Heteroscorpionate‐based heteroleptic copper(II) complexes: Antioxidant,molecular docking and in vitro cytotoxicity studies

Three new heteroscorpionate ligands, (2‐hydroxyphenyl)bis(imidazol‐1‐yl)methane (HL¹), (4‐diethylamino‐2‐hydroxyphenyl)bis(imidazol‐1‐yl)methane (HL²) and (5‐bromo‐2‐hydroxyphenyl)bis(imidazol‐1‐yl)methane (HL³), and their heteroleptic copper(II) complexes of the type [Cu(L^1–3)diimine]ClO₄ ( 1 – 6 ; where diimine =2,2′‐bipyridyl or 1,10‐phenanthroline) have been synthesized and characterized using spectroscopic methods. The molecular structure of ligand HL¹ was determined by single‐crystal X‐ray diffraction. UV–visible, electron paramagnetic resonance and theoretical studies suggest a distorted square pyramidal geometry around copper(II) ion. Analyses of highest occupied and lowest unoccupied molecular orbitals have been used to explain the charge transfer taking place within the complexes. The antioxidant activities of the heteroscorpionate ligands and their heteroleptic copper(II) complexes were determined using ABTS, DPPH and H₂O₂ free radical scavenging assays with respect to standard antioxidant ascorbic acid. In molecular docking studies, the complexes showed π–π, hydrogen bonding, van der Waals and electrostatic interactions with fibroblast growth factor receptor kinase. In vitro cytotoxicity activities of ligands and copper(II) complexes were examined on human breast adenocarcinoma (MCF‐7), cervical (HeLa) and lung (A549) cancer cell lines and normal human dermal fibroblast cell line using MTT assay. Complex 4 exhibited higher anticancer activity than the other complexes against all three cancer lines, being more potent than the standard drug cisplatin.     

Synthesis,characterization and biological applications of new copper(II) complexes of aryl hydrazones

On treatment of copper(II) acetate with aryl hydrazone ligands, four new solid derivatives of copper(II) were produced in appreciable yields. Various characterization techniques including infrared, UV–visible, NMR, electron paramagnetic resonance and mass spectroscopies, elemental analysis, scanning electron microscopy, powder X‐ray diffraction and thermogravimetric analysis revealed a tetra‐coordination in all the mononuclear crystalline complexes with high thermal stability. Further, significant interaction of these novel complexes with calf thymus DNA via intercalative mode of binding was revealed by electronic absorption spectroscopy. The chemical nuclease activity of the complexes on pBR322 DNA was investigated in the presence and absence of oxidizing agent (H₂O₂). A potent nuclease activity was observed only in the presence of H₂O₂. Further, antibacterial and antifungal studies of the new ligands and complexes revealed that the latter possessed comparatively better activity.     

Influence of polymer conformation on the entrance length in capillary flow

An analysis of the flow of polymer solutions through capillaries by means of pressure profiles was performed in this work. The experiments were carried out with aqueous solutions of flexible and semirigid macromolecules, Polyox and Xanthan respectively. The influence of the macromolecules' conformation on the flow field development is reflected on the different magnitudes of the entry length, being of the order of 60 diameters for the solutions of rigid macromolecules, and of the order of 10 diameters for flexible ones. In addition, the calculated end effects were larger for the rigid macromolecules than for the flexible ones. From these results, it is found that an increase in the entrance length is observed when the pseudoplastic behavior of the polymer solutions is increased.Dedicated to Prof. Dr. J. Meissner on the occasion of his retirement from the chair of Polymer Physics at the Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland     

Electron momentum distributions and compton profiles of some molecules with FSGO model

The electron momentum distributions and the Compton profiles (within the impulse approximation) of H₂, LiH, methane, water, acetylene, ethylene, ethane cyclopropane and cyclobutane have been calculated using the floating spherical Gaussian orbital (FSGO) wavefunctions. The agreement of the single-FSGO Compton profiles with the corresponding experimental or the Hartree-Fock (HF-SCF) theoretical ones is fairly good in most of the cases examined. The advantages and drawbacks of using the FSGO model for the calculation of Compton profiles are discussed.     

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define `fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library `diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.     

