Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of nsP2 Cysteine Protease with Antialphavirus Activity.

Despite their widespread impact on human health, there are no approved drugs for combating alphavirus infections. The heterocyclic β-aminomethyl vinyl sulfone RA-0002034 () is a potent irreversible covalent inhibitor of the alphavirus nsP2 cysteine protease with broad-spectrum antiviral activity. Analogs of that varied each of the three regions of the molecule were synthesized to establish structure-activity relationships for the inhibition of (CHIKV) nsP2 protease and viral replication.

Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of nsP2 Cysteine Protease with Anti-alphavirus Activity.

Despite their widespread impact on human health there are no approved drugs for combating alphavirus infections. The heterocyclic β-aminomethyl vinyl sulfone RA-0002034 () is a potent irreversible covalent inhibitor of the alphavirus nsP2 cysteine protease with broad spectrum antiviral activity. Analogs of that varied each of three regions of the molecule were synthesized to establish structure-activity relationships for inhibition of (CHIKV) nsP2 protease and viral replication.

STOPLIGHT: A Hit Scoring Calculator.

We introduce STOPLIGHT, a web portal to assist medicinal chemists in prioritizing hits from screening campaigns and the selection of compounds for optimization. STOPLIGHT incorporates services to assess 6 physiochemical and structural properties, 6 assay liabilities, and 11 pharmacokinetic properties, for any small molecule represented by its SMILES string. We briefly describe each service and illustrate the utility of this portal with a case study.

Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search.

Nearest neighbor-based similarity searching is a common task in chemistry, with notable use cases in drug discovery. Yet, some of the most commonly used approaches for this task still leverage a brute-force approach. In practice this can be computationally costly and overly time-consuming, due in part to the sheer size of modern chemical databases.

Pharmacokinetics Profiler (PhaKinPro): Model Development, Validation, and Implementation as a Web Tool for Triaging Compounds with Undesired Pharmacokinetics Profiles.

Computational models that predict pharmacokinetic properties are critical to deprioritize drug candidates that emerge as hits in high-throughput screening campaigns. We collected, curated, and integrated a database of compounds tested in 12 major end points comprising over 10,000 unique molecules. We then employed these data to build and validate binary quantitative structure-activity relationship (QSAR) models.

Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach.

Unlabelled: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign.

An Improved Metric and Benchmark for Assessing the Performance of Virtual Screening Models.

Structure-based virtual screening (SBVS) is a key workflow in computational drug discovery. SBVS models are assessed by measuring the enrichment of known active molecules over decoys in retrospective screens. However, the standard formula for enrichment cannot estimate model performance on very large libraries.

Synthesis of 5-Benzylamino and 5-Alkylamino-Substituted Pyrimido[4,5-c]quinoline Derivatives as CSNK2A Inhibitors with Antiviral Activity.

A series of 5-benzylamine-substituted pyrimido[4,5-c]quinoline derivatives of the CSNK2A chemical probe SGC-CK2-2 were synthesized with the goal of improving kinase inhibitor cellular potency and antiviral phenotypic activity while maintaining aqueous solubility. Among the range of analogs, those bearing electron-withdrawing ( and ) or donating () substituents on the benzyl ring as well as introduction of non-aromatic groups such as the cyclohexylmethyl () were shown to maintain CSNK2A activity. The CSNK2A activity was also retained with -methylation of SGC-CK2-2, but α-methyl substitution of the benzyl substituent led to a 10-fold reduction in potency.

Changes in Cabernet Sauvignon yield and berry quality as affected by variability in weather conditions in the last two decades in Lebanon.

Cabernet Sauvignon is the most planted cultivar in Lebanese vineyards. This study investigated the variation of its production at two vineyards 'Kanafar' (West Bekaa at 1020 m.a.

BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening.

Deep learning methods that predict protein-ligand binding have recently been used for structure-based virtual screening. Many such models have been trained using protein-ligand complexes with known crystal structures and activities from the PDBBind data set. However, because PDBbind only includes 20K complexes, models typically fail to generalize to new targets, and model performance is on par with models trained with only ligand information.

[Status epilepticus in a pregnant patient with a previously unrecognized POLG-associated disease].

-associated diseases are rare causes of pharmacoresistant epilepsy and status epilepticus, especially in adult patients. Phenotypic and genotypic variability in these conditions causes the complexity of their diagnosis. In the study, we report a case of a 33-year-old female patient who developed recurrent convulsive status epilepticus with focal clonic onset at the week 22/23 of pregnancy.

Enhancement of Polyacrylate Antiscalant Activity during Gypsum Deposit Formation with the Pretreatment of Aqueous Solutions with Spruce Wood Shavings.

Considerable efforts are made worldwide to reduce inorganic scale in reverse osmosis plants, boilers and heat exchangers, evaporators, industrial water systems, geothermal power plants and oilfield applications. These include the development of new environmentally friendly antiscalants and the improvement of conventional ones. The present report is dedicated to the unconventional application of spruce wood shavings in combination with polyacrylate (PAA-F1) in a model case of gypsum scale formation.

HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra-large chemical libraries.

