Farukh Arjmand

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

A novel heterobimetallic Cu(II)-Sn(IV) complex 1 bearing bioactive 1,10-phenanthroline pharmacophore ligand scaffold was synthesized and characterized by elemental analysis, IR, UV-vis spectroscopy, Mass (ESI and FAB) and X-ray crystallography. The in vitro DNA binding studies of complex 1 with CT DNA was carried out by various biophysical and molecular docking techniques which revealed that complex 1 binds to DNA through intercalation in the minor groove having AT-rich sequences. Complex 1 exhibits high chemical nuclease activity cleaving supercoiled pBR322 DNA via hydrolytic pathway which was further evidenced by T4 DNA ligase assay. The complex 1 shows high inhibitory activity against Topo I at a very low concentration (15 μM), suggesting that complex 1 is an efficient catalytic inhibitor of human Topo I and further validated by molecular docking studies.

Interaction with DNA of a heteronuclear [Na2Cu4] coordination cluster obtained from the assembly of two hydroxo-bridged [CuII2] units by a dimeric sodium nitrate template

The heteronuclear [Na(2)Cu(4)(bemp)(2)(OH)(2)(NO(3))(2)(OH(2))(4)] x 5 H(2)O (1 x 5H(2)O; H(3)bemp: 2,6-bis-[(2-hydroxyethylimino)-methyl]-4-methyl-phenol) cluster has been synthesized in aqueous-methanol at room temperature and structurally characterized. The water soluble complex is obtained from the template assembly of two [Cu(2)(bemp)(OH)] neutral fragments through their weak oxophillic interactions with two interconnected NaNO(3) units as core. Four [Na(2)Cu(4)] units form a metal-organic cage arrangement in the crystal lattice that traps a (H(2)O)(7) cluster. Variable-temperature magnetic susceptibility measurements (2-300 K) reveals a strong antiferromagnetic coupling between the Cu(II) ions within the dimers with J = -124.1 cm(-1) (in the H = -2JS(1)S(2) convention). The interaction of complex 1 x 3H(2)O with calf thymus DNA (binding constant K(b), 4.6 x 10(4) M(-1)) in Tris buffer was studied by UV-visible and emission titration, and cyclic voltammetry. The hexanuclear Na(2)Cu(4) complex also binds double-stranded supercoiled plasmid pBR322 DNA and displays efficient hydrolytic cleavage. The hydrolytic mechanism is supported by evidence from DNA relegation employing T4 ligase assay and reactive oxygen species (ROS) quenching cleavage experiments.

Enantiomeric recognition of chiral L– and D–penicillamine Zinc(II) complexes: DNA binding behavior and cleavage studies

Two designed L–/D–penicillamine based enantiomeric Zn(II) complexes 1a and 1b of 1,10–phenanthroline were synthesized and structurally characterized. The interactions of the complexes with CT DNA have been explored by absorption, fluorescence and CD measurements, revealing that both the complexes interact with DNA via electrostatic binding. All the corroborative results indicated the enantiopreferential selective binding of L–form of the complex over the D–form. A gel electrophoretic pictogram of the complexes 1a and 1b demonstrates their ability to cleave pBR322 DNA through hydrolytic process; validated by T4 religation assays; furthermore, the L–form of the complex exhibited more pronounced cleavage than the D–form. However, both complexes preferred the minor groove of the DNA double helix. Interaction studies with mononucleotides revealed that both the enantiomers possess high affinity towards the A–T base pairs of DNA, consistent with the previous reports on stereospecific selectivity of Zn(II) complexes. These studies were further supported by molecular docking studies and the resulting binding energy of docked metal complexes 1a and 1b were found to be −306.4 and −289.1 KJ mol−1, respectively. The more negative relative binding energy of L–form of complex suggests greater propensity for DNA than the D–enantiomer.

