Grid inhomogeneous solvation theory for cross-solvation in rigid solvents.

Grid Inhomogeneous Solvation Theory (GIST) has proven useful to calculate localized thermodynamic properties of water around a solute. Numerous studies have leveraged this information to enhance structure-based binding predictions. We have recently extended GIST toward chloroform as a solvent to allow the prediction of passive membrane permeability.

Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures.

Hydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explicit solvent.

X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy.

is a Python package used to calculate the entropy of a given distribution, in this case, based on the distribution of dihedral angles. The dihedral entropy facilitates an alignment-independent measure of local protein flexibility. The key feature of our approach is a Gaussian kernel density estimation (KDE) using a plug-in bandwidth selection, which is fully implemented in a C++ backend and parallelized with OpenMP.

pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD.

Susceptibility to endosomal degradation is a decisive contribution to a protein's immunogenicity. It is assumed that the processing kinetics of structured proteins are inherently linked to their probability of local unfolding. In this study, we quantify the impact of endosomal acidification on the conformational stability of the major timothy grass pollen allergen Phl p 6.

Conformational Ensembles of Antibodies Determine Their Hydrophobicity.

A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation propensity of antibodies via precalculated scales for the hydrophobicity or aggregation propensity of single amino acids.

Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding.

Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions of proteins in atomistic detail. However, the accuracy of models derived from simulations inevitably relies on the quality of the underlying force field. Here, we present an evaluation of current non-polarizable and polarizable force fields (AMBER ff14SB, CHARMM 36m, GROMOS 54A7, and Drude 2013) based on the long-standing biophysical challenge of protein folding.

Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin.

Biomolecular recognition between proteins follows complex mechanisms, the understanding of which can substantially advance drug discovery efforts. Here, we track each step of the binding process in atomistic detail with molecular dynamics simulations using trypsin and its inhibitor bovine pancreatic trypsin inhibitor (BPTI) as a model system. We use umbrella sampling to cover a range of unbinding pathways.

Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory.

Reliable information on partition coefficients plays a key role in drug development, as solubility decisively affects bioavailability. In a physicochemical context, the partition coefficient of a solute between two different solvents can be described as a function of solvation free energies. Hence, substantial scientific efforts have been made toward accurate predictions of solvation free energies in various solvents.

Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments.

The relation of surface polarity and conformational preferences is decisive for cell permeability and thus bioavailability of macrocyclic drugs. Here, we employ grid inhomogeneous solvation theory (GIST) to calculate solvation free energies for a series of six macrocycles in water and chloroform as a measure of passive membrane permeability. We perform accelerated molecular dynamics simulations to capture a diverse structural ensemble in water and chloroform, allowing for a direct profiling of solvent-dependent conformational preferences.

Charge Anisotropy of Nitrogen: Where Chemical Intuition Fails.

For more than half a century computer simulations were developed and employed to study ensemble properties of a wide variety of atomic and molecular systems with tremendous success. Nowadays, a selection of force-fields is available that describe the interactions in such systems. A key feature of force-fields is an adequate description of the electrostatic potential (ESP).

Catalytic Site p Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations.

Enzymatic function and activity of proteases is closely controlled by the pH value. The protonation states of titratable residues in the active site react to changes in the pH value, according to their p, and thereby determine the functionality of the enzyme. Knowledge of the titration behavior of these residues is crucial for the development of drugs targeting the active site residues.

Hydration thermodynamics of cytosolic phospholipase A GIVA predict its membrane-associated parts and its highly hydrated binding site.

During biological events, the water molecules associated with the protein are re-oriented to adapt to the new conditions, inducing changes in the system's free energy. The characterization of water structure and thermodynamics may facilitate the prediction of certain biological events, such as the binding of a ligand and the membrane-associated parts of a protein. In this computational study, we calculated the hydration thermodynamics of cytosolic phospholipase A group IV (GIVA cPLA) to study the hydration properties of the protein's surface and binding pocket.

Sodium-induced population shift drives activation of thrombin.

The equilibrium between active E and inactive E* forms of thrombin is assumed to be governed by the allosteric binding of a Na ion. Here we use molecular dynamics simulations and Markov state models to sample transitions between active and inactive states. With these calculations we are able to compare thermodynamic and kinetic properties depending on the presence of Na.

Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces.

Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In substrate binding, but also in structure-based drug design, the thermodynamic properties of water molecules surrounding a given protein are of high interest. One of the main algorithms devised in recent years to quantify thermodynamic properties of water is the grid inhomogeneous solvation theory (GIST), which calculates these features on a grid surrounding the protein.

Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases.

β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies.

CDR-H3 loop ensemble in solution - conformational selection upon antibody binding.

We analyzed pairs of protein-binding, peptide-binding and hapten-binding antibodies crystallized as complex and in the absence of the antigen with and without conformational differences upon binding in the complementarity-determining region (CDR)-H3 loop. Here, we introduce a molecular dynamics-based approach to capture a diverse conformational ensemble of the CDR-H3 loop in solution. The results clearly indicate that the inherently flexible CDR-H3 loop indeed needs to be characterized as a conformational ensemble.

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties.

We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies in three pairs differing substantially in their individual promiscuity respectively specificity. For two pairs of antibodies crystal structures are available in different states of maturation and used as starting structures for the analyses.

Electrostatic recognition in substrate binding to serine proteases.

Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes.

Late-Stage Functionalization of Drug-Like Molecules Using Diversinates.

Late-stage functionalization (LSF) is a powerful method to quickly generate new analogues of a lead structure without resorting to de novo synthesis. We have leveraged Baran Diversinates to carry out late-stage functionalizations on lead structures from internal drug discovery projects and accurately predicted regioselectivities using computational methods. Our functionalization successfully afforded specific regioisomers which were in line with our predictions.

Glucocorticoid agonistic and antagonistic effects of mifepristone and onapristone on thymocyte subset composition and CD26/dipeptidyl peptidase IV activity in infant male rats.

Antiglucocorticoid activities of two antigestagens-antiglucocorticoids (AGs)-mifepristone and onapristone-were tested in hydrocortisone-treated suckling male rats. Hydrocortisone (HC) treatment in vivo resulted in (1) reduction of the relative thymus weight and absolute thymocyte counts; (2) relative decrease of the CD4(+)CD8(+) thymocyte proportion accompanied by an increase of single-positive and double negative thymocyte populations, the latter of which contained large CD3-negative cells expressing a high level of CD26 on their surface; (3) increase of specific dipeptidyl peptidase IV (DPP IV) activity in thymocyte homogenates. Both AGs suppressed the systems (1) and (2) to a comparable extent.

Early and delayed effects of hydrocortisone and onapristone on intestinal brush-border enzymes and their sialylation and on thymus growth in suckling rats.

The antigestagen-antiglucocorticoid onapristone (ZK 98.299) was tested on three glucocorticoid-sensitive systems after hydrocortisone (HC) administration to suckling male rats, by determining onapristone (ZK)-induced inhibition of HC-provoked (1) increase of activities of intestinal brush-border enzymes, (2) desialylation of brush-border components and (3) thymolysis. HC acetate (75 mg/kg body weight (b.

Development of gastrointestinal functions.

Data are summarized about digestion and absorption of carbohydrates, lipids and proteins during mammalian perinatal development including human fetuses. Corresponding with the high fat intake in suckling rats, absorption of triglycerides was found to be approximately 2-3 times higher in suckling than in adult rats. Carnitine contents of the small intestinal mucosa of rats decrease postnatally, reaching adult levels at the time of weaning.

The effect of an anti-glucocorticoid (ZK 98299) on thymus evolution and on hydrocortisone-induced thymolysis, intestinal brush-border enzymes and their desialylation in suckling rats.

1. The action in Onapristone infant male rats displays short-term and delayed effects. 2.

Dipeptidyl peptidase IV in cell proliferation and differentiation.

In this short review we discuss the present knowledge of a dipeptidyl peptidase IV (DPP-IV, EC 3.4.14.

Sialic acid--marker of development and differentiation.

The authors discuss the role of structural diversity of various sialic acids in glycoconjugates, i. e. in glycoproteins and glycolipids of cell membranes and of body fluids under various physiologic and pathologic conditions, as summarized in recent reviews.