DNA Minor Groove Research Articles

Abstract 4064: Synergistic activity of Lurbinectidin plus ONC201 in SCLC is associated with ATF4, CHOP and pChk1 induction

Abstract Small cell lung cancer (SCLC) accounts for 15% of lung cancer and is responsive to chemotherapy but most patients relapse with drug-resistant disease and have very poor 5-year survival of less than 7%. One of the most notable advances in the last decade has been the approval of lurbinectedin for platinum resistant SCLC. Lurbinectedin is a small molecule inhibitor, targeting RNA polymerase II, and binding the minor grooves of DNA to induce double-strand breaks. The dismal SCLC survival rate underscores the need for a novel combination to increase patient survival outcomes. ONC201 is a pro-apoptotic TRAIL-inducing compound that activates the integrated stress response and appears to have efficacy in neuroendocrine tumors including paragangliomas. In our preclinical experiments, we explored the combination of ONC201 and lurbinectedin as a potentially effective treatment regimen for SCLC. Lurbinectedin has been shown to have effective cancer cell killing ability in multiple SCLC cell lines (H1048, H1105, H1882, H1417) at sub-nanomolar concentrations, while sparing healthy lung epithelial tissue cells (cell line HSAEC). We hypothesized that combining ONC201 and lurbinectedin will yield synergistic outcomes due to combining drugs that act by different potentially complementary mechanisms. We treated SCLC cell lines with ONC201 and lurbinectedin at increasing concentrations of the drugs. CellTiter Glo was used to perform cell viability assays, and combination index analysis (Combenefit software) revealed the most synergy between the agents occurred at the concentrations of 0.156 uM ONC201 and 0.047 nM lurbinectedin. We are expanding this combination’s efficacy in other SCLC lines and tumor types. Western blotting further examined these synergies and showed that PARP cleavage and expression of ATF4 and TRAIL death receptor DR5 were increased at higher concentrations of these agents. We further noted that combinatorial treatment with these agents induced marked upregulation of Phosphorylated Chk1 and CHOP at the highest treatment concentrations versus lower concentrations and control. These effects indicate effectiveness of the combinatorial treatment in causing DNA damage and instability, inducing double-stranded DNA breaks, as well as initiating the intrinsic apoptosis pathway through the integrated stress response, selectively in the malignant cells. Ongoing directions include testing similar concentrations of both ONC201 and lurbinectedin in additional SCLC cell lines, SCLC patient-derived organoids, and in vivo, as well as exploring immune correlates of the drug treatments. Keywords: SCLC; lurbinectedin; chemotherapy; imipridones; genomics Citation Format: Nicholas R. Liguori, Ashley Fss Uruchurtu, Young Lee, Leiqing Zhang, Abbas Abbas, Varun Prabhu, Lanlan Zhou, Christopher J. Azzoli, Wafik S. El-Deiry. Synergistic activity of Lurbinectidin plus ONC201 in SCLC is associated with ATF4, CHOP and pChk1 induction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4064.

MC1923 phase II clinical trial of durvalumab (MEDI4736) and topotecan or lurbinectedin in patients with relapsed extensive-stage small cell lung cancer previously treated with chemotherapy and immunotherapy.

