Structure-Based Design of a Potent and Selective YTHDC1 Ligand.

N6-Adenosine methylation (m6A) is a prevalent post-transcriptional modification of mRNA, with YTHDC1 being the reader protein responsible for recognizing this modification in the cell nucleus. Here, we present a protein structure-based medicinal chemistry campaign that resulted in the YTHDC1 inhibitor 40, which shows an equilibrium dissociation constant (Kd) of 49 nM. The crystal structure of the complex (1.6 Å resolution) validated the design. Compound 40 is selective against the cytoplasmic m6A-RNA readers YTHDF1-3 and YTHDC2 and shows antiproliferative activity against the acute myeloid leukemia (AML) cell lines THP-1, MOLM-13, and NOMO-1. For the series of compounds that culminated into ligand 40, the good correlation between the affinity in the biochemical assay and antiproliferative activity in the THP-1 cell line provides evidence of YTHDC1 target engagement in the cell. The binding to YTHDC1 in the cell is further supported by the cellular thermal shift assay. Thus, ligand 40 is a tool compound for studying the role of YTHDC1 in AML.

Proteolysis Targeting Chimera Degraders of the METTL3-14 m6A-RNA Methyltransferase.

Methylation of adenine N6 (m6A) is the most frequent RNA modification. On mRNA, it is catalyzed by the METTL3-14 heterodimer complex, which plays a key role in acute myeloid leukemia (AML) and other types of blood cancers and solid tumors. Here, we disclose the first proteolysis targeting chimeras (PROTACs) for an epitranscriptomics protein. For designing the PROTACs, we made use of the crystal structure of the complex of METTL3-14 with a potent and selective small-molecule inhibitor (called UZH2). The optimization of the linker started from a desfluoro precursor of UZH2 whose synthesis is more efficient than that of UZH2. The first nine PROTAC molecules featured PEG- or alkyl-based linkers, but only the latter showed cell penetration. With this information in hand, we synthesized 26 PROTACs based on UZH2 and alkyl linkers of different lengths and rigidity. The formation of the ternary complex was validated by a FRET-based biochemical assay and an in vitro ubiquitination assay. The PROTACs 14, 20, 22, 24, and 30, featuring different linker types and lengths, showed 50% or higher degradation of METTL3 and/or METTL14 measured by Western blot in MOLM-13 cells. They also showed substantial degradation on three other AML cell lines and prostate cancer cell line PC3.

Fragment Ligands of the m6A-RNA Reader YTHDF2.

We report 17 small-molecule ligands that compete with N6-methyladenosine (m6A) for binding to the m6A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol-1 per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.

Heteroaryl sulfonamide synthesis: scope and limitations.

Heteroaryl sulfonamides are important structural motifs in the medicinal and agrochemical industries. However, their synthesis often relies on the use of heteroaryl sulfonyl chlorides, which are unstable and toxic reagents. Herein, we report a protocol that allows direct oxidative coupling of heteroaryl thiols and primary amines, readily available and inexpensive commodity chemicals. The transformation proceeds under mild reaction conditions and yields the desired N-alkylated sulfonamides in good yields. N-alkyl heteroaryl sulfonamides can be further transformed using a microwave-promoted Fukuyama-Mitsunobu reaction to N,N-dialkyl heteroaryl sulfonamides. The developed protocols thus enable the preparation of previously difficult to prepare sulfonamides (toxic reagents, harsh conditions, and low yields) under mild conditions.

Unified Approach to Benzo[d]thiazol-2-yl-Sulfonamides.

In this paper, we report a unified approach to N-substituted and N,N-disubstituted benzothiazole (BT) sulfonamides. Our approach to BT-sulfonamides starts from simple commercially available building blocks (benzo[d]thiazole-2-thiol and primary and secondary amines) that are connected via (a) a S oxidation/S-N coupling approach, (b) a S-N coupling/S-oxidation sequence, or via (c) a S-oxidation/S-F bond formation/SuFEx approach. The labile N-H bond in N-monoalkylated BT-sulfonamides (pKa (BTSO2N(H)Bn) = 3.34 ± 0.05) further allowed us to develop a simple weak base-promoted N-alkylation method and a stereoselective microwave-promoted Fukuyama-Mitsunobu reaction. N-Alkyl-N-aryl BT-sulfonamides were accessed with the help of the Chan-Lam coupling reaction. Developed methods were further used in stereo and chemoselective transformations of podophyllotoxin and several amino alcohols.