Recent rapid expansion of make-on-demand, purchasable, chemical libraries comprising dozens of billions or even trillions of molecules has challenged the efficient application of traditional structure-based virtual screening methods that rely on molecular docking. We present a novel computational methodology termed HIDDEN GEM (HIt Discovery using Docking ENriched by GEnerative Modeling) that greatly accelerates virtual screening. This workflow uniquely integrates machine learning, generative chemistry, massive chemical similarity searching and molecular docking of small, selected libraries in the beginning and the end of the workflow.

Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server.

In the ligand prediction category of CASP15, the challenge was to predict the positions and conformations of small molecules binding to proteins that were provided as amino acid sequences or as models generated by the AlphaFold2 program. For most targets, we used our template-based ligand docking program ClusPro ligTBM, also implemented as a public server available at https://ligtbm.cluspro.

Mixed, nonclassical behavior in a classic allosteric protein.

Allostery is a major driver of biological processes requiring coordination. Thus, it is one of the most fundamental and remarkable phenomena in nature, and there is motivation to understand and manipulate it to a multitude of ends. Today, it is often described in terms of two phenomenological models proposed more than a half-century ago involving only T(tense) or R(relaxed) conformations.

PLANTAIN: Diffusion-inspired Pose Score Minimization for Fast and Accurate Molecular Docking.

Molecular docking aims to predict the 3D pose of a small molecule in a protein binding site. Traditional docking methods predict ligand poses by minimizing a physics-inspired scoring function. Recently, a diffusion model has been proposed that iteratively refines a ligand pose.

Tyrosinase-Catalyzed Peptide Macrocyclization for mRNA Display.

mRNA display of macrocyclic peptides has proven itself to be a powerful technique to discover high-affinity ligands for a protein target. However, only a limited number of cyclization chemistries are known to be compatible with mRNA display. Tyrosinase is a copper-dependent oxidase that oxidizes tyrosine phenol to an electrophilic -quinone, which is readily attacked by cysteine thiol.

Fluorescent-Tagged Antiscalants-The New Materials for Scale Inhibition Mechanism Studies, Antiscalant Traceability and Antiscaling Efficacy Optimization during CaCO and CaSO·2HO Scale Formation.

Equipment scaling leads to reduced production efficiency in a wide range of industrial applications worldwide. Various antiscaling agents are currently commonly used to mitigate this problem. However, irrespective of their long and successful application in water treatment technologies, little is known about the mechanisms of scale inhibition, particularly the localization of scale inhibitors on scale deposits.

Mechanisms of Phototoxic Effects of Cationic Porphyrins on Human Cells In Vitro.

The toxic effects of four cationic porphyrins on various human cells were studied in vitro. It was found that, under dark conditions, porphyrins are almost nontoxic, while, under the action of light, the toxic effect was observed starting from nanomolar concentrations. At a concentration of 100 nM, porphyrins caused inhibition of metabolism in the MTT test in normal and cancer cells.

Harmonically mode-locked laser pulse accumulation in a self-resonating optical cavity.

Optical enhancement cavities enabling laser pulses to be coherently stacked in free space are used in several applications to enhance accessible optical power. In this study, we develop an optical cavity that accumulates harmonically mode-locked laser pulses with a self-resonating mechanism for X-ray sources based on laser-Compton scattering. In particular, a Fabry-Perot cavity composed of 99% reflectance mirrors maintained the optical resonance in a feedback-free fashion for more than half an hour and automatically resumed the accumulation even if the laser oscillation was suspended.

Degradation of polymer banknotes through handling, and effect on fingermark visualisation.

The surface structure of mint (as-issued) and handled polymer five pounds sterling banknotes was studied by atomic force microscopy and laser scanning confocal microscopy. A total of 1856 fingermarks on mint and handled banknotes from four different issuing banks (Bank of England, Bank of Scotland, Royal Bank of Scotland and Clydesdale Bank) were visualised with Vacuum Metal Deposition (VMD), Cyanoacrylate Fuming (CAF) and, on Clydesdale Bank notes, magnetic fluorescent powder. VMD was significantly more effective in developing fingermarks on handled banknotes, across all the banks studied, although effectiveness varied with issuing bank.

Application and Visualization of Fluorescent-Tagged Antiscalants in Electrodialysis Processing of Aqueous Solutions Prone to Gypsum Scale Deposition.

Membrane scaling is a serious problem in electrodialysis. A widely used technique for controlling scale deposition in water treatment technologies is the application of antiscalants (AS). The present study reports on gypsum scale inhibition in electrodialysis cell by the two novel ASs: fluorescent-tagged bisphosphonate 1-hydroxy-7-(6-methoxy-1,3-dioxo-1Hbenzo[de]isoquinolin-2(3H)-yl)heptane-1,1-diyl-bis(phosphonic acid), HEDP-F and fluorescein-tagged polyacrylate, PAA-F2 (molecular mass 4000 Da) monitored by chronopotentiometry and fluorescent microscopy.

Integrated approach to elucidate metal-implant related adverse outcome pathways.

Exogenous metal particles and ions from implant devices are known to cause severe toxic events with symptoms ranging from adverse local tissue reactions to systemic toxicities, potentially leading to the development of cancers, heart conditions, and neurological disorders. Toxicity mechanisms, also known as Adverse Outcome Pathways (AOPs), that explain these metal-induced toxicities are severely understudied. Therefore, we deployed in silico structure- and knowledge-based approaches to identify proteome-level perturbations caused by metals and pathways that link these events to human diseases.