TPS8604 Background: Chemoimmunotherapy followed by durvalumab maintenance yields a median overall survival of 12.9 months in patients with extensive stage Small Cell Lung Cancer (ES SCLC), which is an improvement over chemotherapy alone. However, 90% of these patients will have progressive disease. While topotecan and lurbinectedin have established modest activity in the second line, it is unknown whether continuing immunotherapy in this setting confers additional benefit. In preclinical studies lurbinectedin, a DNA minor groove binder, used with immune checkpoint inhibitors has synergistic effects. Methods: This phase 2 trial is enrolling patients with ES SCLC who have progressed on platinum based chemoimmunotherapy, to three treatment groups. Group 1 includes patients with platinum sensitive SCLC who will receive durvalumab (1500 mg given as an intravenous [IV] infusion once every 3 weeks) and topotecan (1.25 mg/m2/day IV for 5 consecutive days every 3 weeks). In Groups 2A and 2B, patients with platinum sensitive and platinum resistant disease respectively, receive durvalumab and lurbinectedin (3.2 mg/m2 IV on Day 1 of every 21-day cycle). Patients with platinum sensitive disease are assigned to Groups 1 or 2A based on the preferences of the treating physician and the patient. Patients with treated/stable CNS metastases are eligible. The primary endpoint is the proportion of patients who are alive at 6 months (6OS) for Group 1 and the proportion of patients who are alive and progression-free at 6 months (6PFS) in Groups 2A and 2B. Secondary endpoints include safety, adverse event profile, response rate, PFS, and OS. The sample size is based on a 2-stage Simon Optimal Design. For Treatment Group 1, with 22 eligible patients there is 80% power to detect a true 6-month OS rate (6OS) of 75%, with 10% alpha under the null hypothesis that the true 6OS is at most 50%. For Treatment Group 2A, with 20 eligible patients this design has 80% power to detect a true 6-month PFS rate (6PFS) of 65%, with 10% alpha under the null hypothesis that the true 6PFS is at most 40%. For Treatment Group 2B, with 22 eligible patients this design has 80% power to detect a true 6-month PFS rate (6PFS) of 40%, with 10% alpha under the null hypothesis that the true 6PFS is at most 19%. To account for possible drop-outs, accrual targets will be 24, 22, and 24 patients to Groups 1, 2A, and 2B respectively. For the safety analyses, 6 patients will be enrolled at the starting dose level for each treatment group (1, 2) and then briefly closed to accrual to assess adverse events. If we observe 2+ DLTs in these 6 treated patients during Cycle 1 within a treatment group (1 vs. 2), we will declare the combination treatment too toxic and lower the starting dose of chemotherapy for the next 6 patients. The study was open for all 3 groups as of January 2022 and has accrued 2 patients. Clinical trial information: NCT04607954.

Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines

The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5′-GAATTC-3′ binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT–DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT–DNA) was studied using UV–Vis, fluorescence, circular dichroism (CD) and 1H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT–DNA as evidenced by: (1) non–displacement of EB from EB/CT–DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT–DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in 1H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT–DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT–DNA is governed mainly by H–bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT–DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H–bonding and π–π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents.

Ken Breslauer began studies on the thermodynamics of small cationic molecules binding in the DNA minor groove over 30 years ago, and the studies reported here are an extension of those ground-breaking reports. The goals of this report are to develop a detailed understanding of the binding thermodynamics of pyridine-based sequence-specific minor groove binders that have different terminal cationic groups. We apply biosensor-surface plasmon resonance and ITC methods to extend the understanding of minor groove binders in two directions: (i) by using designed, heterocyclic dicationic minor groove binders that can incorporate a G•C base pair (bp), with flanking AT base pairs, into their DNA recognition site, and bind to DNA sequences specifically; and (ii) by using a range of flanking AT sequences to better define molecular recognition of the minor groove. A G•C bp in the DNA recognition site causes a generally more negative binding enthalpy than with most previously used pure AT binding sites. The binding is enthalpy-driven at 25 °C and above. The flanking AT sequences also have a large effect on the binding energetics with the -AAAGTTT- site having the strongest affinity. As a result of these studies, we now have a much better understanding of the effects of the DNA sequence and compound structure on the molecular recognition and thermodynamics of minor groove complexes.

Antiproliferative activity and DNA binding studies of cyclometalated complexes of platinum(II) containing 2-vinylpyridine.

