Molecular drug design, synthesis and crystal structure determination of CuII–SnIV heterobimetallic core: DNA binding and cleavage studies

Synthesis and antitumor activity of copper(II) complexes of imidazole derivatives

Complexes [Cu(PI)2(H2O)](NO3)2 (1), [Cu(PBI)2(NO3)]NO3 (2), [Cu(TBI)2(NO3)]NO3 (3), [Cu(BBIP)2](ClO4)2 (4) and [Cu(BBIP)(CH3OH)(ClO4)2] (5) were synthesized from the reactions of Cu(II) salts with 2-(2'-pyridyl)imidazole (PI), (2-(2'-pyridyl)benzimidazole (PBI), 2-(4'-thiazolyl)-benzimidazole (TBI), 2,6-bis(benzimidazol-2-yl)-pyridine (BBIP), respectively. Their compositions and crystal structures were determined. Their in-vitro antitumor activities were screened on four cancer cell lines and one normal cell line (HL-7702) using cisplatin as the positive control. Complexes 2 and 4 show higher cytotoxicity than the other three complexes. The cytotoxicity of complex 2 are comparable to those for cisplatin, and the cytotoxicity for 4 are much higher than those for cisplatin. From a viewpoint of antitumor, 2 might be a nice choice on the tumor cell line of T24 because its IC50 values on T24 and HL-7702 are 15.03 ± 1.10 and 21.34 ± 0.35, respectively. Thus, a mechanistic study for complexes 2 and 4 on T24 cells was conducted. It revealed that they can reduce mitochondrial membrane potential and increase mitochondrial membrane permeability, resulting in increased intracellular ROS levels, Ca2+ inward flow, dysfunctional mitochondria and the eventual cell apoptosis. In conclusion, they can induce cell apoptosis through mitochondrial dysfunction. These findings could be useful in the development of new antitumor agents.

Anticancer behaviour of 2,2'-(pyridin-2-ylmethylene)bis(5,5-dimethylcyclohexane-1,3-dione)-based palladium(II) complex and its DNA, BSA binding propensity and DFT study

Herein, we report the synthesis and biological evaluation of [Pd(L)(OH2)Cl] complex (where L = 2,2'-(pyridin-2-ylmethylene)bis(5,5-dimethylcyclohexane-1,3-dione) as a novel promising anticancer candidate. The complex was characterized by single-crystal X-ray diffraction and other various spectroscopic techniques. Besides, the optimized structure was determined through DFT calculations revealing that the coordination geometry of [Pd(L)(OH2)Cl] complex is square planar. The binding propensity of [Pd(L)(OH2)Cl] complex with DNA and BSA was assessed by the spectrophotometric method. The antimicrobial profile of the ligand and its [Pd(L)(OH2)Cl] complex was screened against clinically important bacterial strains. [Pd(L)(OH2)Cl] complex showed promising activity against these microorganisms. Pd(L)(OH2)Cl] complex exhibited a potent antiproliferative potential compared to its ligand against different human cancer cells (A549, HCT116, MDA-MB-231, and HepG2) with less toxic effect against normal cells (WI-38). Additionally, [Pd(L)(OH2)Cl] complex exerted its anticancer effects against the most responsive cells (HCT116 cells; IC50 = 11 ± 1 μM) through suppressing their colony-forming capabilities and triggering apoptosis and cell cycle arrest at S phase. Quantitative PCR analysis revealed a remarkable upregulation of the mRNA expression level of p53 and caspase-3 by 4.8- and 5.9-fold, respectively, relative to control. Remarkable binding properties and non-covalent interactions between L and its [Pd(L)(OH2)Cl] complex with the binding sites of different receptors including CDK2, MurE ligase, DNA, and BSA were established using molecular docking. Based on our results, [Pd(L)(OH2)Cl] complex is an intriguing candidate for future investigations as a potential anticancer drug for the treatment of colon cancer.

