AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Development of Activity-Based Probes for Ubiquitin and Ubiquitin-like Protein Signaling Pathways

Ubiquitin and ubiquitin-like (UBL) proteins regulate a vast variety of cellular functions. Some UBL proteins are present in all cell types, while others are expressed only in certain cells or under certain environmental conditions. This highlights the central role of UBL systems in regulation of ubiquitous as well as specific cellular functions. UBL proteins share little amino acid sequence identity to each other, yet they share similar 3D shapes, which is exemplified by the β-grasp fold. Central to UBL protein signaling pathways are UBL protein-activating E1 enzymes that activate the C-terminus of UBL proteins for subsequent conjugation to the protein substrates. Due to their critical roles in biology, E1 enzymes have been recognized as emerging drug targets to treat human diseases. In spite of their biological significance, however, methods to discover UBL proteins and to monitor the intracellular activity of E1 enzymes are lacking. Thus, there is a critical need for methods to evaluate the intracellular mechanisms of action of E1 enzyme inhibitors. Here we describe the development of a mechanism-based small-molecule probe, <b>ABP1</b>, that can be used to discover and to detect active UBL proteins, and to monitor the intracellular activity of E1 enzymes inside intact cells. The developed probe can also be used to profile the selectivity of E1 enzyme-targeting drugs <i>in vitro</i> and inside intact cells

Catalytically Important Residues of E6AP Ubiquitin Ligase Identified Using Acid-Cleavable Photo-Cross-Linkers

Inactivation of the E6AP E3 ubiquitin ligase (UBE3A gene) causes Angelman syndrome, while aberrant degradation of p53 by E6AP is implicated in cervical cancers. Herein, we describe the development of photo-cross-linkers to discover catalytic residues of E6AP. Using these cross-linkers, we identified covalent modifications of the E6AP catalytic cysteine and two lysines: Lys⁸⁴⁷ and Lys⁷⁹⁹. Lys⁸⁴⁷ is required for the formation of Lys⁴⁸-linked polyubiquitin chains, while the K799A E6AP mutant was more active at producing Lys⁴⁸-linked polyubiquitin chains. Thus, opposing roles of Lys⁷⁹⁹ and Lys⁸⁴⁷ pave the path forward to pharmacological inhibitors or activators of E6AP for therapeutic purposes

(E)-1,5-Diphenylpent-2-en-4-yn-1-one

The title compound, C17H12O, has an E conformation about the C=C bond. The C&#8212;C[triple-bond]C&#8212;C torsion angle is 7.7&#8197;(2)&#176;, and the mean planes of the phenylethylenone [r.m.s. deviation&#160;= 0.059&#8197;(1)&#8197;&#197;] and phenylacetylene [r.m.s. deviation&#160;= 0.023&#8197;(1)&#8197;&#197;] fragments form a dihedral angle of 14.16&#8197;(7)&#176;. In the crystal, weak C&#8212;H...O interactions link the molecules into zigzag chains propagated in [010]

Effect of Compactin on the Mycotoxin Production and Expression of Related Biosynthetic and Regulatory Genes in Toxigenic Fusarium culmorum

Zearalenone (ZEN) and deoxynivalenol (DON) are mycotoxins produced by various species of Fusarium fungi. They contaminate agricultural products and negatively influence human and animal health, thus representing a serious problem of the agricultural industry. Earlier we showed that compactin, a secondary metabolite of Penicillium citrinum, is able to completely suppress the aflatoxin B1 biosynthesis by Aspergillus flavus. Using the F. culmorum strain FC-19 able to produce DON and ZEN, we demonstrated that compactin also significantly suppressed both DON (99.3%) and ZEN (100%) biosynthesis. The possible mechanisms of this suppression were elucidated by qPCR-based analysis of expression levels of 48 biosynthetic and regulatory genes. Expression of eight of 13 TRI genes, including TRI4, TRI5, and TRI101, was completely suppressed. A significant down-regulation was revealed for the TRI10, TRI9, and TRI14 genes. TRI15 was the only up-regulated gene from the TRI cluster. In the case of the ZEN cluster, almost complete suppression was observed for PKS4, PKS13, and ZEB1 genes, and the balance between two ZEB2 isoforms was altered. Among regulatory genes, an increased expression of GPA1 and GPA2 genes encoding &alpha;- and &beta;-subunits of a G-protein was shown, whereas eight genes were down-regulated. The obtained results suggest that the main pathway for a compactin-related inhibition of the DON and ZEN biosynthesis affects the transcription of genes involved in the G-protein-cAMP-PKA signaling pathway. The revealed gene expression data may provide a better understanding of genetic mechanisms underlying mycotoxin production and its regulation

