On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility

Although they are both highly polar liquids, there are a number of compounds, such as many pharmaceuticals, which show vastly different solubilities in methanol compared with water. From theories of the hydrophobic effect, it might be predicted that this enhanced solubility is due to association between drugs and the less polar -CH3 groups on methanol. In this work, detailed analysis on the atomic structural interactions between water, methanol and the small molecule indole – which is a precursor to many drugs and is sparingly soluble in water yet highly soluble in methanol – reveal that indole preferentially interacts with both water and methanol via electrostatic interactions rather than with direction interactions to the –CH3 groups. The presence of methanol hydrogen bonds with p electrons of the benzene ring of indole can explain the increase in solubility of indole in methanol relative to water. In addition, the excess entropy calculations performed here suggest that this solvation is enthalpically rather than entropically driven.Postprint (author's final draft

On the atomic structure of cocaine in solution

Cocaine is an amphiphilic drug which has the ability to cross the blood–brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ~5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Å of cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function.Peer ReviewedPostprint (author's final draft

Outstanding performance of PIM-1 membranes towards the separation of fluorinated refrigerant gases

The recycling of depleted high global warming mixtures of fluorinated gases (F-gases) with close-boiling or azeotropic behavior requires advanced separation processes to obtain effectively the pure components. Herein, several types of PIM-1 membranes were tested for the first time towards the separation of hydrofluorocarbons and hydrofluoroolefins, showing extraordinarily high permeability coefficients for the value-added difluoromethane (R-32), up to 4100 barrer, coupled with high selectivity for the F-gas pairs of interest. Additionally, the solubility of selected F-gases in PIM-1 was measured and fitted to the dual-mode and Guggenheim, Anderson and de Boer sorption models. The separation performance of the standard PIM-1 and a highly branched PIM-1 was examined with the mixture R-410A (containing R-32 and pentafluoroethane R-125) to assess the influence of the membrane topology on the mixed-gas permeation properties over time (physical aging). Considering that the branched PIM-1 membrane was the least impacted by the aging phenomena, it was used to recover high purity R-32 (concentration in the permeate side as high as 98.9 vol % was achieved) from refrigerant gas mixtures R-410A and R-454B (mixture of R-32 and R-1234yf) in continuous long-term experiments. Results showed the great potential of PIM-1 membranes for the separation of R-32 from refrigerant mixtures collected from end-of-life equipment.This research is supported by project PID2019-105827RB-I00 funded by MCIN/AEI/10.13039/501100011033. F.P. and S.V.G.H. acknowledge the support of the Spanish State Research Agency and the Spanish Ministry of Science and Innovation (grants IJC2020-043134-I and PRE2020-093568, respectively). A.B.F and P.M.B acknowledge EPSRC Grant ep/v047078/1 (SynHiSel). P.G. is supported by Grant RYC2019-027060-I funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”

Polar-Graded Multiferroic SrMnO3 Thin Films

Engineering defects and strains in oxides provides a promising route for the quest of thin film materials with coexisting ferroic orders, multiferroics, with efficient magnetoelectric coupling at room temperature. Precise control of the strain gradient would enable custom tailoring of the multiferroic properties but presently remains challenging. Here we explore the existence of a polar-graded state in epitaxially strained antiferromagnetic SrMnO3 thin films, whose polar nature was predicted theoretically and recently demonstrated experimentally. By means of aberration-corrected scanning transmission electron microscopy we map the polar rotation of the ferroelectric polarization with atomic resolution, both far from and near the domain walls, and find flexoelectricity resulting from vertical strain gradients. The origin of this particular strain state is a gradual distribution of oxygen vacancies across the film thickness, according to electron energy loss spectroscopy. Herein we present a chemistry-mediated route to induce polar rotations in oxygen-deficient multiferroic films, resulting in flexoelectric polar rotations and with potentially enhanced piezoelectricity

Incorporating Alternative Polygenic Risk Scores into the BOADICEA Breast Cancer Risk Prediction Model

