Developing novel approaches to improve binding energy estimation and virtual screening: a PARP case study

Poly-(ADP-ribose)-polymerase (PARP) is a promising anti-cancer target as it plays a crucial role in the cellular reparation and survival mechanisms. However, the development of a robust and cost effective experimental technique to screen PARP inhibitors is still a scientific challenge owing to the difficulties in quantitative detection of the enzyme activity. In this work we demonstrate that the computational chemistry tools including molecular docking and scoring can perform on par with the experimental studies in assessing binding constants and in the recovery of active compounds in virtual screening. Using the recently introduced Lead Finder software we were able to dock a set of 142 well characterized PARP inhibitors and obtain a good correlation between the calculated and experimentally measured binding energies with the rmsd of 1.67 kcal mol⁻¹. Additionally, fine-tuning of the energy scaling coefficients within the Lead Finder scoring function has further decreased rmsd to the value of 0.88 kcal mol⁻¹. Moreover, we were able to reproduce the selectivity of ligand binding between the two isoforms of the enzyme-PARP1 and PARP2-suggesting that the Lead Finder software can be used to design isoform-selective inhibitors of PARP. An impressive enrichment was obtained in the virtual screening experiment, in which the mentioned set of PARP inhibitors was mixed with a commercial library of 300,000 compounds. We also demonstrate that the virtual screening performance can be significantly improved by an additional structural filtration of the docked ligand poses through detection of the crucial hydrogen bonding interactions with the enzyme.     

Paternity cues and mating opportunities: what makes fathers good?

Human males provide facultative paternal investment to their offspring; that is, the male care is not necessary for the survival of his offspring. It is expected that the degree of male investment (1) increases with growing paternity certainty, (2) increases when investment increases the survival and later reproductive prospect of offspring and (3) declines when there are opportunities to mate with multiple females. Using a large sample of adult offspring and their fathers (n = 245), we first investigated the role of two factors possibly involved in the assessment of paternity and subsequently regulating the level of paternal investment: (a) father–child facial resemblance and (b) assortative mating for eye colour. Second, because mating opportunities are inversely related to paternal investment, we also investigated how male facial attractiveness (a cue of mate opportunities) correlates with paternal investment. In line with paternal investment theory, male investment positively correlated with offspring facial resemblance. However, paternal investment were neither higher among blue-eyed couples, nor there were preferences of blue-eyed men to marry with blue-eyed women. Moreover, father facial attractiveness was unrelated to paternal investment. These results indicate that resemblance between offspring and their fathers still plays an important role in paternal investment decision later in offspring’s life.