Searching Inhibitors of Adenosine Kinase by Simulation Methods

Searching new inhibitors of adenosine kinase （AK） is still drawing attention of experimental scientists. A better and solid model is here proposed by means of simulation methods from different ways, the direct analysis of receptor itself, the conventional 3D-QSAR methods and the integration of docking method and the conventional QSAR analysis.     

Virtual screening of organic molecule databases. Design of focused libraries of potential ligands of NMDA and AMPA receptors

A system of virtual screening of organic molecule databases is designed, which permits preprocessing of databases, molecular docking to a three-dimensional model of receptor, and post-processing of the results obtained. Using this screening system, it is possible to reproduce positions of the known ligands in the glutamate sites of the NMDA and AMPA receptors and in the glycine site of the NMDA receptor, to substantially enrich the database with potentially active compounds, and to distinguish between the agonistic and antagonistic character of the action of these compounds in the case of docking to the open and closed forms of the binding sites. Based on the results of screening of a database of low-molecular-weight organic compounds (total of 135,000 structures) using models of the open and closed forms of the glutamate and glycine sites of the NMDA receptor and of the glutamate site of the AMPA receptor, focused libraries of potential agonists and antagonists of these sites were designed.     

N-Mannich bases of benzimidazole as a potent antitubercular and antiprotozoal agents: Their synthesis and computational studies

Abstract

This article dealing with the microwave assisted synthesis of N-Mannich bases of pyridine clubbed with two different benzimidazole cores with their micromolar biological potency. All the synthesized compounds were evaluated for their in-vitro antibacterial, antimycobacterial and antiprotozoal potency. One of the final compound was found to be most active against M. tuberculosis (MIC = 3.125?µM) in the primary screening. N-Mannich bases of benzimidazole with pyridine-3-amine and 5-methyl-pyridine-2-amine showed potency against L. mexicana and T. cruzi respectively with IC₅₀ value 0.25 and 1.02?µg/mL. Compound 4a showed good binding energy in the active pocket of receptor (PDB: 4cod) with ?11.013 docking score. The stability of docked complex was validated by performing Molecular dynamics (MD) up to 20?ns simulation time. In silico ADME parameters and toxicity predicted that the active compounds belong to the Class IV GHS with LD₅₀ value 1360?mg/kg and hence found to be mildly toxic.     

Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach

The extent to which accuracy of electric charges plays a role in protein-ligand docking is investigated through development of a docking algorithm, which incorporates quantum mechanical/molecular mechanical (QM/MM) calculations. In this algorithm, fixed charges of ligands obtained from force field parameterization are replaced by QM/MM calculations in the protein environment, treating only the ligands as the quantum region. The algorithm is tested on a set of 40 cocrystallized structures taken from the Protein Data Bank (PDB) and provides strong evidence that use of nonfixed charges is important. An algorithm, dubbed "Survival of the Fittest" (SOF) algorithm, is implemented to incorporate QM/MM charge calculations without any prior knowledge of native structures of the complexes. Using an iterative protocol, this algorithm is able in many cases to converge to a nativelike structure in systems where redocking of the ligand using a standard fixed charge force field exhibits nontrivial errors. The results demonstrate that polarization effects can play a significant role in determining the structures of protein-ligand complexes, and provide a promising start towards the development of more accurate docking methods for lead optimization applications.     

Gaussian mapping of chemical fragments in ligand binding sites

We present a new approach to automatically define a quasi-optimal minimal set of pharmacophoric points mapping the interaction properties of a user-defined ligand binding site. The method is based on a fitting algorithm where a grid of sampled interaction energies of the target protein with small chemical fragments in the binding site is approximated by a linear expansion of Gaussian functions. A heuristic approximation selects from this expansion the smallest possible set of Gaussians required to describe the interaction properties of the binding site within a prespecified accuracy. We have evaluated the performance of the approach by comparing the computed Gaussians with the positions of aromatic sites found in experimental protein-ligand complexes. For a set of 53 complexes, good correspondence is found in general. At a 95% significance level, approximately 65% of the predicted interaction points have an aromatic binding site within 1.5 A. We then studied the utility of these points in docking using the program DOCK. Short docking times, with an average of approximately 0.18 s per conformer, are obtained, while retaining, both for rigid and flexible docking, the ability to sample native-like binding modes for the ligand. An average 4-5-fold speed-up in docking times and a similar success rate is estimated with respect to the standard DOCK protocol.