Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network.

Covalent drugs exhibit advantages in that noncovalent drugs cannot match, and covalent docking is an important method for screening covalent lead compounds. However, it is difficult for covalent docking to screen covalent compounds on a large scale because covalent docking requires determination of the covalent reaction type of the compound. Here, we propose to use deep learning of a lateral interactions spiking neural network to construct a covalent lead compound screening model to quickly screen covalent lead compounds. We used the 3CL protease (3CL Pro) of SARS-CoV-2 as the screen target and constructed two classification models based on LISNN to predict the covalent binding and inhibitory activity of compounds. The two classification models were trained on the covalent complex data set targeting cysteine (Cys) and the compound inhibitory activity data set targeting 3CL Pro, respected, with good prediction accuracy (ACC > 0.9). We then screened the screening compound library with 6 covalent binding screening models and 12 inhibitory activity screening models. We tested the inhibitory activity of the 32 compounds, and the best compound inhibited SARS-CoV-2 3CL Pro with an IC50 value of 369.5 nM. Further assay implied that dithiothreitol can affect the inhibitory activity of the compound to 3CL Pro, indicating that the compound may covalently bind 3CL Pro. The selectivity test showed that the compound had good target selectivity to 3CL Pro over cathepsin L. These correlation assays can prove the rationality of the covalent lead compound screening model. Finally, covalent docking was performed to demonstrate the binding conformation of the compound with 3CL Pro. The source code can be obtained from the GitHub repository (https://github.com/guzh970630/Screen_Covalent_Compound_by_LISNN).

New Set of Isobaric Labeling Reagents for Quantitative 16Plex Proteomics.

Peptide labeling by isobaric tags is a powerful approach for the relative quantitative analysis of proteomes in multiple groups. There has been a revolution in the innovation of new isobaric reagents; however, great effort is being made to expand simultaneous labeling groups to identify more labeled peptides and reduce reporter ion signal suppression. We redesigned the original chemical structure of the deuterium isobaric amine-reactive tag developed in our laboratory. We optimized the synthetic pathway to create a new set of 16-plex isobaric tags (IBT-16plex). The novel reagent enabled almost complete labeling of peptides within 90 min, with all labeling reporter ions exhibiting comparable MS/MS signals. Compared to a typical 16plex reagent, TMTpro-16plex, the peptides and proteins identified by IBT-16plex in trypsinized HeLa cells were significantly increased by 14.8 and 8.6%, respectively. Moreover, differences in peptide abundance within 10-fold among multiple groups were barely suppressed in IBT-16plex, whereas the dynamic range in TMTpro-16plex-labeled groups was smaller. After quantitative examination of MCF7 cell proteins, IBT-16plex was confirmed as feasible and useful for evaluating protein responses of glucose-starved MCF7 cells to a glucose-rich medium.

Rh(III)-Catalyzed Oxidative C-H Activation/Annulation of Salicylaldehydes with Masked Enynes for the Synthesis of Chromones.

A rhodium(III)-catalyzed oxidative C-H activation/annulation of salicylaldehydes with propargylic acetates has been developed for the regioselective synthesis of 3-vinyl chromones in good yields with broad functional group tolerance. 3-Vinyl chromones were converted into biologically active benzo[c]xanthone by I2-mediated oxidative electrocyclization.

Atroposelective Synthesis of Axially Chiral Styrenes by Platinum- Catalyzed Stereoselective Hydrosilylation of Internal Alkynes.

Hydrofunctionalization of alkynes is one of the most efficient ways to access axially chiral styrenes with open-chained olefins. While great advances have been achieved for 1-alkynylnaphthalen-2-ols and analogues, atroposelective hydrofunctionalization of unactivated internal alkynes lags. Herein we reported a platinum-catalyzed atroposelective hydrosilylation of unactivated internal alkynes for the first time. With monodentate TADDOL-derived phosphonite L1 used as a chiral ligand, various axially chiral styrenes were achieved in excellent enantioselectivities with high E-selectivities. Control experiments showed that the NH-arylamide groups have significant effects on both the yields and enantioselectivities and could act as directing groups. The potential utilities of the products were shown by the transformations of the amide motifs of the products.

Copper-Catalyzed Enantioselective and Regiodivergent Allylation of Ketones with Allenylsilanes.

We report herein a regiodivergent and enantioselective allyl addition to ketones with allenylsilanes through copper catalysis. With the combination of CuOAc, a Josiphos-type bidentate phosphine ligand and PhSiH3 , allyl addition to a variety of ketones furnishes branched products in excellent enantioselectivities. The regioselectivity is completely reversed by employing the P-stereogenic ligand BenzP*, affording the linear products with excellent enantioselectivities and good Z-selectivities. The linear Z-product could be converted to E-product via a catalytic geometric isomerization of the Z-alkene group. The silyl group in the products could provide a handle for downstream elaboration.

Enantioselective Synthesis of Bicyclo[3.2.1]octadienes via Palladium-Catalyzed Intramolecular Alkene-Alkyne Coupling Reaction.

