Molecular modelling studies on cinnoline-based BTK inhibitors using docking and structure-based 3D-QSAR

ABSTRACT

BTK inhibitors have been proved as an effective target for B-cell malignancies. Ibrutinib is the most advanced irreversible BTK inhibitor for treating mantle cell lymphoma/chronic lymphocytic leukaemia but with existing drug resistance and adverse effects. To design novel effective and safety reversible BTK inhibitors, 115 newly cinnoline analogues were selected to perform molecular docking and 3D-QSAR study because of the main scaffold similarity to Ibrutinib. Both established CoMFA and CoMSIA models obtained high predictive and satisfactory value. CoMFA/CoMSIA contour maps demonstrated that bulky substitutions are preferred at R₁ and R₃ positions, and introducing hydrophilic and negative electrostatic substitutions at R₁ positions is important for improving BTK inhibitory activities. These results will be useful to provide clues for rationally designing novel and high potency BTK inhibitors.     

Structure-Based Discovery and Bioactivity Evaluation of Novel Aurora-A Kinase Inhibitors as Anticancer Agents via Docking-Based Comparative Intermolecular Contacts Analysis (dbCICA)

Aurora-A kinase plays a central role in mitosis, where aberrant activation contributes to cancer by promoting cell cycle progression, genomic instability, epithelial-mesenchymal transition, and cancer stemness. Aurora-A kinase inhibitors have shown encouraging results in clinical trials but have not gained Food and Drug Administration (FDA) approval. An innovative computational workflow named Docking-based Comparative Intermolecular Contacts Analysis (dbCICA) was applied—aiming to identify novel Aurora-A kinase inhibitors—using seventy-nine reported Aurora-A kinase inhibitors to specify the best possible docking settings needed to fit into the active-site binding pocket of Aurora-A kinase crystal structure, in a process that only potent ligands contact critical binding-site spots, distinct from those occupied by less-active ligands. Optimal dbCICA models were transformed into two corresponding pharmacophores. The optimal one, in capturing active hits and discarding inactive ones, validated by receiver operating characteristic analysis, was used as a virtual in-silico search query for screening new molecules from the National Cancer Institute database. A fluorescence resonance energy transfer (FRET)-based assay was used to assess the activity of captured molecules and five promising Aurora-A kinase inhibitors were identified. The activity was next validated using a cell culture anti-proliferative assay (MTT) and revealed a most potent lead 85(NCI 14040) molecule after 72 h of incubation, scoring IC₅₀ values of 3.5–11.0 μM against PANC1 (pancreas), PC-3 (prostate), T-47D and MDA-MB-231 (breast)cancer cells, and showing favorable safety profiles (27.5 μM IC₅₀ on fibroblasts). Our results provide new clues for further development of Aurora-A kinase inhibitors as anticancer molecules.     

Synthesis,structure elucidation,DNA binding and molecular docking studies of novel copper(II) complexes of two 1,3,4-thiadiazolethiosemicarbazone derivatives

Four novel Cu(II) chelates were synthesized by reacting hydrated CuCl₂ and Cu(CH₃COO)₂ with two derivatives of 1,3,4-thiadiazolethiosemicarbazone. The structures and geometries of the synthesized complexes were deduced applying the alternative analytical and spectral tools confirming the complexes to have the formulae [(LH)Cu(Cl)]•0.5H₂O, [(LH)Cu(OAc)(H₂O)₂]•0.5H₂O, [(LCl)Cu(Cl)(H₂O)₂]•H₂O and [(LCl)Cu(OAc)]; where LH and LCl are phenyl and p-chlorophenyl derivatives of 1,3,4-thiadiazolethiosemicarbazone ligands, respectively (deprotonated form). IR spectral data confirmed the coordination of the ligands to the copper center as monobasic tridentate in the thiol form. Thermal analysis, UV–Vis spectra and magnetic moment assured the geometry around the copper center to be square planar, trigonal bipyramid and octahedral which have been confirmed by the computational studies. The two ligand derivatives and their copper complexes were applied to evaluate their binding modes with SS-DNA via UV–Vis spectral titration and viscosity measurements. The DNA-binding constant (k_b) values of the investigated derivatives were calculated and compared with ethidium bromide in order to assess their mode of binding with DNA. Moreover, docking study of these complexes was carried out to recognize the drug–DNA interactions and to calculate their binding energies.     