A nanoscale electrochemical guanine DNA-biosensor based on a flower-like nanocomposite of Tb-doped ZnO for the sensitive determination of pemetrexed

Pemetrexed is an antineoplastic drug used in chemotherapeutic treatments, especially in malignant mesothelioma and non-small cell lung carcinoma, but can also cause a variety of complications, like stomach pain, nausea, burning, vomiting, numbness, and tingling, emphasizing the need for an approach to quantify the drug in biological matrices. Herein, a DNA-based biosensor was introduced for pemetrexed determination. A hydrothermal approach was used for synthesizing flower-like nanoparticles (NPs) of zinc oxide (ZnO) doped with Tb (FL-NP Tb3+/ZnO). Moreover, energy dispersive X-ray (EDX), field-emission scanning electron microscopy (FESEM), zeta potential, Brunauer-Emmett-Teller (BET), and X-ray diffraction (XRD) analyses were used for characterizing the as-prepared nanocomposite. According to the impedance analysis, FL-NP Tb3+/ZnO was accompanied by very good electrochemical functions for a simple transfer of electrons. In the case of the immobilization of double-stranded deoxyribonucleic acid (ds-DNA) on the FL-NP Tb3+/ZnO and polypyrrole (PP)-modified pencil graphite electrode (ds-DNA/PP/FL-NP Tb3+/ZnO/PGE), a considerable enhancement was found in the electrochemical oxidation of guanine in ds-DNA residue bases. Since there was an interaction between ds-DNA and pemetrexed, the voltammetric current of guanine over the ds-DNA/PP/FL-NP Tb3+/ZnO/PGE declined in the presence of pemetrexed in the electrolytic solution. Moreover, under optimum conditions (25 mg L-1 of ds-DNA and 10 min incubation time, in acetate buffer at 25 °C), a linear decrease in the guanine signal was observed on the ds-DNA/PP/FL-NP Tb3+/ZnO/PGE as the pemetrexed concentration increased in the range from 0.001 μM to 175.0 μM with a limit of detection of 0.17 nM. Finally, the new DNA-based biosensor was successfully used for determining pemetrexed in real samples, indicating its application potential.

Sensitive MALDI-TOF MS and 'turn-on' fluorescent genosensor for the determination of DNA damage induced by CNS acting drugs

The genotoxic and carcinogenic adverse effects of various drugs should be considered for assessing drug benefit/risk ratio. On that account, the scope of this study is to examine the kinetics of DNA damage triggered by three CNS acting drugs; carbamazepine, quetiapine and desvenlafaxine. Two precise, simple and green approaches were proposed for probing drug induced DNA impairment; MALDI-TOF MS and terbium (Tb³⁺) fluorescent genosensor. The results revealed that all the studied drugs induced DNA damage manifested by the MALDI-TOF MS analysis as a significant disappearance of the DNA molecular ion peak with the appearance of other peaks at smaller m/z indicating the formation of DNA strand breaks. Moreover, significant enhancement of Tb³⁺ fluorescence occurred, proportional to the amount of DNA damage, upon incubation of each drug with dsDNA. Furthermore, the DNA damage mechanism is examined. The proposed Tb³⁺ fluorescent genosensor showed superior selectivity and sensitivity and is significantly simpler and less expensive than other methods reported for the detection of DNA damage. Moreover, the DNA damaging potency of these drugs was studied using calf thymus DNA in order to clarify the potential safety hazards associated with the studied drugs on natural DNA.

Progress of Metal-Based Anticancer Chemotherapeutic Agents in Last two Decades and their Comprehensive Biological (DNA/RNA Binding, Cleavage and Cytotoxicity Activity) Studies

During last two decades, there has been an enormous growth in the discovery of innovative active inorganic anticancer complexes (exerting remarkable cytotoxicity at sub micro-molar levels) derived from myriad ligand scaffolds, mainly acting on cancerous vs healthy cells by either halting or inhibiting their uncontrolled growth. The phenomenal success of cisplatin to treat numerous forms of solid malignancies has placed metal-based drugs to the forefront of treatment strategies against cancers. More than 10,000 platinum anticancer complexes have been developed during the past 40 years, but only five drugs have been approved for usage in humans while ten more complexes are currently undergoing clinical trials. Most of the compounds have failed either at R&D stages or in preclinical trails. This has led to extensive investigations by researchers of medicinal chemistry, including our group to design and prepare tailored 3d-metallo-drugs and organotin(IV) compounds from some naturally occurring bioactive compounds, such as amino-acids, peptides, chromone derivatives and NSAID's etc. that were used either alone or in cocktail combination, capable of specifically targeting DNA, lnc RNAs and proteins. Furthermore, 3d-metal ions such as copper, cobalt and zinc etc. incorporated in these ligand framework are biocompatible and induce a unique multi-modal mechanism of cytotoxic action involving angiogenesis, ROS-induced DNA damage, apoptosis by p53 mitochondrial genes and caspases etc. The results observed a positive correlation between the binding affinity of complexes with DNA (as quantified by intrinsic binding constant values) and their cytotoxic behavior. Complexes with high DNA binding propensity were typically lethal against a diverse panel of malignant cell types compared to normal cells.

