An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

The interactions among associating (macro)molecules are dynamic, which adds to the complexity of molecular recognition. While ligand flexibility is well accounted for in computational drug design, the effective inclusion of receptor flexibility remains an important challenge. The relaxed complex scheme (RCS) is a promising computational methodology that combines the advantages of docking algorithms with dynamic structural information provided by molecular dynamics (MD) simulations, therefore explicitly accounting for the flexibility of both the receptor and the docked ligands. Here, we briefly review the RCS and discuss new extensions and improvements of this methodology in the context of ligand binding to two example targets: kinetoplastid RNA editing ligase 1 and the W191G cavity mutant of cytochrome c peroxidase. The RCS improvements include its extension to virtual screening, more rigorous characterization of local and global binding effects, and methods to improve its computational efficiency by reducing the receptor ensemble to a representative set of configurations. The choice of receptor ensemble, its influence on the predictive power of RCS, and the current limitations for an accurate treatment of the solvent contributions are also briefly discussed. Finally, we outline potential methodological improvements that we anticipate will assist future development. Rommie E. Amaro and Riccardo Baron contributed equally to this work.     

Errors involved in the existing B-term expressions for the longitudinal diffusion in fully porous chromatographic media Part I: computational data in ordered pillar arrays and effective medium theory

Numerically solving the effective diffusion in a simplified representation of a chromatographic bed, it was found that the B-term expressions that have up to now been used in the literature, and which can all be reduced to either Deff=(gamma mDm+k'gamma sDs)/(1+k') or Deff=(gamma meDm+k'Dpart)/(1+k'), can no longer be considered to be unconditionally valid. This could be demonstrated by showing that the simulated diffusion data are in agreement with the mathematically sound effective medium theory (EMT), whereas the B-term expressions used up to now in literature are in conflict with the EMT, a theory that is widely accepted in all other fields of science. It is also shown that the use of the existing B-term expressions can lead to very large measurement errors (up to a 100% and more) for the determination of the stationary phase diffusion coefficient gamma sDs from peak parking experiments. The representation of the B-term diffusion should in the future hence be based on the Deff expressions that can be derived from the EMT. These are physically sound and are also more accurate than the classical B-term expressions used up to now.     

On the 3-dimensional effects in etched chips for high performance liquid chromatography-separations

In an attempt to quantify the potential of photolithographically etched micro-pillar arrays as a perfectly ordered alternative for the packed bed of spheres, the additional band broadening originating from the top and bottom plate has been investigated using computational fluid dynamics simulations. These calculations provide insight in the theoretical expectations that can be made for the experimental work that is currently being conducted by a number of groups. The calculations show that the additional band broadening contribution can be expected to go through a transient regime as a function of the axial distance along the array. In its fully developed regime and in the most relevant velocity range, the top and bottom wall contribution almost doubles the band broadening compared to the band broadening in a perfectly ordered array of non-porous, non-retentive pillars without top and bottom wall. Compared to the band broadening in an array of porous, retentive pillars on the other hand, the top and bottom wall-effect can be expected to become negligible. A simplified, phenomenological model yielding a first principles prediction of both the transient and the steady-state top and bottom wall band broadening as a function of the inter-pillar distance and the pillar height is proposed and shows good qualitative agreement with the exact calculations.     

Characterization of procyanidin B2 oxidation products in an apple juice model solution and confirmation of their presence in apple juice by high-performance liquid chromatography coupled to electrospray ion trap mass spectrometry

Procyanidins (i.e. condensed tannins) are polyphenols commonly found in fruits. During juice and cider making, apple polyphenol oxidase catalyzes the oxidation of caffeoylquinic acid (CQA) into its corresponding o-quinone which further reacts with procyanidins and other polyphenols, leading to the formation of numerous oxidation products. However, the structure and the reaction pathways of these neoformed phenolic compounds are still largely unknown. Experiments were carried out on a model system to gain insights into the chemical processes occurring during the initial steps of fruit processing. Procyanidin B2 was oxidized by caffeoylquinic acid o-quinone (CQAoq) in an apple juice model solution. The reaction products were monitored using high performance liquid chromatography (HPLC) coupled to ultraviolet (UV)-visible and electrospray tandem mass spectrometry (ESI-MS/MS) in the negative mode. Oxidative conversion of procyanidin B2 ([M-H](-) at m/z 577) into procyanidin A2 at m/z 575 was unambiguously confirmed. In addition, several classes of products were characterized by their deprotonated molecules ([M-H](-)) and their MS/MS fragmentation patterns: hetero-dimers (m/z 929) and homo-dimers (m/z 1153 and 705) resulting from dimerization involving procyanidin and CQA molecules; intramolecular addition products at m/z 575, 573, 927, 1151 and 703. Interestingly, no extensive polymerization was observed. Analysis of a cider apple juice enabled comparison with the results obtained on a biosynthetic model solution. However, procyanidin A2 did not accumulate but seemed to be an intermediate in the formation of an end-product at m/z 573 for which two structural hypotheses are given. These structural modifications of native polyphenols as a consequence of oxidation probably have an impact on the organoleptic and nutritional properties of apple juices and other apple-derived foods.     