Deuteron induced damage in alkali halides

Abstract

The thermoelectric and galvanomagnetic properties in the CdxHg1_xTe solid solution samples (x = 0.12; 0.15) irradiated at 300 K by electrons (3.5 MeV; by integrated fluxes up to 1.46 × 10¹⁸e/cm²) have been investigated in a wide temperature range 4.2–300 K and in magnetic fields 0–22 kOe.

It has been discovered that the electron irradiation of Cd_xHg_1–xTe crystals leads to an increase of the Hall coefficient and a decrease of the thermo e.m.f. sign inversion temperature. The concentrations and mobilities of electron and hole have been calculated on a basis of quantitative analysis of galvanomagnetic data. It has been shown that the kinetic coefficient behavior upon irradiation is due to the Te vacancy-based type radiation defect origin.     

DFT studies on global parameters,antioxidant mechanism and molecular docking of amlodipine besylate

Amlodipine besylate (AMB) is a synthetic dihydropyridine calcium channel blocker with antihypertensive and anti-anginal effects. Quantum computational investigations on AMB were done using DFT/B3LYP/6-311++G (d, p) level of theory, to study the molecular structural properties, nonlinear properties and antioxidant properties of AMB. The electrophilic and nucleophilic sites along with complete NBO analysis helps to locate the intermolecular electronic interactions and their stabilization energies. Complete NBO analysis was additionally done to locate the intermolecular electronic interactions and their stabilization energies. Charge distributions of Mulliken population, NBO and MEP are correlated. Also, the antioxidant properties of AMB were assessed to check whether these antioxidant effects contribute to the effects of antioxidant therapy. Further, the molecular docking studies of these compounds demonstrated a good selectivity profile with Monoamine oxidase B with better binding affinity and confirms AMB is a potent antioxidant.     

Spectroscopic and electrochemical study for evaluating DNA interaction activity of 4‐(3‐halophenyl)‐6‐(pyridin‐2‐yl)pyrimidin‐2‐amine based piano stool Cp* Rh (III) and Ir (III) complexes

Six novel organometallic half sandwich complexes [(η5‐C₅Me₅)M(L^1–3)Cl]Cl.2H₂O were synthesized using [{(η⁵‐C₅Me₅)M(μ‐Cl)Cl₂], where M = Ir (III)/Rh (III) and L^1–3 = three pyridyl pyrimidine based ligands; and characterized by NMR, Infra‐red spectroscopy, conductance, elemental and thermal analysis. The complex‐DNA binding mode and/or strength evaluated using absorption titration, electrochemical studies and hydrodynamic measurement proposed intercalative binding mode, which was also confirmed by molecular docking study. Differential pulse voltammetry and cyclic voltammetry studies indicated an alteration in oxidation and reduction potentials of complexes (M⁺⁴/M⁺³) in presence of CT‐DNA. The metal complexes can cleave plasmid DNA as proposed in gel electrophoretic analysis. The LC₅₀ values of complexes evaluated on brine shrimp suggested their potent cytotoxic nature.     

Spectroscopic investigation,DFT, fluorescence,molecular docking and biological studies of divalent and trivalent binuclear complexes prepared from benzoyl thiosemicarbazide derivative of 2‐benzylmalonohydrazide

The binuclear Cr (III), Mn (II) and Fe (III) complexes of N,N′‐(2,2′‐(2‐benzylmalonyl)bis (hydrazine‐1‐carbonothioyl))dibenzamide (H₄BPCD), which derived from the combination of 2‐benzylmalonohydrazide suspension with benzoyl‐isothiocyanate, have been isolated and investigated by the necessary analytical and spectroscopic techniques. The IR studies show that H₄BPCD dispose as a mono‐negative hexadentate ligand (NOS)₂ towards Mn (II) ion and tetra‐negative hexadentate (NOS)₂ towards both Cr (III) and Fe (III) ions. The values of molar conductance in DMSO suggested the non‐electrolytic nature for all complexes. The magnetic measurements and the electronic transitions data confirmed the hexa‐coordinate geometry of complexes. The DFT geometry optimization of all compounds and IR comparative study of both theoretical and experimental of H₄BPCD were carried out. Moreover, the H₄BPCD and its Cr (III) complex displayed intra ligand (π → π*) fluorescence emission spectra which corroborate their photoactive nature. The coordinated and crystalline water molecules have been investigated by (TG/DTG) studies. The kinetic and thermodynamic parameters were computed using Horowitz‐ Metzger, Coats‐Redfern and Broido methods. Biological studies of DNA binding, minimum inhibitory concentration, in vitro determination of SOD‐like activity and MTT‐cytotoxicity assay as well as molecular docking studies were tested for the ligand and its complexes.     