Biological activity of bis-(morpholineacetato)palladium(II) complex: Preparation, structural elucidation, cytotoxicity, DNA-/serum albumin-interaction, density functional theory, in-silico prediction and molecular modeling

In an effort to discover a novel potential bioactive compound, a mono-nuclear Pd(II) complex with an amino acid derivative as ligand was synthesized and characterized through experimental and computational methodologies. A square-planar configuration was suggested for palladium(II) complex utilizing density functional theory. MEP map and Mulliken atomic charge were detected electrophilic and nucleophilic regions of the compound for reactions. The lipophilicity and cytotoxic activity of the complex was more effective than cisplatin. Also, OSIRIS DataWarrior revealed proper oral bioavailability and good drug-likeness for the compound. In-vitro binding behavior of the Pd(II) complex with DNA and serum albumin (BSA) were fully determined via variety of procedures including fluorescence, UV-Vis, CD, viscosity, gel electrophoresis experiments and molecular simulation. The negative signs of ΔH° and ΔS° for Pd(II) complex-CT-DNA/-BSA systems indicated the existence of hydrogen bonding/van der Waals interactions for both binding systems. Additionally, docking simulation illustrated the interaction of Pd(II) complex with the minor groove of DNA and the hydrophobic cavity of the BSA (drug binding site I).

Exploring inclusion complex of an anti-cancer drug (6-MP) with β-cyclodextrin and its binding with CT-DNA for innovative applications in anti-bacterial activity and photostability optimized by computational study

The co-evaporation approach was used to examine the host-guest interaction and to explore the cytotoxic and antibacterial properties of an important anti-cancer medication, 6-mercaptopurine monohydrate (6-MP) with β-cyclodextrin (β-CD). The UV-Vis investigation confirmed the inclusion complex's (IC) 1 : 1 stoichiometry and was also utilized to oversee the viability of this inclusion process. FTIR, NMR, and XRD, among other spectrometric techniques, revealed the mechanism of molecular interactions between β-CD and 6-MP which was further hypothesized by DFT to verify tentative outcomes. TGA and DSC studies revealed that 6-MP's thermal stability increased after encapsulation. Because of the protection of drug 6-MP by β-CD, the formed IC was found to have higher photostability. This work also predicts the release behavior of 6-MP in the presence of CT-DNA without any chemical changes. An evaluation of the complex's antibacterial activity in vitro revealed that it was more effective than pure 6-MP. The in vitro cytotoxic activity against the human kidney cancer cell line (ACHN) was also found to be significant for the IC (IC₅₀ = 4.18 μM) compared to that of pure 6-MP (IC₅₀ = 5.49 μM). These findings suggest that 6-MP incorporation via β-CD may result in 6-MP stability and effective presentation of its solubility, cytotoxic and antibacterial properties.

Probing the Molecular Assembly of a Metabolizer Drug with β-Cyclodextrin and Its Binding with CT-DNA in Augmenting Antibacterial Activity and Photostability by Physicochemical and Computational Methodologies

The assembly of an inclusion complex in an aqueous medium using a metabolizer drug (dyphylline) as guest and β-cyclodextrin as host has been established, which is extremely appropriate for a variety of applications in modern biomedical sciences. The formation of the inclusion complex is established by ¹H NMR, and surface tension and conductivity measurements demonstrate that the inclusion complex was produced with 1:1 stoichiometry. The thermodynamic parameters based on density, viscosity, and refractive index measurements were used to determine the nature of the complex. This research also forecasts how dyphylline will release in the presence of CT-DNA without any chemical modifications. The produced insertion complex (IC) has a higher photostability due to the drug dyphylline being protected by β-CD. The antibacterial activity of dyphylline greatly improved after complexation and exhibited higher toxicity against Gram-negative (highest against Escherichia coli) in comparison to Gram-positive bacteria. The encapsulation mode of the dyphylline molecule into the cavity of the β-CD was also investigated using DFT to confirm preliminary results.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