Trisubstituted Highly Activated Benzo[d]thiazol-2-yl-sulfone-Containing Olefins as Building Blocks in Organic Synthesis.

In this paper, we report the formation of highly electrophilic 1,1-deactivated olefins, their use as novel synthetic building blocks, and their transformation to structurally diverse molecular scaffolds. Synthesis of 1,1-deactivated olefins substituted with a BT-sulfonyl group and a carbonyl or nitrile, respectively, consists of unusual Ti(OPri)4-mediated Knoevenagel-type condensation and proceed in good to excellent yields. Generated olefins can be further transformed in a highly stereoselective manner and in good yields to various polyfunctionalized heterocycles and acyclic molecular scaffolds. Overall, the obtained structures are accessed in two to four steps starting from the (mostly) commercially available aldehydes. In addition, the presence of the BT-sulfonyl group in prepared structures allows for further chemoselective functionalization/post-synthetic transformations to provide structurally diverse final compounds.

General Synthesis of 1-Aryl-6-azaisocytosines and Their Utilization for the Preparation of Related Condensed 1,2,4-Triazines.

A simple general synthesis of 1-aryl-6-azaisocytosine-5-carbonitriles 4 is described. This method is based on coupling diazonium salts with cyanoacetylcyanamide 2 and then cyclization of the formed 2-arylhydrazono-2-cyanoacetylcyanamides 3. The 6-azaisocytosines 4 were studied with respect to tautomeric equilibrium and the transformation of functional groups, and used in the synthesis of the condensed heterocyclic compounds: Purine isosteric imidazo[2,1-c]-[1,2,4]triazine 8 and the 1,2,4-triazino[2,3-a]quinazolines 9-12.

Lignans and Neolignans: Plant secondary metabolites as a reservoir of biologically active substances.

Lignans and neolignans are plant secondary metabolites derived from the oxidative coupling of phenylpropanoids. Biological activity of these phenolic compounds ranges from antioxidant, antitumor (terminaloside P, IC50 = 10 nM), anti-inflammatory, anti-neurodegenerative (schibitubin B, IC50 = 3.2 nM) and antiviral (patentiflorin A, IC50 = 14-23 nM) to antimicrobial. In addition, it was observed that several members of this group, namely enterolactone and its biochemical precursors also known as phytoestrogens, possess important protective properties. Most of these lignans and neolignans are presented in reasonable amounts in one's diet and thus the protection they provide against the colon and breast cancer, to name a few, is even more important to note. Similarly, neuroprotective properties were observed (schisanwilsonin G, IC50 = 3.2 nM) These structural motives also serve as an important starting point in the development of anticancer drugs. Presumably the most famous members of this family, etoposide and teniposide, synthetic derivatives of podophyllotoxin, are used in the clinical treatment of lymphocytic leukemia, certain brain tumors, and lung tumors already for nearly 20 years. This review describes 413 lignans and neolignans which have been isolated between 2016 and mid-2018 being reported in more than 300 peer-reviewed articles. It covers their source, structure elucidation, and bioactivity. Within the review, the structure-based overview of compounds as well as the bioactivity-based overview of compounds are described.

One and Two-Carbon Homologation of Primary and Secondary Alcohols to Corresponding Carboxylic Esters Using ß-Carbonyl BT Sulfones as a Common Intermediate.

Herein we report the efficient one- and two-carbon homologation of 1° and 2° alcohols to their corresponding homologated esters via the Mitsunobu reaction using ß-carbonyl benzothiazole (BT) sulfone intermediates. The one-carbon homologation approach uses standard Mitsunobu C-S bond formation, oxidation and subsequent alkylation, while the two-carbon homologation uses a less common C-C bond forming Mitsunobu reaction. In this latter case, the use of ß-BT sulfone bearing esters lowers the p Ka sufficiently enough for the substrate to be used as a carbon-based nucleophile and deliver the homologated ß-BT sulfone ester, and this superfluous sulfone group can then be cleaved. In this paper we describe several methods for the effective desulfonylation of BT sulfones and have developed methodology for one-pot alkylation-desulfonylation sequences. As such, overall, a one-carbon homologation sequence can be achieved in a two-pot (four step) procedure and the two-carbon homologation in a two-pot (three step) procedure (three-pot; four step when C-acid synthesis is included). This methodology has been applied to a wide variety of functionality (esters, silyl ethers, benzyls, heteroaryls, ketones, olefins and alkynes) and are all tolerated well providing good to very good overall yields. The power of our method was demonstrated in site-selective ingenol C20 allylic alcohol two-carbon homologation.