Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE) approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-)automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.     

Associative memory with dynamic synapses

We have examined a role of dynamic synapses in the stochastic Hopfield-like network behavior. Our results demonstrate an appearance of a novel phase characterized by quick transitions from one memory state to another. The network is able to retrieve memorized patterns corresponding to classical ferromagnetic states but switches between memorized patterns with an intermittent type of behavior. This phenomenon might reflect the flexibility of real neural systems and their readiness to receive and respond to novel and changing external stimuli.     

Aggressive behaviors in adult SF-1 knockout mice that are not exposed to gonadal steroids during development.

Sex hormones are a major factor responsible for the development of sex differences. Steroidogenic factor 1 (SF-1) is a key regulator of gonadal and adrenal development, and SF-1 knockout mice (SF-1 KO) are born without gonads and adrenal glands. Consequently, these mice are not exposed to gonadal sex steroids. SF-1 KO pups die shortly after birth due to adrenal deficiency. In the present study, SF-1 KO mice were rescued by neonatal corticosteroid injections followed by adrenal transplantations on day 7-8 postnatally. Control mice received corticosteroid injections and were gonadectomized prior to puberty. Mice were observed interacting with ovariectomized hormone primed females and gonad-intact males. In the absence of sex steroid replacement, adult SF-1 KO mice were significantly more aggressive than control mice in tests with stimulus females. After testosterone treatment, control males displayed significantly more aggression towards male intruders than control female mice, or male and female SF-1 KO mice, suggesting a developmental role of gonadal hormones in the expression of aggressive behavior and affirming SF-1 KO mice as a behavioral model to investigate affects of fetal gonad deficiency. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Coincidence detection with dynamic synapses

Recent experimental findings show that the efficacy of transmission in cortical synapses depends on presynaptic activity. In most neural models, however, the synapses are regarded as static entities where this dependence is not included. We study the role of activity-dependent (dynamic) synapses in neuronal responses to temporal patterns of afferent activity. Our results demonstrate that, for suitably chosen threshold values, dynamic synapses are capable of coincidence detection (CD) over a much larger range of frequencies than static synapses. The phenomenon appears to be valid for an integrate-and-fire as well as a Hodgkin-Huxley neuron and various types of CD tasks.     

Realization of the Temperature Scale in the Range from 234.3 K (Hg Triple Point) to 1084.62°C (Cu Freezing Point) in Croatia

This article describes the realization of the International Temperature Scale in the range from 234.3 K (mercury triple point) to 1084.62°C (copper freezing point) at the Laboratory for Process Measurement (LPM), Faculty of Mechanical Engineering and Naval Architecture (FSB), University of Zagreb. The system for the realization of the ITS-90 consists of the sealed fixed-point cells (mercury triple point, water triple point and gallium melting point) and the apparatus designed for the optimal realization of open fixed-point cells which include the gallium melting point, tin freezing point, zinc freezing point, aluminum freezing point, and copper freezing point. The maintenance of the open fixed-point cells is described, including the system for filling the cells with pure argon and for maintaining the pressure during the realization.     

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs), in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE) approach to compute CYP binding affinities from molecular dynamics (MD) simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results ofMDruns starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs.     

Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers: a comparative molecular dynamics study

The disaccharide α,α-trehalose (TRH) is known for its bioprotective action in organisms subject to stressful environmental conditions. However, the mechanisms whereby TRH stabilizes biomolecules remains matter of debate, the five main hypotheses being the water replacement (WRH), headgroup bridging (HBH), vitrification (VIH), water entrapment (WEH) and hydration forces (HFH) hypotheses. Four hypotheses (all except HFH) are in principle compatible with a preferential affinity of the sugar molecules (compared to water) for the biomolecular surface. According to the recently proposed sugar-like mechanism (Pereira and Hünenberger), preferential affinity would result from the entropy gain upon releasing many water molecules from the surface region to the bulk, at the cost of immobilizing and rigidifying fewer sugar molecules. Thus, a more flexible disaccharide such as gentiobiose (GNT) should evidence a weaker preferential affinity, limiting its bioprotective ability. In this work, molecular dynamics (MD) simulations of a dipalmitoyl-phosphatidylcholine (DPPC) bilayer patch in the presence of either pure water or aqueous solutions of GNT or TRH are performed in order to assess the validity of this suggestion. At 475 K and 1.6 m (molal), TRH indeed preserves the bilayer structure to a larger extent compared to GNT. However, the present investigation does not unambiguously indicate which of the above mechanism takes place, since the simulations reveal characteristic features of all of them. This suggests either that multiple mechanisms may be simultaneously active or that their definitions are not precise enough.     

BMP3 Affects Cortical and Trabecular Long Bone Development in Mice

Bone morphogenetic proteins (BMPs) have a major role in tissue development. BMP3 is synthesized in osteocytes and mature osteoblasts and has an antagonistic effect on other BMPs in bone tissue. The main aim of this study was to fully characterize cortical bone and trabecular bone of long bones in both male and female Bmp3^−/− mice. To investigate the effect of Bmp3 from birth to maturity, we compared Bmp3^−/− mice with wild-type littermates at the following stages of postnatal development: 1 day (P0), 2 weeks (P14), 8 weeks and 16 weeks of age. Bmp3 deletion was confirmed using X-gal staining in P0 animals. Cartilage and bone tissue were examined in P14 animals using Alcian Blue/Alizarin Red staining. Detailed long bone analysis was performed in 8-week-old and 16-week-old animals using micro-CT. The Bmp3 reporter signal was localized in bone tissue, hair follicles, and lungs. Bone mineralization at 2 weeks of age was increased in long bones of Bmp3^−/− mice. Bmp3 deletion was shown to affect the skeleton until adulthood, where increased cortical and trabecular bone parameters were found in young and adult mice of both sexes, while delayed mineralization of the epiphyseal growth plate was found in adult Bmp3^−/− mice.