A new bio-active asymmetric-Schiff base: synthesis and evaluation of calf thymus DNA interaction, topoisomerase IIα inhibition, in vitro antiproliferative activity, SEM analysis and molecular docking studies

In this paper, the asymmetric-Schiff base 2-(4-(2-hydroxybenzylideneamino)benzylideneamino)benzoic acid (SB-2) was newly synthesized and characterized by various spectroscopic methods. The interaction of SB-2 with calf thymus DNA was investigated by UV-vis, fluorescence spectroscopy and molecular docking methods. It was determined that SB-2 effectively binds to DNA via the intercalation mode. DNA electrophoretic mobility experiments displayed that topoisomerase IIα could not cleave pBR322 plasmid DNA in the presence of SB-2, confirming that the Schiff base acts as a topo II suppressor. In the molecular docking studies, SB-2 was found to show an affinity for both the DNA-topoisomerase IIα complex and the DNA. In vitro antiproliferative activity of SB-2 was screened against HT-29 (colorectal) and HeLa (cervical) human tumor cell lines by MTT assay. SB-2 diminished the cell viability in a concentration- and incubation time-dependent manner. The ability of SB-2 to measure DNA damage in tumor cells was evaluated with cytokinesis-block micronucleus assay after incubation 24 h and 48 h. Light and scanning electron microscopy experiments of tumor cells demonstrated an incubation time-dependent increase in the proportion of apoptotic cells (nuclear condensation and apoptotic bodies) suggesting that autophagy and apoptosis play a role in the death of cells. Based on the obtained results, it may be considered that SB-2 is a candidate for DNA-targeting antitumor drug.Communicated by Ramaswamy H. Sarma.

Synthesis, Characterization, Biological Evaluation and DNA Interaction Studies of 4-Aminophenol Derivatives: Theoretical and Experimental Approach

In the present study, five 4-aminophenol derivatives (4-chloro-2-(((4-hydroxyphenyl)imino)methyl)phenol(S-1), 4-((4-(dimethylamino)benzylidene)amino)phenol(S-2), 4-((3-nitrobenzylidene)amino)phenol(S-3), 4-((thiophen-2-ylmethylene)amino)phenol(S-4) and 4-(((E)-3-phenylallylidene)amino)phenol(S-5)) were synthesized and characterized by FT-IR, ¹H-NMR, ¹³C-NMR and elemental analyses. The synthesized compounds were tested for their antimicrobial (Gram-positive and Gram-negative bacteria and Saccharomyces cervesea fungus) and antidiabetic (α-amylase and α-glucosidase inhibitory) activities. All the compounds showed broad-spectrum activities against the Staphylococcus aureus (ATCC 6538), Micrococcus luteus (ATCC 4698), Staphylococcus epidermidis (ATCC 12228), Bacillus subtilis sub. sp spizizenii (ATCC 6633), Bordetella bronchiseptica (ATCC 4617) and Saccharomyces cerevisiae (ATCC 9763) strains. The newly synthesized compounds showed a significant inhibition of amylase (93.2%) and glucosidase (73.7%) in a concentration-dependent manner. Interaction studies of Human DNA with the synthesized Schiff bases were also performed. The spectral bands of S-1, S-2, S-3 and S-5 all showed hyperchromism, whereas the spectral band of S-4 showed a hypochromic effect. Moreover, the spectral bands of the S-2, S-3 and S-4 compounds were also found to exhibit a bathochromic shift (red shift). The present studies delineate broad-spectrum antimicrobial and antidiabetic activities of the synthesized compounds. Additionally, DNA interaction studies highlight the potential of synthetic compounds as anticancer agents. The DNA interaction studies, as well as the antidiabetic activities articulated by the molecular docking methods, showed the promising aspects of synthetic compounds.