Enantiomeric Specificity of Biologically Significant Cu(II) and Zn(II) Chromone Complexes Towards DNA

Novel chiral Schiff base ligands (R)/(S)-2-amino-3-(((1-hydroxypropan-2-yl)imino)methyl)-4H-chromen-4-one (L(1) and L(2)) derived from 2-amino-3-formylchromone and (R/S)-2-amino-1-propanol and their Cu(II)/Zn(II) complexes (R1, S1, R2, and S2) were synthesized. The complexes were characterized by elemental analysis, infrared (IR), hydrogen ((1) H) and carbon ((13)C) nuclear magnetic resonance (NMR), electrospray ionization-mass spectra (ESI-MS), and molar conductance measurements. The DNA binding studies of the complexes with calf thymus were carried out by employing different biophysical methods and molecular docking studies that revealed that complexes R1 and S1 prefers the guanine-cytosine-rich region, whereas R2 and prefers the adenine-thymine residues in the major groove of DNA. The relative trend in K(b) values followed the order R1>S1>R2>S2. This observation together with the findings of circular dichroic and fluorescence studies revealed maximal potential of (R)-enantiomeric form of complexes to bind DNA. Furthermore, the absorption studies with mononucleotides were also monitored to examine the base-specific interactions of the complexes that revealed a higher propensity of Cu(II) complexes for guanosine-5-monophosphate disodium salt, whereas Zn(II) complexes preferentially bind to thymidine-5-monophosphate disodium salt. The cleavage activity of R1 and R2 with pBR322 plasmid DNA was examined by gel electrophoresis that revealed that they are good DNA cleavage agents; nevertheless, R1 proved to show better DNA cleavage ability. Topoisomerase II inhibitory activity of complex R1 revealed that the complex inhibits topoisomerase II catalytic activity at a very low concentration (25 μM). Furthermore, in vitro antitumor activity of complexes R1 and S1 were screened against human carcinoma cell lines of different histological origin.

Synthesis, crystal structure and antiproliferative activity of Cu(II) nalidixic acid–DACH conjugate: Comparative in vitro DNA/RNA binding profile, cleavage activity and molecular docking studies

Nalidixic acid-DACH conjugate Cu(II) molecular entity, 1 was synthesized, thoroughly characterized by spectroscopic techniques (FT-IR, EPR and ESI-MS) and single crystal X-ray diffraction technique as a potential chemotherapeutic drug candidate for cancer oncology. Complex 1 was found to be a potent drug-like molecular entity in confirmation with Lipinski rules. 1R,2R-diaminocyclohexane (DACH) ligand scaffold (which reduces the drawbacks of cisplatin analogues) and nalidixic acid pharmacophore make it a suitable drug entity targeting nucleic acids. To evaluate the chemotherapeutic potential of 1 comparative inxa0vitro DNA/RNA interaction studies have been investigated by employing various biophysical techniques (UV-vis, fluorescence, circular dichorism, viscosity, cyclic voltammetry and FT-IR), cleavage activity and Topo-II inhibition assay. Further, mechanistic investigation revealed the efficiency of 1 to cleave pBR322 DNA strands by an oxidative pathway involving the generation of ROS and preferential selectivity towards the A-T region of DNA major groove. Antiproliferative activity in conjugation with flow cytometry analysis of 1 against human osteoblastoma cell line (U2OS) suggested a cell cycle arrest at S phase. This work further advances our knowledge for the development and design of small RNA targeted therapeutic molecules which are under exploited drug targets.

Synthesis of chiral R/S-pseudopeptide-based Cu(II) & Zn(II) complexes for use in targeted delivery for antitumor therapy: enantiomeric discrimination with CT-DNA and pBR322 DNA hydrolytic cleavage mechanism

Chiral pseudopeptide Cu(II) and Zn(II) complexes (1S/R and 2S/R, respectively), were obtained by a de novo synthetic strategy employing pseudopeptide synthons derived from R/S-2-amino-2-phenylethanol and N-methyliminodiacetic acid. The complexes were thoroughly characterized by elemental analysis, mass spectrometry, and IR; the 2S/R complexes were further characterized by 1H, 13C NMR, whereas 1S/R complexes were studied by EPR spectroscopy. In vitro DNA binding studies were carried out by UV-Vis, fluorescence, thermal denaturation and circular dichroic techniques. The experimental results revealed that the complexes strongly bind to DNA via electrostatic interaction. The extent of binding was quantified by computing their intrinsic binding constant (Kb) and binding constant (K) values, which showed that the S-enantiomers of both complexes 1 and 2 exhibited higher binding propensities as compared to their R-enantiomeric analogs, and followed the trend 1S > 2S > 1R > 2R. Thermal denaturation studies of complexes in the absence and presence of CT-DNA have been carried out and the calculated ΔTm was found to be 1–3 °C, depicting the electrostatic mode of binding, which corroborated the results of the UV-Vis, fluorescence and other optical methods. The cleavage efficiencies of 1S and 2S with pBR322 DNA were evaluated by gel electrophoretic assay. S-Enantiomers of both Cu(II) and Zn(II) complexes were found to be efficient cleaving agents and cleavage reactions were mediated by hydrolytic pathways, which were further validated by relegation experiments using the T4 ligase enzyme. The cytotoxic activity of 1S and 2S showed pronounced GI50 values <10 μg mL−1 in the case of the HeLa cancer cell line, whereas for other cell lines, viz. MCF7, Hep-G2 and MIA-Pa-Ca-2, moderate activity was observed, which implicated the selective response of drug entities towards different cancer phenotypes.

