Organic Azide Inhibitors of Cysteine Proteases

Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function

Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.

Mechanism-based inhibition of GH127/146 cysteine glycosidases by stereospecifically functionalized l-arabinofuranosides

To understand the precise mechanism of the glycoside hydrolase (GH) family 127, a cysteine β-l-arabinofuranosidase (Arafase) - HypBA1 - has been isolated from Bifidobacterium longum in the human Gut microbiota, and the design and synthesis of the mechanism-based inhibitors such as l-Araf-haloacetamides have been carried out. The α-l-Araf-azide derivative was used as the monoglycosylamine equivalent to afford the l-Araf-chloroacetamides (α/β-1-Cl) as well as bromoacetamides (α/β-1-Br) in highly stereoselective manner through Staudinger reaction followed by amide formation with/without anomerization. Against HypBA1, the probes 1, especially in the case of α/β-1-Br inhibited the hydrolysis. Conformational implications of these observations are discussed in this manuscript. Additional examinations using l-Araf-azides (α/β-5) resulted in further mechanistic observations of the GH127/146 cysteine glycosidases, including the hydrolysis of β-5 as the substrate and oxidative inhibition by α-5 using the GH127 homologue.

Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity

The main protease (Mpro) is a validated antiviral drug target of SARS-CoV-2. A number of Mpro inhibitors have now advanced to animal model study and human clinical trials. However, one issue yet to be addressed is the target selectivity over host proteases such as cathepsin L. In this study we describe the rational design of covalent SARS-CoV-2 Mpro inhibitors with novel cysteine reactive warheads including dichloroacetamide, dibromoacetamide, tribromoacetamide, 2-bromo-2,2-dichloroacetamide, and 2-chloro-2,2-dibromoacetamide. The promising lead candidates Jun9-62-2R (dichloroacetamide) and Jun9-88-6R (tribromoacetamide) had not only potent enzymatic inhibition and antiviral activity but also significantly improved target specificity over caplain and cathepsins. Compared to GC-376, these new compounds did not inhibit the host cysteine proteases including calpain I, cathepsin B, cathepsin K, cathepsin L, and caspase-3. To the best of our knowledge, they are among the most selective covalent Mpro inhibitors reported thus far. The cocrystal structures of SARS-CoV-2 Mpro with Jun9-62-2R and Jun9-57-3R reaffirmed our design hypothesis, showing that both compounds form a covalent adduct with the catalytic C145. Overall, these novel compounds represent valuable chemical probes for target validation and drug candidates for further development as SARS-CoV-2 antivirals.

Caspase-1 Specific Light-Up Probe with Aggregation-Induced Emission Characteristics for Inhibitor Screening of Coumarin-Originated Natural Products

Caspase-1 is a key player in pyroptosis and inflammation. Caspase-1 inhibition is found to be beneficial to various diseases. Coumarin-originated natural products have an anti-inflammation function, but their direct inhibition effect to caspase-1 remains unexplored. To evaluate their interactions, the widely used commercial coumarin-based probe (Ac-YVAD-AMC) is not suitable, as the background signal from coumarin-originated natural products could interfere with the screening results. Therefore, fluorescent probes using a large Stokes shift could help solve this problem. In this work, we chose the fluorophore of tetraphenylethylene-thiophene (TPETH) with aggregation-induced emission characteristics and a large Stokes shift of about 200 nm to develop a molecular probe. Bioconjugation between TPETH and hydrophilic peptides (DDYVADC) through a thiol-ene reaction generated a light-up probe, C1-P3. The probe has little background signal in aqueous media and exerts a fluorescent turn-on effect in the presence of caspase-1. Moreover, when evaluating the inhibition potency of coumarin-originated natural products, the new probe could generate a true and objective result but not for the commercial probe (Ac-YVAD-AMC), which is evidenced by HPLC analysis. The quick light-up response and accurate screening results make C1-P3 very useful in fundamental study and inhibitior screening toward caspase-1.

