds in this study as the external set, obtaining a Q2ext = 79.99 value. From these results, a molecular similarity analysis (MSA) of the isatin derivatives with a series of DNA intercalating and minor groove-binding agents, and further docking with DNA, suggested that the molecular action mechanism of these compounds may be as DNA minor groove-binder agents in assays with the HeLa cell line.

Correction to Mahanine, A DNA Minor Groove Binding Agent Exerts Cellular Cytotoxicity with Involvement of C-7-OH and -NH Functional Groups.

Correction to Mahanine, A DNA Minor Groove Binding Agent Exerts Cellular Cytotoxicity with Involvement of C-7-OH and -NH Functional Groups.

DNA-Minor Groove Binding Agents as Anti-Tubercular Probes. Old Tools for a New Challenge?

Tuberculosis, an ancient infectious disease caused by Mycobacterium tuberculosis, ranks as one of the top ten killers worldwide. The limited number of validated targets and scarce therapeutic options demand that renewed efforts should be made to identify tuberculosis drugs with novel mechanisms of action. To this end, mycobacterial DNA might represent a potential target for the development of effective anti-tubercular compounds. In particular, the minor groove of DNA offers an important recognition site for small-molecules that can be programmed to bind to this region in a sequence-selective manner to disrupt mycobacterial transcription factors activity and ultimately cause bacterial cell death. This review describes the structural features of the DNA-minor groove, the requirements for small molecules to bind to this site and the remarkable biophysical and antibacterial properties of DNA-minor groove binding agents, including netropsin, distamycin and their poly-heterocyclic analogues, diamidines, benzimidazole-containing molecules, duocarmycins and pyrrolo[2,1-c][1,4]benzodiazepines (PBDs). Furthermore, the ability of selected heterocyclic-polyamides and PBDs to significantly inhibit the growth of pathogenic, slow-growing M. tuberculosis and other non-pathogenic mycobacterial strains is highlighted. In summary, DNA-minor groove binding agents may serve as molecular scaffolds for the design of highly efficient probes to treat M. tuberculosis infections.

Design, Synthesis, and Evaluation of Bis‐Benzothiazole Derivatives as DNA Minor Groove Binding Agents

A series of novel bis‐benzothiazole derivatives with head‐to‐head orientation were designed, synthesized, and evaluated for their anti‐proliferative activities on U937, HL60, and HeLa cells. A significant part of the targets exhibited considerable in vitro anticancer activity, and some of them were more potent than the reference 5‐FU. Molecular modeling, fluorescence, and viscosimetry studies revealed that these compounds could bind into the minor groove of DNA. Amongst them, the most active compound 7 with IC50 in a range of 6.76 to 8.67 μM against the tested three cell lines, which was 1.46–2.47 and 3.48–4.93 times more potent than 5‐FU and Hoechst 33258, respectively, warrant further investigations.

Mahanine, A DNA Minor Groove Binding Agent Exerts Cellular Cytotoxicity with Involvement of C-7-OH and −NH Functional Groups

Mahanine, a carbazole alkaloid is a potent anticancer molecule. To recognize the structure-activity correlation, mahanine was chemically modified. Antiproliferative activity of these derivatives was determined in 19 cancer cell lines from 7 different origins. Mahanine showed enhanced apoptosis compared to dehydroxy-mahanine-treated cells, indicating significant contribution of the C-7-OH group. O-Methylated-mahanine and N-methylated dehydroxy-mahanine-treated cells exhibited apoptosis only at higher concentrations, suggesting additional contribution of 9-NH group. Using biophysical techniques, we demonstrated that mahanine interacts with DNA through strong association with phosphate backbone compared to other derivatives but is unable to induce any conformational change in DNA, hence suggesting the possibility of being a minor groove binder. This was corroborated by molecular modeling and isothermal titration calorimetry studies. Taken together, the results of the current study represent the first evidence of involvement of C-7-OH and 9-NH group of mahanine for its cytotoxicity and its minor groove binding ability with DNA.

Benzothiazole derivatives as human DNA topoisomerase IIα inhibitors

Benzothiazole derivatives resembling the structure of DNA purine bases were tested to determine their topoisomerase inhibition activities. Based on DNA topoisomerase I and II relaxation assay results, all 12 derivatives acted as human topoisomerase IIα inhibitors, whereas only two compounds inhibited Calf thymus topoisomerase I. 3-amino-2-(2-bromobenzyl)-1,3-benzothiazol-3-ium 4-methylbenzensulfonate (BM3) was observed to be the most effective human topoisomerase IIα inhibitor with the lowest IC50 value of 39 nM. The mechanistic studies suggested that BM3 was neither a DNA intercalator nor a topoisomerase poison, it was only a DNA minor groove-binding agent. BM3 initially bound to the DNA topoisomerase IIα enzyme, then to DNA. As a result, the tested benzothiazole derivatives were obtained as strong topoisomerase IIα inhibitors. The benzothiazole tosylated salt form BM3 was found as the most effective topoisomerase IIα inhibitor. BM3’s mechanisms of action might be its direct interaction with the enzyme. BM3’s minor groove-binding property might also contribute to this action. Hence, BM3 could be a good candidate as a new anticancer agent.