Bicyclo[3.2.1]octadiene compounds and derivatives exist in a number of natural products and bioactive compounds. Nevertheless, catalytic enantioselective protocols for the synthesis of these skeletons have not been disclosed. Herein we reported a palladium-catalyzed asymmetric intramolecular alkene-alkyne coupling of alkyne-tethered cyclopentenes, affording a library of enantionenriched bicyclo[3.2.1]octadienes in excellent yields and enantioselectivities (mostly >99 % ee). Moreover, the products could undergo an unusual iodination-induced 1,2-acyl migration, forming iodinated bicyclo[3.2.1]octadienes with three vicinal stereocenters. The enone and isolated olefin motifs embedded in the products provide useful handles for downstream elaboration.

Pd-Catalyzed Asymmetric 5-exo-trig Cyclization/Cyclopropanation/Carbonylation of 1,6-Enynes for the Construction of Chiral 3-Azabicyclo[3.1.0]hexanes.

We herein disclose a mild and efficient access to chiral 3-azabicyclo[3.1.0]hexanes via a Pd-catalyzed asymmetric 5-exo-trig cyclization/cyclopropanation/carbonylation of 1,6-enynes. Various nucleophiles, such as alcohols, phenols, amines and water, are well compatible with the reaction system. This reaction forms three C-C bonds, two rings, two adjacent quaternary carbon stereocenters as well as one C-O/C-N bond with excellent regio- and enantioselectivities. The products could be further functionalized to generate a library of 3-azabicyclo[3.1.0]hexane frameworks.

Palladium-Catalyzed Asymmetric Sequential Hydroamination of 1,3-Enynes: Enantioselective Syntheses of Chiral Imidazolidinones.

Pd-catalyzed sequential hydroamination of readily available 1,3-enynes is reported. The redox-neutral process provides an efficient route to synthesize a broad scope of imidazolidinones, thiadiazolidines, and imidazolidines. Asymmetric sequential hydroamination generates a series of synthetically valuable, enantioenriched imidazolidinones. Mechanistic studies revealed that the transformation occurred via an intermolecular enyne hydroamination pathway to give an allene intermediate. Subsequent intramolecular hydroamination of the allene intermediate proceeded under the Curtin-Hammett principle to provide enantioenriched imidazolidinone products.

Novel and Potent Acetylcholinesterase Inhibitors for the Treatment of Alzheimer's Disease from Natural (±)-7,8-Dihydroxy-3-methyl-isochroman-4-one.

Alzheimer's disease (AD) is a neurodegenerative disease that causes memory and cognitive decline as well as behavioral problems. It is a progressive and well recognized complex disease; therefore, it is very urgent to develop novel and effective anti-AD drugs. In this study, a series of novel isochroman-4-one derivatives from natural (±)-7,8-dihydroxy-3-methyl-isochroman-4-one [(±)-XJP] were designed and synthesized, and their anti-AD potential was evaluated. Among them, compound 10a [(Z)-3-acetyl-1-benzyl-4-((6,7-dimethoxy-4-oxoisochroman-3-ylidene)methyl)pyridin-1-ium bromide] possessed potent anti-acetylcholinesterase (AChE) activity as well as modest antioxidant activity. Further molecular modeling and kinetic investigations revealed that compound 10a was a dual-binding inhibitor that binds to both catalytic anionic site (CAS) and peripheral anionic site (PAS) of the enzyme AChE. In addition, compound 10a exhibited low cytotoxicity and moderate anti-Aß aggregation efficacy. Moreover, the in silico screening suggested that these compounds could pass across the blood-brain barrier with high penetration. These findings show that compound 10a was a promising lead from a natural product with potent AChE inhibitory activity and deserves to be further developed for the prevention and treatment of AD.

Discovery of trans-3-(pyridin-3-yl)acrylamide-derived sulfamides as potent nicotinamide phosphoribosyltransferase (NAMPT) inhibitors for the potential treatment of cancer.

Nicotinamide phosphoribosyltransferase (NAMPT) has emerged as a promising target for the discovery of anticancer drugs. Based on NAMPT inhibitor FK866 that has been advanced into phase II trial, we identified a trans-3-(pyridin-3-yl)acrylamide compound 13 incorporating with a biarylsulfanilamide moiety as a new NAMPT inhibitor. Further structure-activity relationship (SAR) exploration led to additional biarylsulfanilamide-derived compounds with high in vitro NAMPT inhibitory potency and antiproliferative activity. In particular, compound 23, the most potent NAMPT inhibitor (IC50 = 5.08 nM), showed single-digit nanomolar antiproliferative activity against DU145, Hela, and H1975 cells with IC50 values of 2.90 nM, 2.34 nM, and 2.24 nM, respectively, and even subnanomolar level against K562, MCF-7, and HUH7 cells with IC50 values of 0.46 nM, 0.23 nM and 0.53 nM, respectively. Our findings provided promising lead compounds for the discovery of more potent NAMPT inhibitors as anticancer drugs.