Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble

Representing the 3D structures of ligands in virtual screenings via multi-conformer ensembles can be computationally intensive, especially for compounds with a large number of rotatable bonds. Thus, reducing the size of multi-conformer databases and the number of query conformers, while simultaneously reproducing the bioactive conformer with good accuracy, is of crucial interest. While clustering and RMSD filtering methods are employed in existing conformer generators, the novelty of this work is the inclusion of a clustering scheme (NMRCLUST) that does not require a user-defined cut-off value. This algorithm simultaneously optimizes the number and the average spread of the clusters. Here we describe and test four inter-dependent approaches for selecting computer-generated conformers, namely: OMEGA, NMRCLUST, RMS filtering and averaged-RMS filtering. The bioactive conformations of 65 selected ligands were extracted from the corresponding protein:ligand complexes from the Protein Data Bank, including eight ligands that adopted dissimilar bound conformations within different receptors. We show that NMRCLUST can be employed to further filter OMEGA-generated conformers while maintaining biological relevance of the ensemble. It was observed that NMRCLUST (containing on average 10 times fewer conformers per compound) performed nearly as well as OMEGA, and both outperformed RMS filtering and averaged-RMS filtering in terms of identifying the bioactive conformations with excellent and good matches (0.5 < RMSD < 1.0 Å). Furthermore, we propose thresholds for OMEGA root-mean square filtering depending on the number of rotors in a compound: 0.8, 1.0 and 1.4 for structures with low (1–4), medium (5–9) and high (10–15) numbers of rotatable bonds, respectively. The protocol employed is general and can be applied to reduce the number of conformers in multi-conformer compound collections and alleviate the complexity of downstream data processing in virtual screening experiments.     

Exploiting automatic on-line renewable molecularly imprinted solid-phase extraction in lab-on-valve format as front end to liquid chromatography: application to the determination of riboflavin in foodstuffs

In the present work, it is proposed, for the first time, an on-line automatic renewable molecularly imprinted solid-phase extraction (MISPE) protocol for sample preparation prior to liquid chromatographic analysis. The automatic microscale procedure was based on the bead injection (BI) concept under the lab-on-valve (LOV) format, using a multisyringe burette as propulsion unit for handling solutions and suspensions. A high precision on handling the suspensions containing irregularly shaped molecularly imprinted polymer (MIP) particles was attained, enabling the use of commercial MIP as renewable sorbent. The features of the proposed BI-LOV manifold also allowed a strict control of the different steps within the extraction protocol, which are essential for promoting selective interactions in the cavities of the MIP. By using this on-line method, it was possible to extract and quantify riboflavin from different foodstuff samples in the range between 0.450 and 5.00 mg L⁻¹ after processing 1,000 μL of sample (infant milk, pig liver extract, and energy drink) without any prior treatment. For milk samples, LOD and LOQ values were 0.05 and 0.17 mg L⁻¹, respectively. The method was successfully applied to the analysis of two certified reference materials (NIST 1846 and BCR 487) with high precision (RSD < 5.5%). Considering the downscale and simplification of the sample preparation protocol and the simultaneous performance of extraction and chromatographic assays, a cost-effective and enhanced throughput (six determinations per hour) methodology for determination of riboflavin in foodstuff samples is deployed here.     

Enantiodivergent synthesis of P-chirogenic phosphines

Several approaches for the enantiodivergent synthesis of P-chirogenic mono- and diphosphines are described, using ephedrine methodology and phosphine borane chemistry. Firstly, both enantiomers of a tertiary phosphine can be obtained starting from the same oxazaphospholidine borane complex, prepared from (+)-ephedrine, when changing the order of addition of the organolithium reagents during the synthetic pathway. The second approach is based on the chlorophosphine boranes, which react with an organolithium reagent, to afford the corresponding phosphines with inversion of configuration. In the case where the chlorophosphine borane reacts with the t-butyl lithium reagent, a metal-halogen exchange occurs to afford the corresponding phosphide borane with retention of the configuration. The reaction of the phosphide borane with an alkyl halide leads to the same phosphine, but with the opposite configuration. Another approach depends on the diastereoselective preparation of the starting oxazaphospholidine borane complex from (?)-ephedrine, which leads according the case, to either one or the other enantiomer of a phosphine. Finally, the synthesis of (R,R)- and (S,S)-1,2-bis(methylphenylphosphino)ethane is also demonstrated using both enantiomers of the P-chirogenic diphosphinite diborane, which simultaneously allows the introduction of alkyl- or aryl substituents on the phosphorus atoms. In summary, these approaches show the great efficiency of the “ephedrine methodology” for the enantiodivergent synthesis of P-chirogenic mono- and diphosphines, and bearing alkyl or aryl substituents.     

A formal [3+3]-annulation-based approach to pancratistatins: total synthesis of (±)-7-deoxy-pancratistatin and its 2-epi and 2,4-diepi analogues

A full account is given for the total synthesis and the cytotoxic activity against the human lung tumoral cell line NCI-H460 of (±)-7-deoxy-pancratistatin and its 2-epi- and 2,4-diepi- unnatural analogues.     

Partial Hydrolysis of Poly(2‐ethyl‐2‐oxazoline) and Potential Implications for Biomedical Applications?

The hydrolysis of PEtOx is studied to evaluate the potential toxicity of partially hydrolyzed polymers that might interfere with its increasing popularity for biomedical applications. The hydrolysis of PEtOx is studied in the presence of digestive enzymes (gastric and intestinal) and at 5.8 M hydrochloric acid as a function of temperature (57, 73, 90, and 100 °C). It is found that PEtOx undergoes negligible hydrolysis at 37 °C and that thermal and solution properties are not altered when up to 10% of the polymer backbone is hydrolyzed. Mucosal irritation and cytotoxicity is also absent up to 10% hydrolysis levels. In conclusion, PEtOx will not decompose at physiological conditions, and partial hydrolysis will not limit its biomedical applications.

     

Haarlet analysis of Lipschitz regularity in metric measure spaces

In this note we shall give a characterization of Lipschitz spaces on spaces of homogeneous type via Haar coefficients.     

Binding of molecular magnesium hydrides to a zirconocene-enyne template

An enyne-zirconium complex stabilizes molecular magnesium hydride (MgH(2) ) and even a molecular hydride, nC(4) H(9) MgH. These systems feature magnesium olefin π?complexation.