CryptoBench: Cryptic protein-ligand binding sites dataset and benchmark.

Motivation: Structure-based methods for detecting protein-ligand binding sites play a crucial role in various domains, from fundamental research to biomedical applications. However, current prediction methodologies often rely on holo (ligand-bound) protein conformations for training and evaluation, overlooking the significance of the apo (ligand-free) states. This oversight is particularly problematic in the case of cryptic binding sites (CBSs) where holo-based assessment yields unrealistic performance expectations.

4-Oxo-β-lactams as Covalent Inhibitors of the Mitochondrial Intramembrane Protease PARL.

Rhomboid proteases play a variety of physiological roles, but rhomboid protease inhibitors have been mostly developed for the model rhomboid GlpG. In this work, we screened different electrophilic scaffolds against the human mitochondrial rhomboid PARL and found 4-oxo-β-lactams as submicromolar inhibitors. Multifaceted computations suggest explanations for the activity at the molecular scale and provide models of covalently bound complexes.

Photochemical and Collision-Induced Cross-Linking of Lys, Arg, and His to Nitrile Imines in Peptide Conjugate Ions in the Gas Phase.

We report a study of internal covalent cross-linking with photolytically generated diarylnitrile imines of N-terminal arginine, lysine, and histidine residues in peptide conjugates. Conjugates in which a 4-(2-phenyltetrazol-5-yl)benzoyl group was attached to C-terminal lysine, that we call RAAA--K, KAAA--K, and HAAA--K, were ionized by electrospray and subjected to UV photodissociation (UVPD) at 213 nm. UVPD triggered loss of N and proceeded by covalent cross-linking to nitrile imine intermediates that involved the side chains of N-terminal arginine, lysine, and histidine, as well as the peptide amide groups.

Simultaneous treatment with palm-LEAP2(1-14) and feeding high-fat diet attenuates liver lipid metabolism but not obesity: Sign of selective resistance to palm-LEAP2(1-14).

Liver-enriched antimicrobial peptide 2 (LEAP2) is a natural antagonist/inverse agonist of ghrelin receptor GHSR. Its truncated palmitoylated analog palm-LEAP2(1-14) promised anti-obesity properties because it exhibited favourable stability and an acute anorexigenic effect in our previous studies. Here we demonstrate desirable palm-LEAP2(1-14) pharmacokinetics, with significant levels of the peptide persisting in mouse blood 3 hours after its subcutaneous administration.

The zymogenic form of SARS-CoV-2 main protease: A discrete target for drug discovery.

SARS-CoV-2 main protease (M) autocatalytically releases itself out of the viral polyprotein to form a fully active mature dimer in a manner that is not fully understood. Here, we introduce several tools to help elucidate differences between cis (intramolecular) and trans (intermolecular) proteolytic processing and to evaluate inhibition of precursor M. We found that many mutations at the P1 position of the N-terminal autoprocessing site do not block cis autoprocessing but do inhibit trans processing.

The evaluation of DNA-linked inhibitor antibody and AlphaScreen assays for high-throughput screening of compounds targeting the cap-binding domain in influenza a polymerase.

The PB2 subunit of the influenza virus polymerase complex is essential for viral replication, primarily through a mechanism known as cap-snatching. In this process, PB2 binds to the 5' cap structure of host pre-mRNAs, enabling the viral polymerase to hijack the host transcriptional machinery. This binding facilitates the cleavage and integration of the capped RNA fragment into viral mRNA, thereby promoting efficient viral replication.

Prodrugging fungicidal amphotericin B significantly decreases its toxic effects.

Amphotericin B (AmB) is one of the most effective antifungal drugs, with a strong, dose-dependent activity against most Candida and Aspergillus species responsible for life-threatening infections. However, AmB is severely toxic, which hinders its broad use. In this proof-of-concept study, we demonstrate that prodrugging AmB considerably decreases AmB toxicity without affecting its fungicidal activity.

Lipid Demixing Reduces Energy Barriers for High Curvature Vesicle Budding.

Under standard physiological conditions, budding relies on asymmetries, including differences in leaflet composition, area, and osmotic conditions, and involves large curvature changes in nanoscale lipid vesicles. So far, the combined impact of asymmetry and high curvatures on budding has remained unknown. Here, using continuum elastic theory, the budding pathway is detailed under realistic conditions.

CaMKIIα hub ligands are unable to reverse known phenotypes in Angelman syndrome mice.

Angelman Syndrome (AS) is a neurodevelopmental disorder caused by the loss of function of ubiquitin-protein ligase E3A (UBE3A), resulting in marked changes in synaptic plasticity. In AS mice, a dysregulation of Ca/calmodulin-dependent protein kinase II alpha (CaMKIIα) was previously described. This has been convincingly validated through genetic rescue of prominent phenotypes in mouse cross-breeding experiments.

Reduced Radial Electric Quadrupole Moment Function for Diatomic Molecules.

The prospect of constructing global electric quadrupole moment functions (EQMFs) of diatomic molecules by morphing their theoretical approximants within the framework of the reduced radial curve (RRC) approach is explored by performing model calculations for the ground electronic states of H and HF. The reduced quadrupole moment curves probed, constructed for a set of differently accurate theoretical EQMFs, coincide with their best many-parameter analytic counterparts so closely that they can be used as their accurate few-parameter representations. No other such functional representation is available in the literature.

