On the Topological Sub-Structural Molecular Design (TOSS-MODE) in QSPR/QSAR and Drug Design Research

Abstract

A recently introduced graph-theoretical approach to the study of structure-property-activity relationships is presented. The theoretical approach and the computational strategy for the use of the TOSS-MODE approach are given with details. Several QSPR and QSAR applications are reviewed including the study of physical properties of organic compounds, diamagnetic susceptibilities, and biological properties. The applications of the TOSS-MODE approach to discrimination of active/inactive compounds, the virtual screening of compounds with a desired property from databases of chemical structures, identification of active/inactive fragments and its relationships with 2D/3D pharmacophores, and to the design of novel compounds with desired biological activities are also reviewed.     

基于分子参数的药物小肠吸收预测模型

选择100个化合物作为数据集,随机选取其中80个为训练集,其他分子为验证集,并为每个化合物分子计算了30个参数.通过采用五种不同多元线性回归分析方法对其训练模拟,建立了数学模型,并用验证集检验了所建模型的预测能力.结果发现向后筛选法为最优小肠吸收建模方法.由该法所建模型的统计结果良好(R2>0.80),应用于验证集时也表现出较强预测能力.该模型确定了对小肠吸收影响较大的分子参数,有助于指导进一步的新药筛选和开发.     

Dendrimer building toolkit: Model building and characterization of various dendrimer architectures

We have developed a graphical user interface based dendrimer builder toolkit (DBT) which can be used to generate the dendrimer configuration of desired generation for various dendrimer architectures. The validation of structures generated by this tool was carried out by studying the structural properties of two well known classes of dendrimers: ethylenediamine cored poly(amidoamine) (PAMAM) dendrimer, diaminobutyl cored poly(propylene imine) (PPI) dendrimer. Using full atomistic molecular dynamics (MD) simulation we have calculated the radius of gyration, shape tensor and monomer density distribution for PAMAM and PPI dendrimer at neutral and high pH. A good agreement between the available simulation and experimental (small angle X‐ray and neutron scattering; SAXS, SANS) results and calculated radius of gyration was observed. With this validation we have used DBT to build another new class of nitrogen cored poly(propyl ether imine) dendrimer and study it's structural features using all atomistic MD simulation. DBT is a versatile tool and can be easily used to generate other dendrimer structures with different chemistry and topology. The use of general amber force field to describe the intra‐molecular interactions allows us to integrate this tool easily with the widely used molecular dynamics software AMBER. This makes our tool a very useful utility which can help to facilitate the study of dendrimer interaction with nucleic acids, protein and lipid bilayer for various biological applications. © 2012 Wiley Periodicals, Inc.     

Metal adsorption properties of multi-functional PAMAM dendrimer based gels

Metal adsorption studies are getting important and there are many functional adsorbents developed recently. Here, we report the synthesis of multifunctional PAMAM G2 (polyamidoamine) possessing methacryl, amine, hydroxyl and phosphonate groups used in free radical curing gel formulations. UV curable gel is conducted in the presence of acrylamide, bisacrylamide, and polyethylene glycol diacrylate. Adsorption study of the resulting novel sorbents (gels) are carried out with a series of metals. Through a comprehensive study, structure–property relationship of the series gels is conducted by using different amount of amine, hydroxyl, and/or phosphonate ester groups on the PAMAM G2. Selected metals are Cr³⁺, Fe³⁺, Ni²⁺, Cu²⁺, Ag⁺, and Cd²⁺ within a series of hard, intermediate, and soft ionic species. Adsorption study is carried out in pure water environment at neutral pH. Metal ions removal percentages and adsorption capacities of gel adsorbents are calculated by using atomic absorption spectroscopy. There is relationship between the overall functional groups presence in gel formulation and swelling densities for removing the metal ions. Introducing dendrimer into the gel formulation enhanced the metal ions adsorption against to Bare GEL formulation which do not possess dendrimer units. Consequently, the maximum removal efficiency has been obtained for Cr³⁺ and Fe³⁺.     

QSPR Modeling of the Reactivity Parameters of Monomers in Radical Copolymerizations

For a series of monomers, QSPR test analysis is performed by optimizing the correlation weights of the local invariants of molecular graphs representing monomer structures in order to construct models of the reactivity parameters of monomers Q and e. This approach may be used as a tool in reactivity predictions for monomers for which no experimental data on Q and e are available.Original Russian Text Copyright © 2004 by A. A. Toropov, V. O. Kudyshkin, N. L. Voropaeva, I. N. Ruban, and S. Sh. Rashidova__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 994–998, November–December, 2004.     

3D-QSAR and molecular modeling of HIV-1 integrase inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied on a series of inhibitors of HIV-1 integrase with respect to their inhibition of 3-processing and 3-end joining steps in vitro.The training set consisted of 27 compounds belonging to the class of thiazolothiazepines. The predictive ability of each model was evaluated using test set I consisting of four thiazolothiazepines and test set II comprised of seven compounds belonging to an entirely different structural class of coumarins. Maximum Common Substructure (MCS) based method was used to align the molecules and this was compared with other known methods of alignment. Two methods of 3D QSAR: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were analyzed in terms of their predictive abilities. CoMSIA produced significantly better results for all correlations. The results indicate a strong correlation between the inhibitory activity of these compounds and the steric and electrostatic fields around them. CoMSIA models with considerable internal as well as external predictive ability were obtained. A poor correlation obtained with hydrophobic field indicates that the binding of thiazolothiazepines to HIV-1 integrase is mainly enthalpic in nature. Further the most active compound of the series was docked into the active site using the crystal structure of integrase. The binding site was formed by the amino acid residues 64-67, 116, 148, 151-152, 155-156, and 159. The comparison of coefficient contour maps with the steric and electrostatic properties of the receptor shows high level of compatibility.