A Fragment-Based Method to Discover Irreversible Covalent Inhibitors of Cysteine Proteases

A novel fragment-based drug discovery approach is reported which irreversibly tethers drug-like fragments to catalytic cysteines. We attached an electrophile to 100 fragments without significant alterations in the reactivity of the electrophile. A mass spectrometry assay discovered three nonpeptidic inhibitors of the cysteine protease papain. The identified compounds display the characteristics of irreversible inhibitors. The irreversible tethering system also displays specificity: the three identified papain inhibitors did not covalently react with UbcH7, USP08, or GST-tagged human rhinovirus 3C protease

6-(4-Chlorophenyl)-3-methylimidazo[2,1-b]thiazole

In the title compound, C12H9ClN2S, the imidazo[2,1-b]thiazole fragment is planar (r.m.s. deviation = 0.003&#8197;&#197;), and the benzene ring is twisted slightly [by 5.65&#8197;(6)&#176;] relative to this moiety. In the crystal, molecules are linked by &#960;&#8211;&#960; stacking interactions into columns along [010]. The molecules within the columns are arranged alternatively by their planar rotation of 180&#176;. Thus, in the columns, there are the two types of &#960;&#8211;&#960; stacking interactions, namely, (i) between two imidazo[2,1-b]thiazole fragments [interplanar distance = 3.351&#8197;(2)&#8197;&#197;] and (ii) between an imidazo[2,1-b]thiazole fragment and the phenyl ring [interplanar distance = 3.410&#8197;(5)&#8197;&#197;]. There are no short contacts between the columns

3-Bromo-2-[4-(methylsulfanyl)phenyl]-5,6,7,8-tetrahydro-1,3-benzothiazolo[3,2-a]imidazole

In the title molecule, C16H15BrN2S2, the central imidazo[2,1-b]thiazole fragment is almost planar (r.m.s. deviation = 0.012 Å), and the fused 5,6,7,8-tetrahydrobenzene ring adopts an unsymmetrical half-chair conformation. The dihedral angle between the imidazo[2,1-b]thiazole and benzene planes is 18.25 (4)°. The terminal methylsulfanyl substituent lies practically within the benzene plane [the dihedral angle between the corresponding planes is 7.20 (10)°] and is turned toward the C—Br bond. In the crystal, molecules form infinite chains along [100] via secondary Br...N interactions [3.1861 (16) Å]. The chains are arranged at van der Waals distances

7-Nitro-2-phenylimidazo[2,1-b][1,3]benzothiazole

In the title molecule, C15H9N3O2S, the central imidazo[2,1-b][1,3]benzothiazole heterotricyclic unit is essentially planar (r.m.s. deviation = 0.021 Å). The terminal phenyl ring and nitro group are twisted by 9.06 (1) and 11.02 (4)°, respectively, from the mean plane of the heterotricycle. In the crystal, molecules are linked by π–π stacking interactions into columns along [100]; the interplanar distance between neighboring imidazo[2,1-b][1,3]benzothiazole planes within the columns is 3.370 (2) Å. Furthermore, the columns interact with each other by secondary S...O [2.9922 (10) and 3.1988 (11) Å] interactions, forming a three-dimensional framework