Optimization of Covalent MKK7 Inhibitors via Crude Nanomole-Scale Libraries.

High-throughput nanomole-scale synthesis allows for late-stage functionalization (LSF) of compounds in an efficient and economical manner. Here, we demonstrated that copper-catalyzed azide-alkyne cycloaddition could be used for the LSF of covalent kinase inhibitors at the nanoscale, enabling the synthesis of hundreds of compounds that did not require purification for biological assay screening, thus reducing experimental time drastically. We generated crude libraries of inhibitors for the kinase MKK7, derived from two different parental precursors, and analyzed them via the high-throughput In-Cell Western assay. Select inhibitors were resynthesized, validated via conventional biological and biochemical methods such as western blots and liquid chromatography-mass spectrometry (LC-MS) labeling, and successfully co-crystallized. Two of these compounds showed over 20-fold increased inhibitory activity compared to the parental compound. This study demonstrates that high-throughput LSF of covalent inhibitors at the nanomole-scale level can be an auspicious approach in improving the properties of lead chemical matter.

An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor.

Designing covalent inhibitors is increasingly important, although it remains challenging. Here, we present covalentizer, a computational pipeline for identifying irreversible inhibitors based on structures of targets with non-covalent binders. Through covalent docking of tailored focused libraries, we identify candidates that can bind covalently to a nearby cysteine while preserving the interactions of the original molecule. We found âˆ¼11,000 cysteines proximal to a ligand across 8,386 complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In a prospective evaluation, five out of nine predicted covalent kinase inhibitors showed half-maximal inhibitory concentration (IC50) values between 155 nM and 4.5 µM. Application against an existing SARS-CoV Mpro reversible inhibitor led to an acrylamide inhibitor series with low micromolar IC50 values against SARS-CoV-2 Mpro. The docking was validated by 12 co-crystal structures. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.

Electrophilic Natural Products as Drug Discovery Tools.

Electrophilic natural products (ENPs) are a rich source of bioactive molecules with tremendous therapeutic potential. While their synthetic complexity may hinder their direct use as therapeutics, they represent tools for elucidation of suitable molecular targets and serve as inspiration for the design of simplified synthetic counterparts. Here, we review the recent use of various activity-based protein profiling methods to uncover molecular targets of ENPs. Beyond target identification, these examples also showcase further development of synthetic ligands from natural product starting points. Two examples demonstrate how ENPs can progress the emerging fields of targeted protein degradation and molecular glues. Though challenges still remain in the synthesis of ENP-based probes, and in their synthetic simplification, their potential for discovery of novel mechanisms of action makes it well worth the effort.

Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.

Efficient Targeted Degradation via Reversible and Irreversible Covalent PROTACs.

Proteolysis targeting chimeras (PROTACs) represent an exciting inhibitory modality with many advantages, including substoichiometric degradation of targets. Their scope, though, is still limited to date by the requirement for a sufficiently potent target binder. A solution that proved useful in tackling challenging targets is the use of electrophiles to allow irreversible binding to the target. However, such binding will negate the catalytic nature of PROTACs. Reversible covalent PROTACs potentially offer the best of both worlds. They possess the potency and selectivity associated with the formation of the covalent bond, while being able to dissociate and regenerate once the protein target is degraded. Using Bruton's tyrosine kinase (BTK) as a clinically relevant model system, we show efficient degradation by noncovalent, irreversible covalent, and reversible covalent PROTACs, with <10 nM DC50's and >85% degradation. Our data suggest that part of the degradation by our irreversible covalent PROTACs is driven by reversible binding prior to covalent bond formation, while the reversible covalent PROTACs drive degradation primarily by covalent engagement. The PROTACs showed enhanced inhibition of B cell activation compared to ibrutinib and exhibit potent degradation of BTK in patient-derived primary chronic lymphocytic leukemia cells. The most potent reversible covalent PROTAC, RC-3, exhibited enhanced selectivity toward BTK compared to noncovalent and irreversible covalent PROTACs. These compounds may pave the way for the design of covalent PROTACs for a wide variety of challenging targets.

Tandem Acyl Substitution/Michael Addition of Thioesters with Vinylmagnesium Bromide.

A tandem reaction of thioesters with vinylmagnesium bromide is reported. The initial acyl substitution provides an α,ß-unsaturated ketone which further reacts with the liberated thiolate. This transition-metal-free synthesis of ß-sulfanyl ketones takes place under mild reaction conditions, whereas the addition of a second Grignard molecule is almost completely suppressed. The carefully chosen parameters enabled the transformation of different substrates in moderate to good yields.

Cross-Coupling of Chloro(hetero)arenes with Thiolates Employing a Ni(0)-Precatalyst.

A general and efficient Ni-catalyzed coupling of challenging aryl chlorides and in situ generated aliphatic and aromatic thiolates is described. The employed on-cycle, air-stable defined Ni precatalysts allow for transformation of a broad scope of substrates. A variety of functional groups and heterocyclic motifs as well as structurally varied thiols are tolerated at unprecedented moderate catalyst loadings and reaction temperatures. Depending on reaction conditions, aryl thiols can selectively undergo C-S or C-C couplings.

Nickel-Catalyzed Coupling of Arylzinc Halides with Thioesters.

The Pd-catalyzed Fukuyama reaction of thioesters with organozinc reagents is a mild, functional-group-tolerant method for acylation chemistry. Its Ni-catalyzed variant might be a sustainable alternative to expensive catalytic Pd sources. We investigated the reaction of S-ethyl thioesters with aryl zinc halides with hetero- and homotopic Ni precatalysts and several ligands. The results show that both homo- and heterotopic species may contribute to catalysis. The substrate scope using an operationally homogeneous defined Ni complex was established. Acyl radicals are postulated as short-lived intermediates.

Metal-Catalyzed Synthesis and Use of Thioesters: Recent Developments.

While thioesters are common intermediates in biochemical processes, they are much less appreciated in organic synthesis, also compared to other carboxylic acid derivatives. However, their chemistry and reactivity is intriguing and diversified, reaching much further than the acyl substitution and aldol chemistry. Herein, we focus on metal-catalyzed reactions for the synthesis of thioesters as well as their transformations. Reactions such as thiocarbonylation, cross-coupling, decarbonylation, allylic substitution or dual photoredox/metal catalysis are discussed. On one hand, new atom economic methods allow for convenient synthesis of thioesters from well available starting materials. On the other hand, various synthetically important compounds can by synthesized due to the multifaceted reactivity of thioesters that we aimed to depict.

Regioselective Thiocarbonylation of Vinyl Arenes.

A palladium-catalyzed thiocarbonylation of styrene derivatives is reported for the first time. The combination of thiols as nucleophiles and a bidentate ligand ensures a unique reaction outcome with high regioselectivity toward the more valuable branched isomer and new reactivity. The ambient reaction conditions (temperature, catalyst loading) and the use of a CO surrogate render this transformation a useful method for the synthesis of thioesters from available feedstock. Various functional groups on arene and thiol substituents are tolerated by the system. Notably, challenging ortho-substituted styrenes are converted with unprecedentedly high regioselectivity.