An electrospray ionization mass spectrometry study of azidoacetic acid/transition metal complexes

RATIONALE

The complexation behavior of transition metals with organic azides by electrospray ionization (ESI) tandem mass spectrometry (MS/MS) is not completely understood. In this study, fragmentation patterns of complex ions having azidoacetic acid coordinated to Ni/Co/Fe were elucidated. The role of transition metals in the mediation of ligand rearrangements in gas phase is experimentally supported.

METHODS

The complexation of some transition metals, nickel, cobalt and iron, by azidoacetic acid was studied by means of ESI and MS/MS. Fragmentation patterns were discerned via consecutive MS/MS experiments on an ion trap mass spectrometer and confirmed by high-resolution (HR) Fourier transform ion cyclotron resonance MS. Density functional theory (DFT) calculations were used to characterize the major ions observed in MS.

RESULTS

Only singly positively charged complex ions were detected presenting various stoichiometries. MS/MS and theoretical calculations allowed us to confirm assignments and coordination sites. Structural evidence suggested that the azidoacetic acid can behave as monodentate and/or bidentate and coordination through the oxygen and nitrogen atoms are both possible. Experimental evidence strongly points to a role of Ni/Co/Fe, in oxidative state (I), in mediating C-C bond activation in the gas phase.

CONCLUSIONS

MS/MS and HRMS experiments were able to elucidate azidoacetic acid complexation with Ni/Co/Fe and several gas-phase processes involving metal reduction and rearrangements. The definition of the coordination pattern dictated by the competition between the nitrogen and the oxygen atoms is also dependent on the metal centre in a very dynamic process. Copyright © 2017 John Wiley & Sons, Ltd.

Microbial transglutaminase displays broad acyl-acceptor substrate specificity

The great importance of amide bonds in industrial synthesis has encouraged the search for efficient catalysts of amide bond formation. Microbial transglutaminase (MTG) is heavily utilized in crosslinking proteins in the food and textile industries, where the side chain of a glutamine reacts with the side chain of a lysine, forming a secondary amide bond. Long alkylamines carrying diverse chemical entities can substitute for lysine as acyl-acceptor substrates, to link molecules of interest onto peptides or proteins. Here, we explore short and chemically varied acyl-acceptor substrates, to better understand the nature of nonnatural substrates that are tolerated by MTG, with the aim of diversifying biocatalytic applications of MTG. We show, for the first time, that very short-chain alkyl-based amino acids such as glycine can serve as acceptor substrates. The esterified α-amino acids Thr, Ser, Cys, and Trp--but not Ile--also showed reactivity. Extending the search to nonnatural compounds, a ring near the amine group--particularly if aromatic--was beneficial for reactivity, although ring substituents reduced reactivity. Overall, amines attached to a less hindered carbon increased reactivity. Importantly, very small amines carrying either the electron-rich azide or the alkyne groups required for click chemistry were highly reactive as acyl-acceptor substrates, providing a robust route to minimally modified, "clickable" peptides. These results demonstrate that MTG is tolerant to a variety of chemically varied natural and nonnatural acyl-acceptor substrates, which broadens the scope for modification of Gln-containing peptides and proteins.

Azidoacetone as a complexing agent of transition metals Ni2+/Co2+ promoted dissociation of the C-C bond in azidoacetone

The relevance of metal interactions with azides has led us to the study of the complexation of some transition metals, nickel and cobalt, by azidoacetone by means of electrospray ionization mass spectrometry (ESI-MS). Complexes were obtained from solutions of NiCl(2) and CoCl(2) , in methanol/water. Nickel was electrosprayed with other counter ion, bromide (Br), as well as other solvent (ethanol/water). For nickel and cobalt, the complexes detected were single positively charged, with various stoichiometries, some resulted from the fragmentation of the ligand, the loss of N(2) being quite common. The most abundant species were [Ni(II)Az(2)X](+) where X = Cl, Br and Az = azidoacetone. Some of the complexes showed solvation with the solvent components. Metal reduction was observed in complexes where a radical was lost, resulting from the homolytic cleavage of a metal coordination bond. Collision-induced dissociation (CID) experiments followed by tandem mass spectrometry (MS-MS) analysis were not absolutely conclusive about the coordination site. However, terminal ions of the fragmentation routes were explained by a gas-phase mechanism proposed where a C-C bond was activated and the metal inserted subsequently. Density functional theory calculations provided structures for some complexes. In [Ni(II)Az(2)X](+) species, one azidoacetone ligand is monodentate and the dominant binding location is the alkylated nitrogen and not the carbonyl group. The other azidoacetone ligand is bidentate showing coordination through alkylated nitrogen and the carbonyl group. These are also the preferential binding sites for the most stable isomer of [Ni(II)AzX](+) species.

