Mutations of the androgen receptor (AR) associated with prostate cancer and androgen insensitivity syndrome may profoundly influence its structure, protein interaction network, and binding to chromatin, resulting in altered transcription signatures and drug responses. Current structural information fails to explain the effect of pathological mutations on AR structure–function relationship. Here, we have thoroughly studied the effects of selected mutations that span the complete dimer interface of AR ligand–binding domain (AR-LBD) using x-ray crystallography in combination with in vitro, in silico, and cell-based assays. We show that these variants alter AR-dependent transcription and responses to anti-androgens by inducing a previously undescribed allosteric switch in the AR-LBD that increases exposure of a major methylation target, Arg ⁷⁶¹ . We also corroborate the relevance of residues Arg ⁷⁶¹ and Tyr ⁷⁶⁴ for AR dimerization and function. Together, our results reveal allosteric coupling of AR dimerization and posttranslational modifications as a disease mechanism with implications for precision medicine.

Over 750 million cases of COVID-19, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), have been reported since the onset of the global outbreak. The need for effective treatments has spurred intensive research for therapeutic agents based on pharmaceutical repositioning or natural products. In light of prior studies asserting the bioactivity of natural compounds of the autochthonous Peruvian flora, the present study focuses on the identification SARS-CoV-2 M^pro main protease dimer inhibitors. To this end, a target-based virtual screening was performed over a representative set of Peruvian flora-derived natural compounds. The best poses obtained from the ensemble molecular docking process were selected. These structures were subjected to extensive molecular dynamics steps for the computation of binding free energies along the trajectory and evaluation of the stability of the complexes. The compounds exhibiting the best free energy behaviors were selected for in vitro testing, confirming the inhibitory activity of Hyperoside against M^pro, with a K_i value lower than 20 µM, presumably through allosteric modulation.

The use of small organic molecules has become one of the most popular strategies in computer-aided drug design (CADD) to facilitate the identification of potential drug-like compounds in the early stages of drug development. In this scenario, novel computational approaches such as the use of the fragment dissolved molecular dynamics (fdMD) methodology emerged as a new framework for the modeling of ligand-receptor interactions. Consisting of molecular dynamics (MD) simulations of the target protein solvated with multiple copies of the same fragment, the original approach is able to identify the most favorable binding site for the system studied in a reasonable simulation time scale (0.2-1 μs). In the present work, we have introduced the use of Gaussian accelerated molecular dynamics (GaMD) to facilitate system exploration, accelerate binding site identification and additionally enhance binding mode elucidation. For this purpose, up to 12 different systems with crystallographic information available have been employed for validation.

The development of specific antiviral therapies targeting SARS-CoV-2 remains fundamental because of the continued high incidence of COVID-19 and limited accessibility to antivirals in some countries. In this context, dark chemical matter (DCM), a set of drug-like compounds with outstanding selectivity profiles that have never shown bioactivity despite being extensively assayed, appears to be an excellent starting point for drug development. Accordingly, in this study, we performed a high-throughput screening to identify inhibitors of the SARS-CoV-2 main protease (M^pro) using DCM compounds as ligands. Multiple receptors and two different docking scoring functions were employed to identify the best molecular docking poses. The selected structures were subjected to extensive conventional and Gaussian accelerated molecular dynamics. From the results, four compounds with the best molecular behavior and binding energy were selected for experimental testing, one of which presented inhibitory activity with a K_i value of 48 ± 5 μM. Through virtual screening, we identified a significant starting point for drug development, shedding new light on DCM compounds.

Palytoxin (PLTX) and its analogues from Ostreopsis cf. ovata are significant health concerns. They show potent vasoconstrictive properties, often causing seafood poisoning. PLTX analogues have chiral centers, resulting in many isomers, making their separation by liquid chromatography and identification/characterization by mass spectrometry challenging. This study explores for the first time the ion mobility spectrometry (IMS) behavior of these compounds to address these analytical challenges. Drift tube ion mobility spectrometry (DTIMS) and traveling wave ion mobility spectrometry (TWIMS) were used and compared. Additionally, trapped ion mobility spectrometry (TIMS) and molecular dynamics simulation were employed to explain unexpected results. TIMS provided higher resolution, distinguishing isomeric ions generated in the electrospray source by losing water molecules from different toxin sites. Computational studies offered theoretical insights into the ion mobility of triply charged calcium and sodium adduct ions, suggesting a folded conformation. ^DT CCS _N2 (collisional cross section using DTIMS and nitrogen as buffer gas) values were obtained for PLTX (standard), ovatoxin-a, and ovatoxin-b from microalgae samples in Sant Andreu de Llavaneres (Barcelona, Spain). These values were comparable (ΔCCSs < 2%) to those measured with TWIMS calibrated using PLTX (standard). The study provides 102 CCS values from DTIMS and TWIMS data for adducts and fragment ions of PLTX analogues, which can be used as reference values in databases for toxin screening in complex samples. Graphical Abstract