Design and synthesis of fatty acid derived 4-methoxybenzylamides as antimicrobial agents

A new series of fatty acid amides viz. N-(4-methoxybenzyl)undec-10-enamide (5), (9Z, 12R)-12-Hydroxy-N-(4-methoxybenzyl)octadec-9-enamide (6) and N-(4-methoxy benzyl)oleamide (7) were synthesized by using a suitable synthetic route involving DCC and DMAP as catalysts. The synthesized compounds were characterized through FTIR, NMR spectroscopy, and mass spectrometry. DNA binding studies through spectroscopy and molecular docking were performed to evaluate the binding mechanism of molecules (5-7) with (ctDNA). The inhibition zone with reference to standards, Minimum Inhibitory Concentration (MIC) and Minimum Killing Concentration (MKC) values were determined to study the in vitro antimicrobial activity for tested compounds. Among all the tested compounds, the compound 6 containing hydroxy group at the fatty acid chain showed most powerful antifungal as well as antibacterial activity.

Molecular docking, DFT and antimicrobial studies of Cu(II) complex as topoisomerase I inhibitor

Herein, we report the synthesis and single crystal X-ray structure of Cu(II)-picolinic acid complex, 1 as a potent topoisomerase I inhibitor. The complex 1 crystallized in the triclinic crystal system with space group P-1. Comparative in vitro binding studies of complex 1 with CT DNA and tRNA were carried out revealing an electrostatic binding mode with higher binding propensity towards tRNA. The intrinsic bonding constant value, K_b was calculated to be 4.36 × 10⁴ and 8.78 × 10⁴ M^-1 with CT DNA and tRNA respectively. DNA cleavage activity was carried out with a pBR322 plasmid DNA substrate to ascertain the cleaving ability. Furthermore, Topo-I inhibition assay of complex 1, performed via gel electrophoresis revealed a significant inhibitory effect on the enzyme catalytic activity at a minimum concentration of 15 µM. The DFT studies were carried out to provide better insight in the electronic transitions observed in the absorption spectrum of the complex 1. Molecular docking studies were carried out with DNA, RNA and Topo-I to determine the specific binding preferences at the target site and complement the spectroscopic studies. The antimicrobial potential of complex 1 was screened against E. coli, S. aureus, P. aeruginosa, B. subtilis and C. albicans; and compared with doxycycline, exhibiting an excellent maximum zone of inhibition of 28 mm against E. coli.Communicated by Ramaswamy H. Sarma.

Structural characterization of new zinc(ii) complexes with N2O2 chelating thiosemicarbazidato ligands; investigation of the relationship between their DNA interaction and in vitro antiproliferative activity towards human cancer cells

New candidates to become DNA-targeting antiproliferative agents: Zinc(ii) complexes bearing N₂O₂-thiosemicarbazidato ligands.

Spectroscopic and In Silico DNA Binding Studies on the Interaction of Some New N-Substituted Rhodanines with Calf-thymus DNA: In Vitro Anticancer Activities

BACKGROUND

In this era of science, cancer is a black dot on the face of humankind. Consequently, the search of promising anticancer agents continues.

AIMS

Here we designed and synthesized new N-substituted rhodanines (RD1-7), evaluated their multispectroscopic interaction with calf thymus DNA, in silico and anticancer studies against MDA-MB-231cancer cell line.

METHODS

By MTT assay rhodanine RD1 was found to be the most potent with IC50 value of 72.61 μM. In addition, DNA binding studies (UV-vis and fluorescence) revealed strong binding affinity of RD1-7 with DNA (Kb in the range of 1.5-7.4 × 105 M-1). Moreover, molecular docking study, experimental DNA binding and anticancer studies are all well agreed to each other.

RESULTS

It was observed that H-bonding and hydrophobic attractions were responsible for stability of DNAcompound adducts. Besides, the reported rhodanines (RD1-7) were found as minor groove binders of DNA. Concisely, RD1-7 indicated promising pharmacological properties and hence, shows auspicious future for the development of novel anticancer agents.

CONCLUSION

The reported rhodanines showed excellent anticancer properties. Therefore, the described rhodanines may be used as potential anticancer agents in the future.