Hoechst increases adeno‐associated virus‐mediated transgene expression in airway epithelia by inducing the cytomegalovirus promoter

In airway epithelia, the kinetics of recombinant adeno-associated virus (AAV) transgene expression is slow. This has negative practical implications for research, as well as for translation into therapy. The DNA minor groove-binding agent Hoechst-33342 has been shown to enhance AAV transgene expression. In the present study, we investigated the mechanism of Hoechst-related augmentation of AAV-mediated transgene expression. We investigated the effect of Hoechst-33342 on HT1080, COS-7, mouse and human airway epithelia transduced with different AAV serotypes encoding enhanced green fluorescent protein (eGFP). We exposed cells to increasing concentrations of Hoechst-33342 at different time points. We evaluated the effect on second-strand DNA synthesis using AAV with a self-complementary genome. We also investigated the effect on expression from transfected plasmids with and without AAV2 inverted terminal repeats (ITRs). We found that Hoechst-33342 significantly accelerated AAV transgene expression for all serotypes tested. Hoechst-33342 only had an effect when the treatment was given during or after transduction, even 120 days post-transduction, suggesting an effect on transgene expression regulation. Hoechst-33342 increased transgene expression when cells were transduced with a self-complementary AAV with the cytomegalovirus promoter, although there was no effect on cells transduced with conventional single-stranded AAV encoding the Rous sarcoma virus promoter. Finally, Hoechst-33342 increases gene expression from transfected plasmids regardless of the presence of AAV2 ITRs. Hoechst dramatically augments and accelerates AAV-mediated transgene expression in airway epithelia without altering AAV-mediated gene transfer. Hoechst activation of the cytomegalovirus promoter is seen in plasmids, although it is drastically enhanced in the context of AAV.

Probing Platinum−Adenine-N3 Adduct Formation with DNA Minor-Groove Binding Agents

Me-lex(py/py), an adenine-N3-selective alkylating agent, and the reversible minor-groove binder netropsin were used to probe the formation of unusual minor-groove adducts by the cytotoxic hybrid agent PT-ACRAMTU ([PtCl(en)(ACRAMTU)](NO(3))(2); en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea). PT-ACRAMTU was found by chemical footprinting to inhibit specific Me-lex-mediated DNA cleavage at several adenine sites but not at nonspecific guanine, which is consistent with the platination of adenine-N3. In a cell proliferation assay, a significant decrease in cytotoxicity was observed for PT-ACRAMTU, when cancer cells were pretreated with netropsin, suggesting that minor-groove adducts in cellular DNA contribute to the biological activity of the hybrid agent.

N-[3-(tert-Butyldimethylsiloxymethyl)-5-nitrophenyl]acetamide

The title compound, C15H24N2O4Si, was prepared by the reaction of (3-acetamido-5-nitro­benz­yl)methanol with tert-butyl­dimethyl­silyl chloride and is a key inter­mediate in the synthesis of novel nonsymmetrical DNA minor groove-binding agents. There are two independent mol­ecules in the structure, which differ primarily in the rotation about the C—O bond next to the Si atom. Two strong N—H⋯O hydrogen bonds align the mol­ecules into a wide ribbon extending approximately parallel to the b axis.

Use of KW-2189, a DNA Minor Groove-Binding Agent, in Patients with Hepatocellular Carcinoma: A North Central Cancer Treatment Group (NCCTG) Phase II Clinical Trial

Hepatocellular carcinoma (HCC) is a common cancer in certain portions of the world. Currently no effective therapies exist for patients with advanced or metastatic HCC. KW-2189, a DNA minor groove-binding agent, has shown promising activity against HCC in preclinical evaluations. A phase II study was conducted to evaluate the activity of KW-2189 in patients with histologic or cytologic confirmed advanced or metastatic HCC who had no prior systemic therapy. Patients received KW-2189 at a dose of 0.5 mg/m2 administered on day 1 of a 6-week cycle. The primary endpoint of the trial was objective regression. Other endpoints included toxicity, disease-free survival, and overall survival. Due to hematologic toxicity the dose of KW-2189 was reduced to 0.375 mg/m2 after 11 patients had been enrolled into the trial. Due to continued significant hematologic toxicity in the next five patients enrolled at the lower dose the trial was closed to accrual. Two responses were seen in patients enrolled at the higher dose, including one sustained CR. KW-2189 showed evidence of anti-tumor activity in HCC. However, because of significant and prolonged hematologic toxicity, when given as a single dose every 6 weeks, further development of this drug in HCC is not possible. Further exploration of DNA minor groove-binding agents in the treatment of HCC appears warranted.