The cytotoxic activity of four cyclometalated platinum(II) complexes [PtMe(vpy)(L)], containing 2-vinylpyridine (vpy) and the phosphine ligands (L) PMe2Ph (1a), PPh3 (1b), PMePh2 (1c), and P(c-Hex)3 (1d), were evaluated against human breast cancer (MDA-MB-231), human lung cancer (A549), human colon cancer (SW1116), and non-tumor epithelial breast (MCF-10A) cell lines. The highest activity was found for 1c with IC50 values of 21.10 µM, 23.36 µM, and 12.96 µM, compared to cisplatin, which was 10.12 µM, 47.57 µM, and 19.50 µM against the A549, SW1116, and MDA-MB-231 cell lines, respectively. 1a-d showed a higher selectivity index (SI) than cisplatin. Docking studies confirmed interaction to the DNA minor groove for all complexes. Genotoxicity studies on 1c showed interactions with the genomic content of malignant cells. Compared with cisplatin as a positive control, a slight shift was found in the electrophoresis mobility, which was utilized further to study the direct interaction of 1c with DNA.

Application of amino acid ionic liquids for increasing the stability of DNA in long term storage

The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM]+ cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM]+ cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage. Communicated by Ramaswamy H. Sarma

Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors

DNMT1 maintains the parental DNA methylation pattern on newly replicated hemimethylated DNA. The failure of this maintenance process causes aberrant DNA methylation that affects transcription and contributes to the development and progression of cancers such as acute myeloid leukemia. Here, we structurally characterized a set of newly discovered DNMT1-selective, reversible, non-nucleoside inhibitors that bear a core 3,5-dicyanopyridine moiety, as exemplified by GSK3735967, to better understand their mechanism of inhibition. All of the dicyanopydridine-containing inhibitors examined intercalate into the hemimethylated DNA between two CpG base pairs through the DNA minor groove, resulting in conformational movement of the DNMT1 active-site loop. In addition, GSK3735967 introduces two new binding sites, where it interacts with and stabilizes the displaced DNMT1 active-site loop and it occupies an open aromatic cage in which trimethylated histone H4 lysine 20 is expected to bind. Our work represents a substantial step in generating potent, selective, and non-nucleoside inhibitors of DNMT1.

In vitro biological and in silico molecular docking and ADME studies of a substituted triazine-coordinated cadmium(II) ion: efficient cytotoxicity, apoptosis, genotoxicity, and nuclease-like activity plus binding affinity towards apoptosis-related proteins.

A cadmium(II) complex containing dppt ligand with the formula [CdCl2(dppt)2], where dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine was synthesized, elucidated and submitted to in vitro cytotoxicity studies against human breast (MCF-7), glioblastoma (U-87), and lung (A549) cancer cell lines as well as mouse embryo normal cell line (NIH/3T3), in comparison with cisplatin employing MTT assay over 24 and 48h. The complex exhibited the highest cytotoxic effect against MCF-7 cells among the other three cell lines with IC50 values of 8.7 ± 0.5 (24h) and 1.2 ± 0.7µM (48h). Significantly, flow cytometric assessment of the complex-treated MCF-7 and U-87 cells demonstrated a dose-dependent induced apoptotic cell death. The cellular morphological changes were in concord with cytotoxicity and flow cytometric results. The results of comet assay showed that the complex is able to induce DNA damage in MCF-7 cells. These observations are of importance, as sustained damage to cellular DNA could lead to apoptotic cell death. The results of DNA-binding studies indicated that the complex fits into the DNA minor groove and interacts with DNA via a partial intercalation. Moreover, the complex was able to efficiently cleave pUC19 DNA through a hydrolytic mechanism. The binding affinity between the complex and apoptosis-relevant protein targets including APAF1, Bax, Bcl-2, Cas3, Cas7, and Cas9 was evaluated through molecular docking studies. In silico virtual studies revealed the complex's strong affinity towards apoptosis-related proteins; therefore the complex can act as a potential apoptosis inducer. Physicochemical, pharmacokinetics, lipophilicity, drug-likeness, and medicinal chemistry properties of the complex were also predicted through in silico absorption, distribution, metabolism and excretion studies.