Critical Assessment of the Interaction between DNA and Choline Amino Acid Ionic Liquids: Evidences of Multimodal Binding and Stability Enhancement

Long-term storage and stability of DNA is of paramount importance in biomedical applications. Ever since the emergence of ionic liquids (ILs) as alternate green solvents to aqueous and organic solvents, their exploration for the extraction and application of DNA need conscientious understanding of the binding characteristics and molecular interactions between IL and DNA. Choline amino acid ILs (CAAILs) in this regard seem to be promising due to their non-cytotoxic, completely biobased and environment-friendly nature. To unravel the key factors for the strength and binding mechanism of CAAILs with DNA, various spectroscopic techniques, molecular docking, and molecular dynamics simulations were employed in this work. UV-Vis spectra indicate multimodal binding of CAAILs with DNA, whereas dye displacement studies through fluorescence emission confirm the intrusion of IL molecules into the minor groove of DNA. Circular dichorism spectra show that DNA retains its native B-conformation in CAAILs. Both isothermal titration calorimetry and molecular docking studies provide an estimate of the binding affinity of DNA with CAAILs ≈ 4 kcal/mol. The heterogeneity in binding modes of CAAIL-DNA system with evolution of time was established by molecular dynamics simulations. Choline cation while approaching DNA first binds at surface through electrostatic interactions, whereas a stronger binding at minor groove occurs via van der Waals and hydrophobic interactions irrespective of anions considered in this study. We hope this result can encourage and guide the researchers in designing new bio-ILs for biomolecular studies in future.

Synthesis, anti-bacterial and anti-protozoal activities of amidinobenzimidazole derivatives and their interactions with DNA and RNA

Amidinobenzimidazole derivatives connected to 1-aryl-substituted 1,2,3-triazole through phenoxymethylene linkers 7a-7e, 8a-8e, and 9a-9e were designed and synthesised with the aim of evaluating their anti-bacterial and anti-trypanosomal activities and DNA/RNA binding affinity. Results from anti-bacterial evaluations of antibiotic-resistant pathogenic bacteria revealed that both o-chlorophenyl-1,2,3-triazole and N-isopropylamidine moieties in 8c led to strong inhibitory activity against resistant Gram-positive bacteria, particularly the MRSA strain. Furthermore, the non-substituted amidine and phenyl ring in 7a induced a marked anti-bacterial effect, with potency against ESBL-producing Gram-negative E. coli better than those of the antibiotics ceftazidime and ciprofloxacin. UV-Vis and CD spectroscopy, as well as thermal denaturation assays, indicated that compounds 7a and 8c showed also binding affinities towards ctDNA. Anti-trypanosomal evaluations showed that the p-methoxyphenyl-1,2,3-triazole moiety in 7b and 9b enhanced inhibitory activity against T. brucei, with 8b being more potent than nifurtimox, and having minimal toxicity towards mammalian cells.

Carbohydrate-based heteronuclear complexes as topoisomerase Iα inhibitor: approach toward anticancer chemotherapeutics

Due to the critical role of cellular enzymes necessary for cell proliferation by deciphering topological hurdles in the process of DNA replication, topoisomerases have been one of the major targets in the anticancer drug development area. A need, therefore, arises for new metallodrugs that specifically recognizes DNA and inhibits the activity of topoisomerase enzymes, herein, we report the synthesis and characterization of new metal-based glycoconjugate entities containing heterobimetallic core Cu^II-Sn^IV (1) and Ni^II-Sn^IV (2) derived from N-glycoside ligand (L). The optimized structure of complex 1 and other significant vibrational modes have been explained using dispersion corrected B3LYP/DFT calculations. In vitro DNA binding profile of the L and both the complexes 1 and 2 were done by various biophysical studies. Complex 1 breaks pBR322 DNA via a hydrolytic means which was validated by T4 DNA enzymatic assay. To get a mechanistic insight of mode of action topoisomerase I (Topo I) inhibition assay was carried out. Also, we have taken the help of molecular modeling studies in accordance with experimental findings. In vitro cytotoxicity of the complex 1 was evaluated against a panel of cancer cells which exhibited remarkably good anticancer activity (GI₅₀ values <10 μg/ml). Moreover, intracellular localization of the complex 1 was visualized by confocal microscopy against HeLa cells.