The expression of topoisomerase II alpha mRNA is increased by the minor groove DNA‐binding drug Hoechst 33258 in African green monkey kidney (Vero) cells

Topoisomerase IIα is a gene that plays a critical role in the replication of DNA. Several anti-tumor chemotherapeutic agents selectively target the topoisomerase IIαprotein and promote the death of rapidly dividing tumor cells. In many drug resistant tumors, topoisomerase IIαhas been shown to be transcriptionally down regulated. This lowered level of topoisomerase IIαexpression has an adverse effect on the chemosensitivity of tumors to anti-tumor chemotherapeutic agents. In this study, we examined the effect of the DNA minor groove-binding agent Hoechst 33258 on the expression of topoisomerase IIα mRNA in subconfluent Vero and MCF-7 cell lines. While we did not detect endogenous expression of topoisomerase IIα mRNA in the MCF-7 cells, the addition of hoechst 33258 to Vero cells resulted in increased expression of topoisomerase IIα mRNA. In order to further investigate these results, we have amplified and cloned the promoter regions of topoisomerase IIα from both Vero and human genomic DNA into the luciferase reporter vector pGL3. Transient transfection analysis and sequence comparisons of the promoter regions from both human and monkey genomic DNA will provide additional information as to the role conserved promoter elements have in promoting the up regulation of topoisomerase IIα in response to Hoechst 33258. Results from these studies will help to identify sequence specific promoter elements that can be targeted for modifying the expression of genes known to be influential in the chemosensitivity of cancer cells. This research was supported through funding from NIH Grant 1R15CA096723-01

Synthesis and Cellular Uptake of Fluorescently Labeled 1-Chloromethyl-5- Hydroxy-1, 2-Dihydro-3H-Benz [e] Indole (Seco-CBI)- Pyrrole Polyamide Conjugates

The synthesis is described of 1-chloromethyl-5-hydroxy-1, 2-dihydro-3H-benz [e] indole (seco- CBI)- pyrrole polyamide conjugates (1-4) which were labeled with a fluorescent Fmoc moiety to evaluate their cellular uptake. Confocal laser scanning microscopy (CLSM) indicates that these DNA minor groove-binding agents localize in the cytoplasm and organelles. Keywords: 1-chloromethyl-5-, hydroxy-1, 2-dihydro-3h-benz [e] indole, pyrrole polyamide conjugates, fluorescent fmoc, groove-binding agents

ChemInform Abstract: Polyhydroxylated Azepanes as New Motifs for DNA Minor Groove Binding Agents.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Transcriptional regulation of topoisomerase II alpha at confluence and pharmacological modulation of expression by bis-benzimidazole drugs.

Topoisomerase II alpha is a critical gene involved in DNA replication and maintenance of genomic stability. Several chemotherapeutic agents target topoisomerase II and levels of expression are an important factor in chemosensitivity. Transcriptional regulation has been demonstrated to regulate topoisomerase II alpha levels under several circumstances, including cellular confluence, heat shock, and expression of oncogenes including ras and myb. Expression of topoisomerase II alpha is regulated by cellular proliferation; transcriptional down-regulation in confluent cells is modulated through sequences within the promoter. In this study, we examined DNA-protein interactions within the topoisomerase II alpha promoter in exponential and confluent phase NIH3T3 cells. Using electrophoretic mobility shift assay and in vitro DNase I footprint experiments, the involvement of NF-Y in transcriptional regulation was established. Incubation of the DNA minor groove-binding agents Hoechst 33342 and Hoechst 33258 with nuclear extracts revealed drug binding to regions surrounding the inverted CCAAT boxes within the topoisomerase II alpha promoter and displacement of proteins binding to these elements. Addition of both Hoechst 33342 and Hoechst 33258 to NIH3T3 cells at confluence resulted in increased expression of topoisomerase II alpha. In addition, MTT cytotoxicity assays in confluent cells showed an additive effect of incubation with Hoechst 33342 and the topoisomerase II alpha poison etoposide. Therefore, DNA binding drugs which block transcription factor activation of the promoter may deregulate topoisomerase II alpha and this strategy may be of value in modifying gene expression and modulating chemosensitivity.

A new class of symmetric bisbenzimidazole-based DNA minor groove-binding agents showing antitumor activity.

The synthesis and evaluation of the novel head-to-head bisbenzimidazole compound 2,2-bis[4'-(3' '-dimethylamino-1' '-propyloxy)phenyl]-5,5-bi-1H-benzimidazole is described. An X-ray crystallographic study of a complex with the DNA dodecanucleotide sequence d(CGCGAATTCGCG) shows the compound bound in the A/T minor groove region of a B-DNA duplex and that the head-to-head bisbenzimidazole motif hydrogen-bonds to the edges of all four consecutive A:T base pairs. The compound showed potent growth inhibition with a mean IC(50) across an ovarian carcinoma cell line panel of 0.31 microM, with no significant cross-resistance in two acquired cisplatin-resistant cell lines and a low level of cross-resistance in the P-glycoprotein overexpressing acquired doxorubicin-resistant cell line. Studies with the hollow fiber assay and in vivo tumor xenografts showed some evidence of antitumor activity.

ChemInform Abstract: Design, Synthesis, and Evaluation of DNA Minor Groove Binding Agents

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.