Complexes of 1-(2-R(F, CH3, Cl)-phenyl)-1,4-dihydro-5H-tetrazole-5-thiones with cadmium chloride: Synthesis, molecular, crystal structures and computational investigation approach

New complex compounds (I) - (IV) were synthesized by the reaction of 1-(2-fluorofluorophenyl) -1,4-dihydro-5H-tetrazole-5-thione (HL1), 1-(2-methylphenyl)-1,4-dihydro-5H-tetrazole-5-thione (HL2) and 1-(2-chlorochlorophenyl)-1,4-dihydro-5H-tetrazole-5-thione (HL3) with cadmium chloride. By X-ray diffraction analysis, molecular and crystal structures of complexes (I), (II), (III) and (IV) are determined. (CIF files CCDC № 2,003,797 (I), 1,993,454 (II), 2,151,359 (III), 2,098,997 (IV)). Hirshfeld surface analysis, frontier orbital analysis, atomic charges, electrostatic potential, nonlinear optical properties, and natural bond analysis of all three‑cadmium metal-organic complexes were discussed. A molecular docking study was used to investigate compounds' binding and interactions with DNA molecules, which predicted compound I as the best binder at the DNA minor groove and demonstrated closed distance interactions. In a long run of molecular dynamics simulations, the compound I complex was also depicted with good dynamics.

Binding and thermodynamic study of thalidomide with calf thymus DNA: Spectroscopic and computational approaches

The thalidomide-DNA interactions have been investigated in detail by numerous biophysical techniques such as UV‐vis, dye displacement assay, viscosity, cyclic voltammetry, circular dichroism, molecular docking, molecular dynamic simulation, FT-IR and 1H NMR spectroscopy. CD spectroscopy, thermal denaturation and viscosity measurement explained that thalidomide is groove binder. Molecular docking analysis highlighted that thalidomide binds trough minor groove of calf thymus DNA which also confirmed from dye displacement experiment. To our knowledge, this is the first instance thalidomide was shown to binds with calf thymus DNA. Molecular dynamic simulation indicated that the thalidomide-DNA system was stabilized by electrostatic attraction as the main interaction and mode of binding is minor groove. Our study provides a better understanding to the DNA-thalidomide binding affinity and it mechanism. Overall, all these in formations can be used for further understanding the pharmacological effects of thalidomide.

Non-covalent binding interaction between phthalic acid esters and DNA.

The interaction of phthalic acid esters (PAEs) with DNA is known to be responsible for the disruption of endocrine functions and the teratogenic and carcinogenic effects. However, the binding strength and mechanism of this important process has often been neglected. Here, we confirmed the binding interaction between PAEs and DNA via fluorescence titration quenching experiment. The linear fitting curve proved that PAEs could bind to DNA, and the binding constants (KA) were 4.11×105, 1.04×105, 7.60×104, 1.99×104, and 1.42×103 L/mol for diethyl phthalate (DEP), bis(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), dimethyl phthalate (DMP), and benzyl butyl phthalate (BBP), respectively. DNA melting point, UV-vis spectra and Fourier transform infrared spectroscopy (FTIR) analyses revealed that PAEs interact predominantly with thymines in the DNA minor groove. Quantum chemical calculations showed that hydrogen bonding and van der Waals force formation between PAEs and DNA bases dominated the binding interaction. However, PAEs-DNA binding did not induce any DNA conformation change since the circular dichroism and FTIR spectra of B-DNA were not change. The electrostatic surface potential (ESP) might act an important role in PAEs-DNA binding interaction. This work will broaden our understanding of the interaction between PAEs and genetic materials.

Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA.

In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.

Discovery of DNA-Targeting HDAC Inhibitors with Potent Antitumor Efficacy In Vivo That Trigger Antitumor Immunity.