Surface structure of cationic surfactant solutions investigated by angular resolved X‐ray photoelectron spectroscopy with calibrated transmission function

The main goal of the present work is to investigate the surface structure of cationic surfactant solutions by angular resolved X‐ray photoelectron spectroscopy (ARXPS) after calibrating transmission function of the spectrometer. We have estimated the transmission function of the ARXPS spectrometer, and with it, we investigated solution of tetrabutylammonium iodide in a nonaqueous polar solvent. By genetic algorithm, the fractional concentration‐depth profiles of constituents were reconstructed. These depth profiles evidence the enrichment of surfactant and the depletion of solvent in the surface regime and verify the separate distributions of oppositely charged surfactant ions. From those profiles we draw a conclusion that there is a preferred orientation for cation present at the surface, and the possibility for cation to take this orientation is related to its surface amount. Copyright © 2010 John Wiley & Sons, Ltd.     

Chromium‐metformin ternary complexes: Thermal,DNA interaction and Docking studies

Three chromium ternary complexes with metformin (met) as a primary ligand and bipyridine (bipy) or ortho‐phenylenediamine (opda) or ortho‐phenanthroline (phen) as secondary ligand were synthesized. These complexes [Cr (Cl)₂(Hmet)(bipy)]‐( 1 ), [Cr (Cl)₂(Hmet)(opda)]‐( 2 ) and [Cr (Cl)₂(Hmet)(phen)]‐( 3 ) were characterized by LC–MS, elemental analysis, molar conductance, thermal analysis, infrared spectroscopy, electronic spectroscopy. The geometrical structures have been found to be octahedral. Degradation pattern of the compounds is shown by thermal studies. The Kinetic parameters‐ energy of activation (E_a), enthalpy (ΔH), entropy (ΔS) and free energy changes (ΔG) have been determined by thermogravimetric data. Coats‐Redfern integration method with thirteen kinetic models was used to calculate the kinetic and thermodynamic parameters for the degradation of all the complexes. The stabilities of the complexes were obtained from their molecular orbital structures from which the quantum chemical parameters were calculated using the HOMO‐LUMO energies. UV–Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV–Vis spectrum with DNA. The binding constants K_b from UV–Vis absorption studies were 3.1x10⁴, 4.4x10⁴, 5x10⁴ M^?1 for 1, 2, 3 respectively and Stern–Volmer quenching constants (K_sq) from fluorescence studies were 0.137, 0.532, 0.631 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT‐DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decrease in the order of 3 > 2 > 1.The light switching properties of the complexes were also evaluated. The complexes were docked in to B‐DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)‐3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.     

The solvent‐free synthesis of polysubstituted pyrroles by a reusable copper Schiff base complex immobilized on silica coated Fe3O4, and DNA binding study of one resulting derivative as a potential anticancer drug

We demonstrate herein the synthesis of a new copper Schiff base complex immobilized on silica‐coated Fe₃O₄ nanoparticles. The structure and composition of this magnetic nanocatalyst were analyzed using Fourier transform infrared (FT‐IR), X‐ray powder diffraction (XRD), vibrating sample magnetometry (VSM), scanning electron microscopy (SEM), energy dispersive X‐ray (EDX) and inductively coupled plasma atomic emission spectroscopy (ICP‐AES). This nanocomposite was found to be an efficient nanocatalyst for the synthesis of polysubstituted pyrrole derivatives and the products were isolated with high turnover number (TON) and high to excellent yields. Among the new synthesized polysubstituted pyrrole derivatives, we explored the first computational and experimental binding study of methyl 1‐benzyl‐4‐(furan‐2‐yl)‐2‐methyl‐1H‐pyrrole‐3‐carboxylate (SP‐10) with calf thymus deoxyribonucleic acid (ct‐DNA), suggesting their application as potential anticancer activity. In addition, the binding modes of SP‐10 with DNA and human serum albumin (HSA) were verified by molecular docking technique.