Carbohydrate-derived amphiphilic macromolecules: a biophysical structural characterization and analysis of binding behaviors to model membranes.

The design and synthesis of enhanced membrane-intercalating biomaterials for drug delivery or vascular membrane targeting is currently challenged by the lack of screening and prediction tools. The present work demonstrates the generation of a Quantitative Structural Activity Relationship model (QSAR) to make a priori predictions. Amphiphilic macromolecules (AMs) "stealth lipids" built on aldaric and uronic acids frameworks attached to poly(ethylene glycol) (PEG) polymer tails were developed to form self-assembling micelles. In the present study, a defined set of novel AM structures were investigated in terms of their binding to lipid membrane bilayers using Quartz Crystal Microbalance with Dissipation (QCM-D) experiments coupled with computational coarse-grained molecular dynamics (CG MD) and all-atom MD (AA MD) simulations. The CG MD simulations capture the insertion dynamics of the AM lipophilic backbones into the lipid bilayer with the PEGylated tail directed into bulk water. QCM-D measurements with Voigt viscoelastic model analysis enabled the quantitation of the mass gain and rate of interaction between the AM and the lipid bilayer surface. Thus, this study yielded insights about variations in the functional activity of AM materials with minute compositional or stereochemical differences based on membrane binding, which has translational potential for transplanting these materials in vivo. More broadly, it demonstrates an integrated computational-experimental approach, which can offer a promising strategy for the in silico design and screening of therapeutic candidate materials

Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships III: Modeling hydrophobic interactions

In an earlier article 8 the need was demonstrated for atomic physicochemical properties for three dimensional structure directed quantitative structure-activity relationships, and it was shown how atomic parameters can be developed for successfully evaluating the molecular octanol-water partition coefficient, which is a measure of hydrophobicity. In this work we report more refined atomic values of octanol-water partition coefficients derived from nearly twice the number of compounds. Carbon, hydrogen, oxygen, nitrogen, sulfur and halogens are divided into 110 atom types of which 94 atomic values are evaluated from 830 molecules by least squares. These values gave a standard deviation of 0.470 and a correlation coefficient of 0.931. These parameters predicted the octanol-water partition coefficient of 125 compounds with a standard deviation of 0.520 and a correlation coefficient of 0.870. There is only a correlation coefficient of 0.432 between the atomic octanol-water partition coefficients and the atomic contributions to molar refractivity over the 93 atom types used for both the properties. This suggests that both parameters can be used simultaneously to model intermolecular interactions. We evaluated the CNDO/2 gross atomic charge distribution over several molecules to check the validity of our classification. We found that the charge density on the heteroatoms in conjugated systems is strongly affected by the presence of similar atoms in the conjugation which suggests it should be incorporated as a separate parameter in evaluating the partition coefficient.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38278/1/540090111_ftp.pd

Estimating the Octanol/Water Partition Coefficient for Aliphatic Organic Compounds Using Semi-Empirical Electrotopological Index

A new possibility for estimating the octanol/water coefficient (log P) was investigated using only one descriptor, the semi-empirical electrotopological index (ISET). The predictability of four octanol/water partition coefficient (log P) calculation models was compared using a set of 131 aliphatic organic compounds from five different classes. Log P values were calculated employing atomic-contribution methods, as in the Ghose/Crippen approach and its later refinement, AlogP; using fragmental methods through the ClogP method; and employing an approach considering the whole molecule using topological indices with the MlogP method. The efficiency and the applicability of the ISET in terms of calculating log P were demonstrated through good statistical quality (r > 0.99; s < 0.18), high internal stability and good predictive ability for an external group of compounds in the same order as the widely used models based on the fragmental method, ClogP, and the atomic contribution method, AlogP, which are among the most used methods of predicting log P

Relationship Between Physicochemical Properties and Herbicidal Activity of 1,2,5-Oxadiazole N-Oxide Derivatives

The relationship between the herbicidal activity of a number of novel 1,2,5-oxadiazole N-oxides and some physicochemical properties potentially related with this bioactivity, such as polarity, molecular volume, proton acceptor ability, lipophilicity, and reduction potential were studied. The semiempirical molecular orbital method AM1 was used to calculate theoretical descriptors such as dipolar moment, molecular volume, Mulliken´s charge and the octanol/water partition coefficients (log Po/w). The values of the reduction potentials (Er) were obtained by cyclic voltammetry. In addition, the retention factors (log k’w) on a reversed-phase high-performance liquid chromatography (RP-HPLC) column in pure aqueous mobile phases were measured for several N-oxide derivatives. The log k’w values show good correlation with the calculated values of log Po/w, showing that the chromatographic parameter can be used as lipophilicity descriptor for these compounds. The multiple regression analysis between the descriptors for the N-oxide derivatives and the herbicide activity indicate that the variance in the biological activity can be explained by changes in the lipophilicity and in the reduction potential.Fil: Fernandez, Luciana Andrea. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Tecnologías Energéticas y Materiales Avanzados; ArgentinaFil: Santo, Marisa Rosana. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; ArgentinaFil: Reta, Mario Roberto. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Giacomelli, Liliana. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; ArgentinaFil: Cattana, Rosa Irene. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; ArgentinaFil: Silber, Juana. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; ArgentinaFil: Risso, Mariela. Universidad de la República; UruguayFil: Cerecetto, Hugo. Universidad de la República; UruguayFil: Gonzalez, Mercedes. Universidad de la República; UruguayFil: Olea-Azar, Claudio. Universidad de Chile; Chil