Modeling the effect of structural changes during dynamic separation processes on MOFs

A model able to describe the effect of structural changes in the adsorbent or adsorbed phase during the dynamic (breakthrough) separation of mixtures on metal-organic frameworks (MOFs) is presented. The methodology is exemplified for a few pertinent case studies: the separation of xylene isomers and ethylbenzene on the flexible MOF MIL-53 and the rigid MOF MIL-47. At low pressures, no preferential adsorption of any component occurs on both MOFs. Contrarily, at higher pressures separation of ethylbenzene (EB) from o-xylene (oX) occurs on MIL-53 as a result of the breathing phenomenon within the MIL-53 structure. The increase in selectivity, starting from the gate-opening pressure, could be modeled by using a pressure-dependent saturation capacity for the most strongly adsorbed component oX. In the separation of m-xylene (mX) from p-xylene (pX) on the rigid MOF MIL-47, separation at higher pressures is a result of preferential stacking of pX. Here, the selectivity increases once the adsorption of pX switches from a single to a double file adsorption. By implementing a loading dependent adsorption constant for pX, the different unconventional breakthrough profiles and the observed selectivity profile on MIL-47 can be simulated. A similar methodology was used for the separation of EB from pX on MIL-47, where the separation is a result from steric constraints imposed onto the adsorption of EB.     

Identification of the Binding Site of Brucella VirB8 Interaction Inhibitors

Secretion systems translocate virulence factors of many bacterial pathogens, enabling their survival inside the host organism. Consequently, inhibition strongly attenuates pathogenicity and can be considered a target for novel antimicrobial drugs. The type IV secretion system (T4SS) of the intracellular pathogen Brucella is a prerequisite for its virulence, and in this work we targeted the interactions of the?essential assembly factor protein, VirB8, using small-molecule inhibitors. High-throughput screening identified several potent and specific inhibitors, and the target-binding site of these inhibitors was identified by X-ray crystallography, in?silico docking, and analysis of the derivates of the inhibitor B8I-2. VirB8 interaction inhibitors bind to a surface groove opposite to the dimerization interface, and by varying the binding-site residues, we were able to determine which residues are required for inhibitor activity. E115 and K182 were found to be especially important, and changes at R114, Y229, and L151 also reduced inhibitor efficiency.     

Solvent-free Michael addition to non-protected 3-(2-nitrovinyl)indole by ultrasound activation

A variety of nucleophiles provided by activated methylenes have been added on 3-(2-nitrovinyl)-1H-indole in very good to excellent yields, under sonication and solvent-free conditions, using solid potassium carbonate or sodium acetate as a base. Direct synthesis avoiding preliminary NH protection is reported and exemplified to 15 molecules.     

Static heterogeneity in metallic glasses and its correlation to physical properties

Glasses exhibit intriguing physical and mechanical properties resulting from their structure. We have investigated metal-glass dynamics using inelastic X-ray scattering and ultrasonic techniques for several Pd-, Pt-, and Zr-based glasses with varying fragility. In some cases we have observed a faster phase velocity at short wavelengths than long wavelengths, or positive dispersion. Here we apply elastic wave scattering theory to suggest that the behavior of acoustic phonons can be understood by considering the presence of intrinsic nanoscale elastic inhomogeneity with a certain correlation length, i.e., “static heterogeneity”. Furthermore, we suggest that such an elastic inhomogeneity could be the origin of many of the interesting physical and mechanical properties of metallic glasses.     

Adenine and RNA in mineral samples. Surface-enhanced Raman spectroscopy (SERS) for picomole detections

Studies on the interactions of biological macromolecules with mineral surfaces are crucial for the detecting biomarkers. But before this can be done for real samples like rocks or sediments, rational methods based on mineral models plus known amounts of nucleic acids must be developed. The methods must be very sensitive, as the amount of bound macromolecule may be very small. Surface-enhanced Raman spectroscopy (SERS) is perfect for detecting picomolar amounts of nucleic acid materials. In this study, the models used were adenine and GAAA hairpin for nucleic acids materials and a clay (montmorillonite) plus colloidal silver (used for SERS detection) for mineral supports. We have shown that OH(-) anions compete with adenine and the adenyl residues in the GAAA loop for adsorption onto nano-sized silver particles in basic medium. The GAAA adenyl moieties are less well adsorbed onto either clay or silver than is adenine. Also, the transfer of either adenine or the RNA hairpin from the clay to the silver aggregates is pH-dependent. Contact between adenine and the montmorillonite also seems to disperse adenine aggregates. The clay could also increase the flexibility of the RNA hairpin so that it is released from the clay at pH 10, and the affinity of its adenyl moieties for the metallic substrate is enhanced.