Correlation Between Molecular Modelling and Spectroscopic Techniques in Investigation With DNA Binding Interaction of Ruthenium(II) Complexes

The DNA binding studies of rutheniumu(II) polypyridyl complexes {[Ru(phen)₂Mipc]²⁺, [Ru(bpy)₂Mipc]²⁺, [Ru(dmb)₂Mipc]²⁺, [Ru(phen)₂BrIPC]²⁺, [Ru(bpy)₂BrIPC]²⁺, [Ru(dmb)₂BrIPC]²⁺, [Ru(phen)₂PIP-Cl]²⁺, [Ru(bpy)₂PIP-Cl]²⁺, [Ru(dmb)₂PIP-Cl]²⁺, [Ru(phen)₂IPPBA]²⁺, [Ru(bpy)₂IPPBA]²⁺, [Ru(dmb)₂IPPBA]²⁺} with DNA investigated by electronic absorption titration, emission and molecular modelling studies to identify the binding interactions. All these complexes are showing good binding constant values ~10⁴ to 10⁵. The intercalative ligands makes the binding of the ruthenium(II) complex with DNA as intercalation mode. The ancillary ligands 1,10-phenanthroline (phen), 4,4'-Dimethyl-2,2'-dipyridyl (dmb) and 2,2'-dipyridine (bpy) having been discovered found to be involved in bond formation with the phosphate backbone of nucleotide base pairs in ruthenium(II) complex-DNA docked complex. The molecular docking results are good agreement with experimental results. The molecular modelling technic should help to extend knowledge about the nature (or) mode of binding of these ruthenium(II) complexes with (calf thymus) CT-DNA.

When DNA repair goes wrong: BER-generated DNA-protein crosslinks to oxidative lesions

Free radicals generate an array of DNA lesions affecting all parts of the molecule. The damage to deoxyribose receives less attention than base damage, even though the former accounts for ∼20% of the total. Oxidative deoxyribose fragments (e.g., 3'-phosphoglycolate esters) are removed by the Ape1 AP endonuclease and other enzymes in mammalian cells to enable DNA repair synthesis. Oxidized abasic sites are initially incised by Ape1, thus recruiting these lesions into base excision repair (BER) pathways. Lesions such as 2-deoxypentos-4-ulose can be removed by conventional (single-nucleotide) BER, which proceeds through a covalent Schiff base intermediate with DNA polymerase β (Polβ) that is resolved by hydrolysis. In contrast, the lesion 2-deoxyribonolactone (dL) must be processed by multinucleotide ("long-patch") BER: attempted repair via the single-nucleotide pathway leads to a dead-end, covalent complex with Polβ cross- linked to the DNA by an amide bond. We recently detected these stable DNA-protein crosslinks (DPC) between Polβ and dL in intact cells. The features of the DPC formation in vivo are exactly in keeping with the mechanistic properties seen in vitro: Polβ-DPC are formed by oxidative agents in line with their ability to form the dL lesion; they are not formed by non-oxidative agents; DPC formation absolutely requires the active-site lysine-72 that attacks the 5'-deoxyribose; and DPC formation depends on Ape1 to incise the dL lesion first. The Polβ-DPC are rapidly processed in vivo, the signal disappearing with a half-life of 15-30min in both mouse and human cells. This removal is blocked by inhibiting the proteasome, which leads to the accumulation of ubiquitin associated with the Polβ-DPC. While other proteins (e.g., topoisomerases) also form DPC under these conditions, 60-70% of the trapped ubiquitin depends on Polβ. The mechanism of ubiquitin targeting to Polβ-DPC, the subsequent processing of the expected 5'-peptidyl-dL, and the biological consequences of unrepaired DPC are important to assess. Many other lyase enzymes that attack dL can also be trapped in DPC, so the processing mechanisms may apply quite broadly.

Synthesis, spectral characterization, DNA interaction, anticancer and molecular docking studies on some transition metal complexes with bidentate ligand

The ligand, N(2),N(3)-bis(3-nitrophenyl)quinoxaline-2.3-diamine was prepared by the condensation of quinoxaline-2.3(1,4H)-dione with 3-nitroaniline. It was treated with Co(II), Ni(II), Cu(II) and Zn(II) acetates to form the metal complexes. These were characterized by elemental analysis, molar conductance, magnetic moment, UV-Vis., IR, (1)H NMR, ESR and mass spectral data. Octahedral geometry has been assigned to Co(II), Ni(II) and Zn(II) complexes, whereas Cu(II) complex has distorted octahedral geometry. From the powder XRD data, crystallite size and unit cell parameters were calculated. The surface morphology of the synthesized compounds were determined using SEM analysis. The antimicrobial activity of the compounds against some bacterial species viz. Escherichiacoli, Klebsiella pneumoniae, Pseudomonas aeuruginosa and Staphylococcus aureus; also the fungal species, Aspergillus niger, and Candida albicans were done by disc diffusion method. DNA binding, cleavage and super oxide anion scavenging activities were also evaluated. The DNA binding activity of the compounds were identified using electronic absorption titrations and DNA cleavage was determined using gel electrophoresis. The anticancer activities of the compounds against HeLa cell line were determined using MTT assay. The highly potent compound among the five against HeLa cell line is subjected to molecular docking study against human papilloma virus receptor molecule and ATP binding site of telomerase.