Lipophilicity in drug design: an overview of lipophilicity descriptors in 3D-QSAR studies

The pharmacophore concept is a fundamental cornerstone in drug discovery, playing a critical role in determining the success of in silico techniques, such as virtual screening and 3D-QSAR studies. The reliability of these approaches is influenced by the quality of the physicochemical descriptors used to characterize the chemical entities. In this context, a pivotal role is exerted by lipophilicity, which is a major contribution to host-guest interaction and ligand binding affinity. Several approaches have been undertaken to account for the descriptive and predictive capabilities of lipophilicity in 3D-QSAR modeling. Recent efforts encode the use of quantum mechanical-based descriptors derived from continuum solvation models, which open novel avenues for gaining insight into structure-activity relationships studies

Molecular Modeling on Structure-Function Analysis of Human Progesterone Receptor Modulators

Considering the significance of progesterone receptor (PR) modulators, the present study is explored to envisage the biophoric signals for binding to selective PR subtype-A using ligand-based quantitative structure activity relationship (QSAR) and pharmacophore space modeling studies on nonsteroidal substituted quinoline and cyclocymopol monomethyl ether derivatives. Consensus QSAR models (Training set (Tr): nTr=100, R2pred=0.702; test set (Ts): nTs=30, R2pred=0.705, R2m=0.635; validation set (Vs): nVs=40, R2pred=0.715, R2m=0.680) suggest that molecular topology, atomic polarizability and electronegativity, atomic mass and van der Waals volume of the ligands have influence on the presence of functional atoms (F, Cl, N and O) and consequently contribute significant relations on ligand binding affinity. Receptor independent space modeling study (Tr: nTr=26, Q2=0.927; Ts: nTs=60, R2pred=0.613, R2m=0.545; Vs: nVs=84, R2pred=0.611, R2m=0.507) indicates the importance of aromatic ring, hydrogen bond donor, molecular hydrophobicity and steric influence for receptor binding. The structure-function characterization is adjudged with the receptor-based docking study, explaining the significance of the mapped molecular attributes for ligand-receptor interaction in the catalytic cleft of PR-A

VASCo: computation and visualization of annotated protein surface contacts

<p>Abstract</p> <p>Background</p> <p>Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions.</p> <p>Results</p> <p>VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in.</p> <p>Conclusion</p> <p>VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.</p

Molecular docking studies of curcumin derivatives with multiple protein targets for procarcinogen activating enzyme inhibition

Curcumin derivatives which are very potent antioxidant, free radical scavenger and known inhibitor of dioxygenases have been extensively studied to explore their potential utilization in chemoprevention. The main objective of the present work is to perform a docking analysis of curcumin derivatives: Tetrahydrocurcumin (THC), Bisdemethoxy curcumin (BDC). Docking studies of these were performed using GOLD and AutoDock into a few well validated targets of anticancer therapy (COX-2, PhenolsulphoTransferases, Matrix metalloproteinases (MMPs), P450 and TNF-alpha). A good correlation was observed in binding affinity of THC and BDC against the targets indicating these derivatives are potent procarcinogen activating enzyme inhibitors. © 2010 Girija CR, et al

Octanol-water partition coefficients of highly hydrophobic photodynamic therapy drugs: a computational study

Photodynamic therapy is a novel treatment for solid tumorsbased on the selective induction of cell death by the generation of cytotoxic reactive oxygen species within neoplastic tissues. Oxygen photosensitization is promoted as a consequence of the activation (using light) of a photosensitizer, which must reach the desired tissue by cellular transport. Hydrophobicity (expressed as the logarithm of octanol/water partition coefficient, logP), becomes a key factor in these processes. Unfortunately, there is no computational method to unambiguously predict the logP value for high hydrophobic photosensitizers. In this study, a total of 12 computational methods have been tested for predicting the logP value of tetrapyrrolic derivatives. Furthermore, in the attempt to correlate logP with experimental HPLC measurements (log(k’)), validation of the results leads to the proposal of a sigmoidal regression for the two parameters (log(k’) and logP)