Polygenic risk; Prediction; Breast cancerRiesgo poligénico; Predicción; Cáncer de mamaRisc poligènic; Predicció; Càncer de mamaBackground: The multifactorial risk prediction model BOADICEA enables identification of women at higher or lower risk of developing breast cancer. BOADICEA models genetic susceptibility in terms of the effects of rare variants in breast cancer susceptibility genes and a polygenic component, decomposed into an unmeasured and a measured component - the polygenic risk score (PRS). The current version was developed using a 313 SNP PRS. Here, we evaluated approaches to incorporating this PRS and alternative PRS in BOADICEA. Methods: The mean, SD, and proportion of the overall polygenic component explained by the PRS (α2) need to be estimated. α was estimated using logistic regression, where the age-specific log-OR is constrained to be a function of the age-dependent polygenic relative risk in BOADICEA; and using a retrospective likelihood (RL) approach that models, in addition, the unmeasured polygenic component. Results: Parameters were computed for 11 PRS, including 6 variations of the 313 SNP PRS used in clinical trials and implementation studies. The logistic regression approach underestimates α⁠, as compared with the RL estimates. The RL α estimates were very close to those obtained by assuming proportionality to the OR per 1 SD, with the constant of proportionality estimated using the 313 SNP PRS. Small variations in the SNPs included in the PRS can lead to large differences in the mean. Conclusions: BOADICEA can be readily adapted to different PRS in a manner that maintains consistency of the model.This work has been supported by grants from Cancer Research UK (PPRPGM-Nov20\100002); the European Union's Horizon 2020 Research and Innovation Programme under grant agreement numbers 633784 (B-CAST) and 634935 (BRIDGES); the PERSPECTIVE I&I project which is funded by the Government of Canada through Genome Canada (#13529) and the Canadian Institutes of Health Research (#155865), the Ministère de l’Économie et de l'Innovation du Québec through Genome Québec, the Quebec Breast Cancer Foundation, the CHU de Quebec Foundation and the Ontario Research Fund; and by the NIHR Cambridge Biomedical Research Centre (BRC-1215–20014). BCAC is funded by the European Union's Horizon 2020 Research and Innovation Programme (grant numbers 634935 and 633784 for BRIDGES and B-CAST respectively), and the PERSPECTIVE I&I project. Additional funding for BCAC is provided via the Confluence project which is funded with intramural funds from the NCI Intramural Research Program, NIH. Genotyping of the OncoArray was funded by the NIH Grant U19 CA148065, and Cancer Research UK Grant C1287/A16563 and the PERSPECTIVE project supported by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research (grant GPH-129344) and, the Ministère de l’Économie, Science et Innovation du Québec through Genome Québec and the PSRSIIRI-701 grant, and the Quebec Breast Cancer Foundation. MT was supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215–20014) and Cancer Research UK C22770/A31523 (International Alliance for Cancer Early Detection programme). The PRISMA study has been funded by Instituto de Salud Carlos III through the project " PI19/01195″ (Co-funded by European Regional Development Fund "A way to make Europe") and it received the institutional support of CERCA Program (Generalitat de Catalunya). The publication costs of this article were defrayed in part by the payment of publication fees. Therefore, and solely to indicate this fact, this article is hereby marked “advertisement” in accordance with 18 USC section 1734

On the structure of prilocaine in aqueous and amphiphilic solutions

The solvation of prilocaine has been investigated in pure water and in an amphiphilic methanol/water solution using a combination of neutron diffraction with isotopic substitution augmented by Empirical Potential Structure Refinement (EPSR) simulations. This combination of techniques allows for details of the solvation structure on the atomic scale to be unravelled. The hydration of prilocaine is significantly altered relative to when this molecule is in pure water (as a hydrochloride salt) or in an amphiphilic environment (as a freebase compound). Interestingly, there is not a significant change in hydration around the amine group on prilocaine hydrochloride compared with prilocaine as a freebase. Despite this group being an ammonium group in water and an amine group in methanol/water solutions, the hydration of this motif remains largely intact. The changes in hydration between prilocaine as a free base and prilocaine·HCl instead appears to arise from a change in hydration around the aromatic ring and the amide group in the prilocaine molecule.Peer ReviewedPostprint (published version

Efficient photochemical synthesis of peptide-α-phenylthioesters

Low yields and substantial epimerization of peptide-α-thioesters often compromise the overall efficiency of native chemical ligation (NCL). Peptide arylthioesters are more reactive than peptide alkylthioesters in NCL, but are also more difficult to handle due to their propensity to hydrolyze, and are therefore often generated in situ. However, pre-prepared peptide arylthioesters are required for some NCL applications. Here we present a 7-nitroindoline-based photochemical method that generates protected peptide phenylthioesters under neutral reaction conditions via their activated esters from photoreactive peptide precursors in high isolated yields, and with low levels of epimerization. This method is fully compatible with Fmoc-strategy solid-phase peptide synthesis. Global deprotection with trifluoroacetic acid furnishes peptide phenylthioesters for NCL. Photoreactive peptide precursors can also be converted into their hydrazides in two steps by this method

The size matters? A computational tool to design bivalent ligands

Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands. Bivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site