Synthesis, characterization, DNA/protein interaction and cytotoxicity studies of Cu(II) and Co(II) complexes derived from dipyridyl triazole ligands

Four different transition metal complexes containing dipyridyl triazole ligands, namely [Cu(abpt)2Cl2]·2H2O (1), [Cu(abpt)2(ClO4)2] (2), [Co2(abpt)2(H2O)2Cl2]·Cl2·4H2O (3) and [Co2(Hbpt)2(CH3OH)2(NO3)2] (4) have been designed, synthesized and further structurally characterized by X-ray crystallography, ESI-MS, elemental analysis, IR and Raman spectroscopy. In these complexes, the both ligands act as bidentate ligands with N, N donors. DNA binding interactions with calf thymus DNA (ct-DNA) of the ligand and its complexes 1~4 were investigated via electronic absorption, fluorescence quenching, circular dichroism and viscosity measurements as well as confocal Laser Raman spectroscopy. The results show these complexes are able to bind to DNA via the non-covalent mode i.e. intercalation and groove binding or electrostatic interactions. The interactions with bovine serum albumin (BSA) were also studied using UV-Vis and fluorescence spectroscopic methods which indicated that fluorescence quenching of BSA by these compounds was the presence of both static and dynamic quenching. Moreover, the in vitro cytotoxic effects of the complexes against four cell lines SK-OV-3, HL-7702, BEL7404 and NCI-H460 showed the necessity of the coordination action on the biological properties on the respective complex and that all four complexes exhibited substantial cytotoxic activity.

Theoretical studies on binding modes of copper-based nucleases with DNA

In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.

Studying non-covalent drug-DNA interactions

Drug-DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.

Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA

The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH<0 and ΔS<0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb=2×10(3)M(-1)). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.

Design and synthesis of enantiomeric (R)- and (S)-copper(II) and diorganotin(IV)-based antitumor agents: their in vitro DNA binding profile, cleavage efficiency and cytotoxicity studies

New chiral reduced Schiff base ligands (R)/(S)-2-(2-hydroxy-1-phenylethylaminomethyl)phenol (L), (R)/(S)-2-(benzylamino)-2-phenylethanol (L') and their Cu(II)/organotin(IV) complexes (1-4) were synthesized and thoroughly characterized. Preliminary in vitro DNA binding studies of (R)- and (S)-enantiomeric pairs of ligands L, L' and complexes 1-4 were carried out employing UV-vis, fluorescence and circular dichroic techniques to evaluate their enantioselective DNA binding potential, thereby to act as antitumor chemotherapeutic drug entities. The observations demonstrated that S-enantiomer of Cu(II) complex, 1 binds more avidly to DNA in comparison to its R-enantiomeric form and organotin(IV) complex 2. This was further established by Kb and Ksv values of ligands L and L' and (S)-/(R)-1-4 complexes, which demonstrated multifold increase in case of S-enantiomer of copper complex 1 in comparison to its R-enantiomeric form. This clearly demonstrates the chiral preference of S-enantiomer over R-enantiomer and its potency to act as a chemotherapeutic agent. Cleavage studies of 1-4 with pBR322 plasmid DNA were carried out, noticeably, S-enantiomer of complex 1 exhibited effective DNA cleavage efficiency in absence of external agents. The cytotoxicity of ligands L and L' and (S)-/(R)-1-4 complexes was examined on a panel of 19 human tumor cell lines of different histological origins by SRB assay. In the both the cases, the S-enantiomer of complex 1 and 3 revealed remarkably good cytotoxic activity (GI50 values <10) against T24 (Urinary Bladder), DU145 (Prostate), U373MG (Astrocytoma) and HCT15, SW620 (Colon) clearly underlining the influence of enantiomeric discrimination. Interestingly, ligands L, L' and rest of the complexes demonstrated moderate cytotoxic activity (GI50 values <40).