Synthesis and characterization of Co(II) and Fe(II) peptide conjugates as hydrolytic cleaving agents and their preferential enantiomeric disposition for CT-DNA: structural investigation of L-enantiomers by DFT and molecular docking studies

Enantiomeric Boc L/D-valine derived peptide conjugate complexes of Co(II) L/D-1 and Fe(II) L/D-2 were synthesised and thoroughly characterized by spectroscopic techniques, elemental analysis, molar conductance and magnetic moment measurements. Peptide complexes L/D-1 and L/D-2 were titrated with CT-DNA by employing various biophysical methods viz., UV-vis, fluorescence and circular dichroic studies and viscosity measurements to envisage their binding mode and binding strength; the experimental results revealed strong preferential disposition of L-enantiomeric complexes via electrostatic binding mode with DNA helix. The structures of L-1 and L-2 were further optimized by applying DFT and molecular docking studies to validate their interaction by electrostatic bonding with DNA. Since L-enantiomers exhibited greater binding propensity than D-enantiomers, therefore, the cleavage efficiency of L-1 and L-2 with pBR322 DNA was evaluated by gel electrophoretic assay. L-Enantiomers of both Co(II) and Fe(II) complexes were found to be efficient cleaving agents and cleavage reactions were mediated by hydrolytic pathway, which were further validated by religation experiments using T4 ligase enzyme.

Single X-ray crystal structure, DFT studies and topoisomerase I inhibition activity of a tailored ionic Ag(I) nalidixic acid–piperazinium drug entity specific for pancreatic cancer cells

Novel ionic Ag(I)−piperazinium nalidixic acid conjugate 1 was synthesized as a potential antitumor agent and was thoroughly characterized by elemental analysis, FT-IR, 1H and 13C NMR and single X-ray crystal diffraction studies. Complex 1 crystallized in the triclinic space group P1 and comprises a dipiperazinium–Ag(I) cationic unit, two nalidixate (naI−) anionic moieties and a nitrate ion. The Ag(I) ion adopted a linear configuration upon coordination with two nitrogen atoms of piperazinium cations (pipzH+) arranged in a trans fashion. The density functional theory (DFT) studies of 1 revealed the HOMO and LUMO to be localized on the metal center viz., the dx2−y2 orbital and partially localized on the C27, C28, C29, C30, C31, C32, N7 and N6 atoms of the piperazinium moiety. Non covalent interaction (NCI) calculations were carried out to identify the weak non-covalent interactions from the topological analysis and reduced gradient of the electron density of complex 1. Our results revealed significant inter- and intramolecular non-covalent interactions between the naI− and [Ag(pip)2]2+ units. Furthermore, an analysis of Hirshfeld surfaces and fingerprint plots were carried out to ascertain a comparison between intermolecular interactions which provide interesting supramolecular architectures involving combinations of N–H⋯O, O–H⋯O and C–H⋯O linkages into a two-dimensional framework. In vitro binding studies of 1 with ct-DNA and tRNA revealed higher binding propensity for tRNA which was evidenced from its higher intrinsic binding constant, Kb and binding constant, K values and the mode of binding was found to be groove binding in nature. The catalytic activity of topoisomerase I enzyme in the presence of complex 1 was ascertained by gel electrophoretic assay which demonstrated significant inhibitory effects at a low concentration of 25 μM. The cytotoxicity activity of 1 was determined by SRB assay on MIA-PA-CA-2, HepG2, HeLa and MCF7 human cancer cell lines; these results exhibited specific and selective antitumor activity for the MIA-PA-CA-2 cancer cell line with a GI50 value <10.