We observed a synergistic antiproliferation effect with combined use of a DNA minor groove binder and a histone deacetylase (HDAC) inhibitor. Inspired by this result, a new series of benzimidazole-hydroxamate hybrids were designed and synthesized to target both DNA minor groove and HDAC. The most active compounds 9k and 9l not only exhibited improved HDAC inhibitory activities compared to SAHA but also possessed potent antiproliferation activities against tumor cells. Importantly, compounds 9k and 9l showed good in vivo antitumor efficacies in both HEL xenograft model and murine melanoma model. We also found that 9k and 9l promote the antigen presentation and activate T cells, thereby triggering antitumor immunity. Moreover, these inhibitors reshaped the tumor immune microenvironment by inhibiting the recruitment of Treg cells and promoting the polarization of tumor-infiltrating macrophages to M2 type with antitumor activity. Our study validated the effectiveness of incorporating a DNA-binding fragment in HDAC inhibitors as novel multitargeting antitumor agents.

Anticancer evaluation of the selected tetrahydropyrimidines: 3D-QSAR, cytotoxic activities, mechanism of action, DNA, and BSA interactions

Selected tetrahydropyrimidines (THPMs) were investigated by means of cytotoxic activities on selected cancer (HeLa, A549, and LS174) and non-cancerous cell lines (MRC-5). Among evaluated compounds, two of them (B7 and B8) showed good cytotoxic activity on the tested cell lines and were selected for further evaluation that included mechanism of action, DNA and BSA interactions and molecular docking study. Calculated parameters from fluorescence quenching studies indicated that B7 and B8 bind on minor groove of DNA and have great ability to bind on carrier protein. Three-dimensional quantitative structure anti-HeLa activity study was performed with data set of THPMs. Molecular Interaction Fields were used to derive Grid independent descriptors (GRIND), as independent variables in Pentacle software. The quality and predictive capacity of the model was proved by internal statistical parameters: R2 = 0.992, Q2= 0.51, as well as external parameters such as R2pred = 0.804 and rm2, r/2 m and rm2¯, that were higher than 0.5. The structural determinants significant for anti-HeLa activity of compounds were identified by using developed 3D-QSAR model. Interpretation of the most impactful GRIND variables on the anti-HeLa activity generated several hypotheses for design of novel and more potent anti-HeLa tetrahydropyrimidines. Additional molecular targets for the most active synthesized derivatives (B7 and B8) are predicted by use of online web-based tool-SwissTargetPrediction.

Novel Pyridazin-3(2H)-one-Based Guanidine Derivatives as Potential DNA Minor Groove Binders with Anticancer Activity.

Novel aryl guanidinium analogues containing the pyridazin-3(2H)-one core were proposed as minor groove binders (MGBs) with the support of molecular docking studies. The target dicationic or monocationic compounds, which show the guanidium group at different positions of the pyridazinone moiety, were synthesized using the corresponding silyl-protected pyridazinones as key intermediates. Pyridazinone scaffolds were converted into the adequate bromoalkyl derivatives, which by reaction with N,N’-di-Boc-protected guanidine followed by acid hydrolysis provided the hydrochloride salts 1–14 in good yields. The ability of new pyridazin-3(2H)-one-based guanidines as DNA binders was studied by means of DNA UV-thermal denaturation experiments. Their antiproliferative activity was also explored in three cancer cell lines (NCI-H460, A2780, and MCF-7). Compounds 1–4 with a bis-guanidinium structure display a weak DNA binding affinity and exhibit a reasonable cellular viability inhibition percentage in the three cancer cell lines studied.

Evaluation of Docking Machine Learning and Molecular Dynamics Methodologies for DNA-Ligand Systems.

