Computational studies of biologically active alkaloids of plant origin: an overview

Computational studies nowadays constitute a crucial source of information for drug development, because they provide information on many molecular properties and also enable predictions of the properties of not-yet-synthesized compounds. Alkaloids are a vast group of natural products exhibiting a variety of biological activities, many of which are interesting for drug development. On the other hand, computational studies of biologically active alkaloids have so far mostly focused on few particularly relevant or “popular” molecules, such as quinine, caffeine, or cocaine, with only few works on the other molecules. The present work offers an overview of existing computational studies on alkaloid molecules, from the earliest ones to the most recent, and considering all the theoretical approaches with which studies have been performed (both quantum mechanics and molecular dynamics). The considered studies are grouped according to their objectives and outcomes, such as conformational analysis of alkaloid molecules, effects of selected solvents on their properties, docking studies aimed at better understanding of the interactions between alkaloid molecules and biological targets, studies focusing on structure activity relationships, and computational studies performed to confirm experimental results. It is concluded that it would be important that computational studies on many other alkaloid molecules are performed and their results made available, covering their different classes as well as the variety of their biological activities, to attain better understanding of the properties not only of individual molecules, but also of groups of related molecules and of the overall alkaloids family.

Conformational properties of chiral tobacco alkaloids by DFT calculations and vibrational circular dichroism: (-)-S-anabasine

A thorough DFT and MM study of the conformational landscape, molecular and electronic structures of (-)-S-anabasine is reported aimed to reveal the mechanism controlling its conformational preference. Although the conformational flexibility and diversity of this system is quite extensive, only two structures are populated both in gas-phase and solution (CCl4 and DMSO). NBO-aided electronic structure analyses performed for the eight conformers representing minima in the potential energy surface of (-)-S-anabasine indicate that both steric and electrostatic factors are determinant in the conformational distribution of the sample in gas phase. Nonetheless, hyperconjugative effects are the key force tipping the balance in the conformational equilibrium between the two main rotamers. Increasing the polarity of the medium (using the IEF-PCM formalism) barely affect the conformational energy profile, although a slight increase in the theoretical population of those structures more affected by electrostatic interactions is predicted. The validity of the theoretical models and calculated conformers populations are endorsed by the accurate reproduction of the IR and VCD spectra (recorded in pure liquid and in CCl4 solution) of the sample (that have been firstly recorded and assigned in the present work) which are consistent with the occurrence of a 2:1 conformational ratio.

Vibrational circular dichroism and theoretical study of the conformational equilibrium in (-)-S-nicotine

We report an extensive study of the molecular and electronic structure of (-)-S-nicotine, to deduce the phenomenon that controls its conformational equilibrium and to solve its solution-state conformer population. Density functional theory, ab initio, and molecular mechanics calculations were used together with vibrational circular dichroism (VCD) and Fourier transform infrared spectroscopies. Calculations and experiments in solution show that the structure and the conformational energy profile of (-)-S-nicotine are not strongly dependent on the medium, thus suggesting that the conformational equilibrium is dominated by hyperconjugative interactions rather than repulsive electronic effects. The analysis of the first recorded VCD spectra of (-)-S-nicotine confirmed the presence of two main conformers at room temperature. Our results provide further evidence of the hypersensitivity of vibrational optical activity spectroscopies to the three-dimensional structure of chiral samples and prove their suitability for the elucidation of solution-state conformer distribution.