Phytochemical -methyl-L-cysteine sulfoxide from Brassicaceae: a key to health or a poison for bees?

Intensive agricultural practices impact the health and nutrition of pollinators like honey bees (). Rapeseed ( L.) is widely cultivated, providing diverse nutrients and phytochemicals, including -methyl-L-cysteine sulfoxide (SMCSO).

Undescribed and known phenolic acid derivatives with significant antioxidant activity from the Scorzonera parviflora Jacq. roots.

The antioxidant activity of Scorzonera parviflora Jacq. roots were assessed by measuring their ability to scavenge ABTS and DPPH radicals. Bioactivity-guided fractionation was utilized to identify the compound(s) responsible for this activity.

Vicinal Bis(methylene) Heterocyclic Diene in Natural Product Synthesis: A Convergent Biomimetic Total Synthesis of Prunolactone A.

The first total syntheses of the natural isocoumarin prunolactone A with a 6/6/6/6/6 spiropentacyclic skeleton and its unnatural (3')-epimer in 10 and 8 steps, respectively, are reported. The syntheses feature generation of a reactive 3,4-bis(methylene)isocoumarin intermediate, its biomimetic Diels-Alder reactions with the shikimic-acid-derived scytolide and (8)-scytolide, and a Mitsunobu reaction allowing access to scytolide in a stereochemically pure form. Computational support for the selectivity of the Diels-Alder reaction is provided.

Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration.

For drugs to be active they have to reach their targets. Within cells this requires crossing the cell membrane, and then free diffusion, distribution, and availability. Here, we explored the in-cell diffusion rates and distribution of a series of small molecular fluorescent drugs, in comparison to proteins, by microscopy and fluorescence recovery after photobleaching (FRAP).

Topical siRNA therapy of diabetic-like wound healing.

Non-healing wounds are a serious complication in diabetic patients. One of the detrimental factors contributing to limited wound healing is the accumulation of metalloproteinase-9 (MMP-9) in the wound. Selective inhibition of MMP-9 is one of the established therapeutic targets for diabetic wound healing.

Enhancing optical absorbance and accelerating rotational speed in molecular motors through oriented external electric fields.

Accelerating the rotational speed of light-driven molecular motors is among the foremost concerns in molecular machine research, as this speed directly influences the performance of a motor. Controlling the motor's rotation is crucial for practical applications, and using an oriented external electric field (OEEF) represents a feasible method to achieve this objective. We have investigated the impact of an OEEF on the optical and kinetic properties of a novel π-donor/acceptor di-substituted molecular motor, R2,3-(NH2, CHO).

MolAR: Memory-Safe Library for Analysis of MD Simulations Written in Rust.

Transition to the memory safe natively compiled programming languages is a major software development trend in recent years, which eliminates memory-related security exploits, enables a fearless concurrency and parallelization, and drastically improves ergonomics and speed of software development. Modern memory-safe programing languages, such as Rust, are currently not used for developing molecular modeling and simulation software despite such obvious benefits as faster development cycle, better performance and smaller amount of bugs. This work introduces MolAR-the first memory-safe library for analysis of MD simulations written in Rust.

Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

A DNA sequence pattern, or "motif", is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and computational motif discovery algorithm. As a part of the Codebook/GRECO-BIT initiative, here we evaluated at large scale the cross-platform recognition performance of positional weight matrices (PWMs), which remain popular motif models in many practical applications.

Identification of methylation-sensitive human transcription factors using meSMiLE-seq.

Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assayed 284 mostly poorly characterized, putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 72 new DNA binding motifs. To investigate whether some of the 158 TFs for which we did not find motifs preferably bind epigenetically modified DNA (i.

Coordination of transporter, cargo, and membrane properties during non-vesicular lipid transport.

Homeostasis of cellular membranes is maintained by fine-tuning their lipid composition. Yeast lipid transporter Osh6, belonging to the oxysterol-binding protein-related proteins family, was found to participate in the transport of phosphatidylserine (PS). PS synthesized in the endoplasmic reticulum is delivered to the plasma membrane, where it is exchanged for phosphatidylinositol 4-phosphate (PI4P).

Photochemical and Collision-Induced Cross-Linking of Asp, Glu, Asn, and Gln Residues in Peptide-Nitrile Imine Conjugate Ions in the Gas Phase.

Peptide conjugates furnished with a 2,5-diaryltetrazolecarbonyl tag at the C-terminal lysine, which we call peptide--K, were found to undergo efficient cross-linking of Asp, Glu, Asn, and Gln residues to transient nitrile-imine intermediates produced by photodissociation and collision-induced dissociation (CID) of the tetrazole ring in gas-phase ions. UV photodissociation (UVPD) at 213 nm achieved cross-linking conversion yields of 37 and 61% for DAAAK--K and EAAAK--K, respectively. The yields for NAAAK--K and QAAAK--K were 29 and 57%, respectively.

From boom to bloom: synthesis of diazidodifluoromethane, its stability and applicability in the 'click' reaction.

Diazidodifluoromethane was prepared from dibromodifluoromethane, sodium azide and an alkanethiolate initiator. It represents the first example of a diazidomethane that is stable enough to be used in synthesis. The stability of (poly)azidomethanes was explored with calculations.