International Journal of Molecular Sciences

302 KiB

Open AccessArticle

Total and Local Quadratic Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”. Application to Prediction of Caco-2 Permeability of Drugs

by Yovani Marrero Ponce, Miguel Angel Cabrera Pérez, Vicente Romero Zaldivar, Ernest Ofori and Luis A. Montero

Int. J. Mol. Sci. 2003, 4(8), 512-536; https://doi.org/10.3390/i4080512 - 30 Aug 2003

Cited by 60 | Viewed by 8031

Abstract

The high interest in the prediction of the intestinal absorption for New Chemical Entities (NCEs) is generated by the increasing rate in the synthesis of compounds by combinatorial chemistry and the extensive cost of the traditional evaluation methods. Quantitative Structure–Permeability Relationships (QSPerR) of the intestinal permeability across the Caco-2 cells monolayer (P_Caco-2) could be obtained by the application of new molecular descriptors. In this sense, quadratic indices of the “molecular pseudograph’s atom adjacency matrix” and multiple linear regression analysis were used to obtain good quantitative models to determine the P_Caco-2. QSPerR models found are significant from a statistical point of view. The total and local quadratic indices were calculated with the TOMO-COMD software. A leave-one-out cross-validation procedure (internal validation) and the evaluation of external test set of 20 drugs (external validation) revealed that regression models had a good predictive power. A comparison with results derived from other theoretical studies shown a quite satisfactory behavior of the present method. The descriptors included in the prediction models permitted the interpretation in structural terms of the permeability process, evidencing the main role of H-bonding and size properties. The models found were used in virtual screening of drug intestinal permeability and a relationship between P_Caco-2 calculated and percentage of human intestinal absorption for the 72 compounds was established. These results suggest that the proposed method is able to predict P_Caco-2, being a good tool for screening of P_Caco-2 for large sets of NCEs synthesized via combinatorial chemistry approach. Full article

► Show Figures

Figure 1

183 KiB

Open AccessArticle

Modelling of Octahedral Manganese II Complexes with Inorganic Ligands: A Problem with Spin-States

by Bartosz Trzaskowski, Andrzej Les and Ludwik Adamowicz

Int. J. Mol. Sci. 2003, 4(8), 503-511; https://doi.org/10.3390/i4080503 - 30 Aug 2003

Cited by 19 | Viewed by 10964

Abstract

Quantum mechanical ab initio UHF, MP2, MC-SCF and DFT calculations with moderate Gaussian basis sets were performed for MnX₆, X = H₂O, F-, CN-, manganese octahedral complexes. The correct spin-state of the complexes was obtained only when the counter [...] Read more.

► Show Figures

Figure 1

532 KiB

Open AccessArticle

Structure, Stability and Interaction Studies on Nucleotide Analogue Systems

by P. Kolandaivel and R. Kanakaraju

Int. J. Mol. Sci. 2003, 4(8), 486-502; https://doi.org/10.3390/i4080486 - 30 Aug 2003

Cited by 6 | Viewed by 8719

Abstract

Most of the biological molecules have a good interaction with water molecules. The hydrogen bonding interactions with the structural analogues of nucleic acid phosphate group namely dimethyl phosphate anion (DMP) and diethyl phosphate anion (DEP) are studied employing the ab initio and density functional theory methods. Inspections have been made to locate the reactive sites for the interactions of isomeric forms of mono, di and tri hydrates of alkyl phosphate anion using the above theories. It reveals, water molecules have a very strong interaction with the phosphate group in both the molecules and their interactions induce the changes in the structural parameters of the PO₄ group for both the DMP and DEP anions. The optimized structural parameters, total energy, dipole moment and rotational constants are calculated and are compared with the available experimental values. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed the conformational stability of these complexes. Full article

► Show Figures

Figure 1

Journal Menu

Journal Browser

Int. J. Mol. Sci., Volume 4, Issue 8 (August-September 2003) – 3 articles , Pages 486-536

Further Information

Guidelines

MDPI Initiatives

Follow MDPI