Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

Binary-QSAR guided virtual screening of FDA approved drugs and compounds in clinical investigation against SARS-CoV-2 main protease

With the emergence of the new SARS-CoV-2 virus, drug repurposing studies have gained substantial importance. Combined with the efficacy of recent improvements in ligand- and target-based virtual screening approaches, virtual screening has become faster and more productive than ever. In the current study, an FDA library of approved drugs and compounds under clinical investigation were screened for their antiviral activity using the antiviral therapeutic activity binary QSAR model of the MetaCore/MetaDrug platform. Among 6733-compound collection, we found 370 compounds with a normalized therapeutic activity value greater than a cutoff of 0.75. Only these selected compounds were used for molecular docking studies against the SARS-CoV-2 main protease (M^pro). After initial short (10 ns) molecular dynamics (MD) simulations with the top-50 docking scored compounds and following molecular mechanics generalized born surface area (MM/GBSA) calculations, top-10 compounds were subjected to longer (100 ns) MD simulations and end-point MM/GBSA estimations. Our virtual screening protocol yielded Cefuroxime pivoxetil, an ester prodrug of second-generation cephalosporin antibiotic Cefuroxime, as being a considerable molecule for drug repurposing against the SARS-CoV-2 M^pro.

Does the donor–acceptor concept work for designing synthetic metals?

Homopolymers of quinoxaline (QX), benzothiadiazole (BT), benzobisthiadiazole (BBT), thienopyrazine (TP), thienothiadiazole (TT), and thienopyrazinothiadiazole (TTP) and copolymers of these acceptors with thiophene (TH) and pyrrole (PY) were investigated with density functional theory. Theoretical band-gap predictions reproduce experimental data well. For all but six copolymers, band-gap reductions with respect to either homopolymer are obtained. Four of the acceptors, BBT, TP, TT, and TTP, give rise to copolymers with band gaps that are smaller than that of polyacetylene. BBT and TTP copolymers with PY in 1:2 stoichiometry are predicted to be synthetic metals. Band-gap reductions result from upshifts of HOMO energies and much smaller upshifts of LUMO values. The smallest band gaps are predicted with TTP, since changes in LUMO energies upon copolymerization are particularly small. The consequence of the small interactions between LUMO levels of donor and acceptor are vanishingly small conduction bandwidths.