Klopman described the chemical reaction of metal ions and base ions in term of softness, E^‡_n and E^‡_m, respectively. By simple modification of known methods, Singh et al. made it applicable for neutral Lewis acids (transition metal salts) and bases (organic molecules) and also extended its application to biological systems for site selectivity and to explain reaction mechanism (markovnikov and anti-markovnikov rule), ligand-receptor interaction of testosterones, estrogens and tetrahydroimidazobenzodiazepinone. In this study effective atomic softness E^‡_n(eff) and E^‡_m(eff), and their change ΔE^‡_nm have been used for site selectivity and polar interaction between 51 peptidic HIV-1 protease inhibitors and receptor amino acids. ΔE^‡_nm values derived from drug-receptor interaction show that when one moiety on receptor behaves as nucleophile (O of valine amino acid) at the same time maximum electrophilic site of the drug (C-atom of the maximum E^‡_n(eff) value) orient itself to come close the respective site and make maximum interaction, while when another moiety on receptor behaves as electrophilic site (C of isoleucine amino acid), at the same time maximum nucleophilic site of the drug (O-atom of the maximum E^‡_m(eff) value) also orient itself to come close the respective site and make maximum interaction.

In this research work, we have applied “Lipinski’s RO5” for pharmacokinetics (PK) study and to predict the activity of peptidic HIV-1 protease inhibitors. Peptidic HIV-1-PRIs have been taken from literature with their observed biological activities (OBAs) in term of IC50. The logarithms of the inverse of IC50 have been used as biological end point o(log1/C) in the study. For calculation of physicochemical parameters, the molecular modeling and geometry optimization of all the derivatives have been carried out with CAChe Pro software using semiempirical PM3 method. Prediction of the biological activity of the inhibitors has shown that the best QSAR model is constructed from pharmacokinetic properties, molecular weight and hydrogen bond acceptor. This also proved that these properties play important role to describe the PKs of the drugs. On the basis of the derived models one can build up a theoretical basis to access the biological activity of the compounds of the same series.

Polychlorinated biphenyls (PCBs) are important class of persist organic pollutants that were used as a component of paints especially in printings, as plastificator of plastics and insulating materials in transformers and capacitors, heat transfer fluids, additives in hydraulic fluids in vacuum and turbine pumps. There is always a need to establish reliable procedures for predicting the bioconcentration potential of chemicals from the knowledge of their molecular structure, or from readily measurable properties of the substance. Hence, correlation and prediction of biococentration factors (BCFs) based on λ_max and vibration frequencies of various bonds viz υ(C-H) and υ(C=C) of biphenyl and its fifty-seven derivatives have been made. For the study, the molecular modeling and geometry optimization of the PCBs have been performed on workspace program of CAChe Pro 5.04 software of Fujitsu using DFT method. UV-visible spectra for each compound were created by electron transition between molecular orbitals as electromagnetic radiation in the visible and ultraviolet (UV-visible) region is absorbed by the molecule. The energies of excited electronic states were computed quantum mechanically. IR spectra of transitions for each compound were created by coordinated motions of the atoms as electromagnetic radiation in the infrared region is absorbed by the molecule. The force necessary to distort the molecule was computed quantum mechanically from its equilibrium geometry and thus frequency of vibrational transitions was predicted. Project Leader Program associated with CAChe has been used for multiple linear regression (MLR) analysis using above spectroscopic data as independent variables and BCFs of PCBs as dependent variables. The reliability of correlation and predicting ability of the MLR equations (models) are judged by R², R²_adj, se, q²_L10O and F values. This study reflected clearly that UV and IR spectroscopic data can be used to predict BCFs of a large number of related compounds within limited time without any difficulty.

When a drug interacts with its receptor, the nonpolar substituent of drug and receptor proteins attract each other because they have opposite magnitude with respect to each other. X-rays structure studies reflected that the S2/S2’ pocket in HIV-1 protease enzyme are essentially hydrophobic. The residues that make up these pockets are Val-32, Ile-47, Ile-50, and Ile-84 in each monomeric polypeptidic unit of the protease enzyme. Δπ_dr and ΔSASA_dr have been used to measure the extent of hydrophobic interaction between peptidic protease inhibitors and receptor proteins (binding site: valine‒isoleucine; and catalytic site: glycine‒aspartic acid‒threonine) on the HIV-1 protease enzyme. For measurement of hydrophobic interaction, the molecular modeling and geometry optimization of all the inhibitors and the receptor amino acids have been carried out with CAChe Pro software by opting semiempirical PM3 methods. Log P was calculated using the atom-typing scheme of Ghose and Crippen, while solvent accessible surface area by conductor likes screening model. π_d, π_r, SASA_Sd and SASA_Sr well describe the hydrophobicities of the substituents and play the effective role for site selectivity for interaction of the drug with the receptor. Comparative study of values of Δπ_dr and ΔSASA_dr show the order of hydrophobic interaction with respect to amino acids: Asp > Thr > Val > Ile and Thr > Val > Asp > Ile, respectively. Further, comparative study of the values of (ΣΔπ_dr)_binding-site, (ΣΔπ_dr)_{catalytic-site}, (ΣΔSASA_dr)_binding-site, (ΣΔSASA_dr)_{catalytic-site} shows that peptidic HIV-1-PRIs interact with binding site rather than catalytic site as binding site have lower value of ΣΔπ_dr and ΣΔSASA_dr. Among the binding site, Val has maximum interaction than Ile, as it has lower vale of Δπ_dr and ΔSASA_dr.