DNA is a molecular target for the treatment of several diseases, including cancer, but there are few docking methodologies exploring the interactions between nucleic acids with DNA intercalating agents. Different docking methodologies, such as AutoDock Vina, DOCK 6, and Consensus, implemented into Molecular Architect (MolAr), were evaluated for their ability to analyze those interactions, considering visual inspection, redocking, and ROC curve. Ligands were refined by Parametric Method 7 (PM7), and ligands and decoys were docked into the minor DNA groove (PDB code: 1VZK). As a result, the area under the ROC curve (AUC-ROC) was 0.98, 0.88, and 0.99 for AutoDock Vina, DOCK 6, and Consensus methodologies, respectively. In addition, we proposed a machine learning model to determine the experimental ∆Tm value, which found a 0.84 R2 score. Finally, the selected ligands mono imidazole lexitropsin (42), netropsin (45), and N,N′-(1H-pyrrole-2,5-diyldi-4,1-phenylene)dibenzenecarboximidamide (51) were submitted to Molecular Dynamic Simulations (MD) through NAMD software to evaluate their equilibrium binding pose into the groove. In conclusion, the use of MolAr improves the docking results obtained with other methodologies, is a suitable methodology to use in the DNA system and was proven to be a valuable tool to estimate the ∆Tm experimental values of DNA intercalating agents.

Fluorinated N-quinoxaline-based boron complexes: Synthesis, photophysical properties, and selective DNA/BSA biointeraction

A series of six examples of 1,1-difluoro-3,5-diaryl-1H [1,2,3,5] oxadiazaborinino[3,4-a]quinoxalin-11-ium-1-uides as a new N-quinoxaline-based boron complex with variable structures was synthesized at 65–70% yields from the reaction of the respective N-(3-arylquinoxalin-2-yl)benzamides with BF3·Et2O — in which aryl = phenyl, 4-ClC6H4, 4-CH3C6H4, and 4-NMe2C6H4. All new benzamides and BF2-complexes were fully characterized by 1H-, 13C, 19F-, and 11B-NMR spectroscopy and single-crystal X-ray diffraction. Moreover, the photophysical properties, TD-DFT analysis, DNA and BSA-binding experiments, and molecular docking studies for these new organoboron complexes were studied. The new BF2-heterocycles demonstrated to be weak generators of 1O2, although their solutions at 5.0 µM showed great photostability over the investigated irradiation. Additionally, the results of the DNA and BSA-binding studies indicated that the greatest interactions were selective in the minor groove of DNA and by the tryptophan site in the BSA albumin pocket.

Half-Sandwich Cyclometalated RhIII Complexes Bearing Thiolate Ligands: Biomolecular Interactions and In Vitro and In Vivo Evaluations.

A class of cyclometalated RhIII complexes [Cp*Rh(ppy)(SR)] bearing thiolate ligands, Cp* = pentamethylcyclopentadienyl, ppy = 2-phenylpyridinate, and R = pyridyl (Spy, 2), pyrimidyl (SpyN, 3), benzimidazolyl (Sbi, 4), and benzothiazolyl (Sbt, 5), were produced and identified by means of spectroscopic methods. The in vitro cytotoxicity of the RhIII compounds in three different human mortal cancerous cell lines (ovarian, SKOV3; breast, MCF-7; lung, A549) and a normal lung (MRC-5) cell line were evaluated, indicating the selectivity of these cyclometalated RhIII complexes to cancer cells. Complex 5, selected for in vivo experiment, has shown an effective inhibition of tumor growth in SKOV3 xenograft mouse model relative to control (p-values < 0.05 and < 0.01). Importantly, the outcomes of H&E (hematoxylin and eosin) staining and hematological analysis revealed negligible toxicity of 5 compared to cisplatin on a functioning of the main organs of mouse. Molecular docking, UV-vis, and emission spectroscopies (fluorescence, 3D fluorescence, synchronous) techniques were carried out on 1-5 to peruse the mechanism of the anticancer activities of these complexes. The obtained data help to manifest the binding affinity between the rhodium compounds and calf thymus DNA (CT-DNA) through the interaction by DNA minor groove and moderate binding affinity with bovine serum albumin (BSA), particularly with the cavity in the subdomain IIA. It can be concluded that the Rh-thiolate complexes are highly promising leads for the development of novel effective DNA-targeted anticancer drugs.

RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im-induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im-induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides-dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im-induced transcriptional arrest.