A highly potent and selective caspase 1 inhibitor that utilizes a key 3-cyanopropanoic acid moiety

Herein, we examine the potential of a nitrile-containing propionic acid moiety as an electrophile for covalent attack by the active-site cysteine residue of caspase 1. The syntheses of several cyanopropanate-containing small molecules based on the optimized peptidic scaffold of prodrug VX-765 were accomplished. These compounds were found to be potent inhibitors of caspase 1 (IC(50) values < or =1 nM). Examination of these novel small molecules against a caspase panel demonstrated an impressive degree of selectivity for caspase 1 inhibition over other caspase isozymes. Assessment of hydrolytic stability and selected ADME properties highlighted these agents as potentially useful tools for studying caspase 1 down-regulation in various settings, including in vivo analyses.

Synthesis and biological evaluation of reversible inhibitors of IdeS, a bacterial cysteine protease and virulence determinant

Analogues of the irreversible protease inhibitors TPCK and TLCK have been synthesized and tested as inhibitors of the bacterial cysteine protease IdeS excreted by Streptococcuspyogenes. Eight compounds were identified as inhibitors of IdeS in an in vitro assay. The most potent compounds contained an aldehyde function, thus acting as efficient reversible inhibitors, nitrile and azide derivatives showed moderate activity.

Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening

The cysteine protease cathepsin S (CatS) is involved in the pathogenesis of autoimmune disorders, atherosclerosis, and obesity. Therefore, it represents a promising pharmacological target for drug development. We generated ligand-based and structure-based pharmacophore models for noncovalent and covalent CatS inhibitors to perform virtual high-throughput screening of chemical databases in order to discover novel scaffolds for CatS inhibitors. An in vitro evaluation of the resulting 15 structures revealed seven CatS inhibitors with kinetic constants in the low micromolar range. These compounds can be subjected to further chemical modifications to obtain drugs for the treatment of autoimmune disorders and atherosclerosis.

Study of doubly charged alkaline earth metal and 3-azidopropionitrile complexes by electrospray ionization mass spectrometry

The present work describes a study of the complexation of calcium and magnesium by 3-azidopropionitrile by means of electrospray ionization mass spectrometry (ESI-MS). Complexes were obtained from solutions of calcium and magnesium salts of the type CaX2 and MgX2 (where X = Cl or NO3) in water and methanol/water. The complexes detected were mainly double positively charged, with various stoichiometries not depending on the solvent, since water and 3-azidopropionitrile were always the main ligands. Solvation with methanol was not observed unlike in a previous study of complexation of nickel and cobalt by 3-azidopropionitrile. The complex ions [M(II)Az4(H2O)](2+), [M(II)Az5](2+) (where M = Ca and Mg) are the most abundant for both metals, and both counter ions. Tandem mass spectrometric (MS/MS) analysis showed that, under collision-induced dissociation (CID) conditions, the most important processes occurring were loss of neutral ligands and the replacement of 3-azidopropionitrile by water. A complex species containing reduced alkaline earth metal was due to radical loss, resulting from homolytic cleavage in the azide ligand. Some terminal ions, in the fragmentation sequences, point to the nitrile group as the coordination site in the 3-azidopropionitrile. Density functional theory (DFT) calculations confirmed this coordination site and proved that 3-azidopropionitrile behaves as a monodentate ligand in the systems under study. Moreover, the theoretical study proved that the presence of water ligand introduces stability through a hydrogen bond established between the water molecule and one nitrogen atom of the azido group. In addition, the strong dipole moment of 3-azidopropionitrile (4.76 D), which is mainly related to presence of the nitrile group, favors the stabilization of the metal-ligand complexes through charge-dipole interactions and the coordination of the metal to the nitrile group.