Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness.

Adequate bioavailability is one of the essential properties for an orally administered drug. Lipinski and others have formulated simplified rules in which compounds that satisfy selected physiochemical properties, for example, molecular weight (MW) ≤ 500 or the logarithm of the octanol-water partition coefficient, log P(o/w) < 5, are anticipated to likely have pharmacokinetic properties appropriate for oral administration. However, these schemes do not simultaneously consider the combination of the physiochemical properties, complicating their application in a more automated fashion. To overcome this, we present a novel method to select compounds with a combination of physicochemical properties that maximize bioavailability and druglikeness based on compounds in the World Drug Index database. In the study four properties, MW, log P(o/w), number of hydrogen bond donors, and number of hydrogen acceptors, were combined into a 4-dimensional (4D) histogram, from which a scoring function was defined on the basis of a 4D dependent multivariate Gaussian model. The resulting equation allows for assigning compounds a bioavailability score, termed 4D-BA, such that chemicals with higher 4D-BA scores are more likely to have oral druglike characteristics. The descriptor is validated by applying the function to drugs previously categorized in the Biopharmaceutics Classification System, and examples of application of the descriptor are given in the context of previously published studies targeting heme oxygenase and SHP2 phosphatase. The approach is anticipated to be useful in early lead identification studies in combination with clustering methods to maximize chemical and structural diversity when selecting compounds for biological assays from large database screens. It may also be applied to prioritize synthetically feasible chemical modifications during lead compound optimization.

Substituent effects in sandwich configurations of multiply substituted benzene dimers are not solely governed by electrostatic control.

Noncovalent interactions between pi systems are central to understanding protein folding and the stability of DNA. Considerable controversy exists about whether substituent effects in pi-pi interactions can be understood purely on the basis of electrostatic interactions or whether other effects must be included to understand observed trends. In this work, we show that in general, pi-pi interactions are not governed solely by electrostatic control. We do not observe a linear correlation between the relative interaction energies and the sums of Hammett parameters in the case of multiply substituted face-to-face benzene dimers. Instead, differential dispersion effects can be so large that even molecules with wildly different electrostatic potentials can exhibit similar attractions to benzene.

Models of S/pi interactions in protein structures: comparison of the H2S benzene complex with PDB data.

S/pi interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H(2)S-benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H(2)S-benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems.

Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach.

The proper description of the electric environment of condensed phases is a critical challenge for force field methods. To test and validate the ability of the CHARMM additive force field to describe the electric environment in aqueous solution combined QM/MM calculations have been used to calculate the vibrational Stark effect (VSE). We utilized a first principles methodology using correlated electronic structure techniques to compute the Stark shift between the gas phase and solvent environments and between two different solvent environments of three VSE probes containing acetonitrile or fluorine functionalities which have been well-characterized experimentally. Reasonable agreement with the experimentally determined Stark shifts is obtained when the MM atoms are described by the CHARMM additive force field, though it is essential to employ an anharmonic correction in the frequency calculation. In addition, the electric field created by the solvent is computed along the CN bond and a theoretical Stark tuning rate is determined for acetonitrile and shown to be in satisfactory agreement with experiment.

First principles computation of lattice energies of organic solids: the benzene crystal.

We provide a first-principles methodology to obtain converged results for the lattice energy of crystals of small, neutral organic molecules. In particular, we determine the lattice energy of crystalline benzene using an additive system based on the individual interaction energies of benzene dimers. Enthalpy corrections are estimated so that the lattice energy can be directly compared to the experimentally determined sublimation energy. Our best estimate of the sublimation energy is 49.4 kJ mol(-1), just over the typical experimentally reported values of 43-47 kJ mol(-1). Our results underscore the necessity of using highly correlated electronic structure methods to determine thermodynamic properties within chemical accuracy. The first coordination sphere contributes about 90 % of the total lattice energy, and the second coordination sphere contributes the remaining 10 %. Three-body interactions are determined to be negligible.

Conventional strain energy in dimethyl-substituted cyclobutane and the gem-dimethyl effect.

The gem-dimethyl effect is the acceleration of cyclization by substituents in the chain and is often used in organic synthesis as a ring-closing effect. Calculations on cyclobutane, methylcyclobutane, and 1,1-dimethylcyclobutane are performed. 1,1-Dimethylcyclobutane is a four-membered carbon ring with gem-dimethyl substituents. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, density functional theory (DFT), and second-order perturbation theory (MP2) with two triple-zeta quality basis sets, 6-311G(d,p) and 6-311G+(2df,2pd). Additional single-point calculations are performed using the optimized MP2/6-311G+(2df,2pd) geometries and coupled-cluster theory including single and double excitations and noniterative, linear triple excitations (CCSD(T)). Calculations indicate that 1,1-dimethylcyclobutane is more than 8 kcal mol-1 less strained than cyclobutane, that is, there is at least some thermodynamic component to the gem-dimethyl effect.

Aliphatic C-H/pi interactions: Methane-benzene, methane-phenol, and methane-indole complexes.

Noncovalent C-H/pi interactions are prevalent in biochemistry and are important in molecular recognition. In this work, we present potential energy curves for methane-benzene, methane-phenol, and methane-indole complexes as prototypes for interactions between C-H bonds and the aromatic components of phenylalanine, tyrosine, and tryptophan. Second-order perturbation theory (MP2) is used in conjunction with the aug-cc-pVDZ and aug-cc-pVTZ basis sets to determine the counterpoise-corrected interaction energy for selected complex configurations. Using corrections for higher-order electron correlation determined with coupled-cluster theory through perturbative triples [CCSD(T)] in the aug-cc-pVDZ basis set, we estimate, through an additive approximation, results at the very accurate CCSD(T)/aug-cc-pVTZ level of theory. Symmetry-adapted perturbation theory (SAPT) is employed to determine the physically significant components of the total interaction energy for each complex.

The effect of multiple substituents on sandwich and T-shaped pi-pi interactions.

Sandwich and T-shaped configurations of substituted benzene dimers were studied by second-order perturbation theory to determine how substituents tune pi-pi interactions. Remarkably, multiple substituents have an additive effect on the binding energy of sandwich dimers, except in some cases when substituents are aligned on top of each other. The energetics of substituted T-shaped configurations are more complex, but nevertheless a simple model that accounts for electrostatic and dispersion interactions (and direct contacts between substituents on one ring and hydrogen atoms on the other), provides a good match to the quantum mechanical results. These results provide insight into the manner by which substituents csan be utilized in supramolecular design.