In-silico guided design, screening, and molecular dynamic simulation studies for the identification of potential SARS-CoV-2 main protease inhibitors for the targeted treatment of COVID-19.

COVID-19, the disease responsible for the recent pandemic, is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) of SARS-CoV-2 is an essential proteolytic enzyme that plays a number of important roles in the replication of the virus in human host cells. Blocking the function of SARS-CoV-2 Mpro offers a promising and targeted, therapeutic option for the treatment of the COVID-19 infection. Such an inhibitory strategy is currently successful in treating COVID-19 under FDA's emergency use authorization, although with limited benefit to the immunocompromised along with an unfortunate number of side effects and drug-drug interactions. Current COVID vaccines protect against severe disease and death but are mostly ineffective toward long COVID which has been seen in 5-36% of patients. SARS-CoV-2 is a rapidly mutating virus and is here to stay endemically. Hence, alternate therapeutics to treat SARS-CoV-2 infections are still needed. Moreover, because of the high degree of conservation of Mpro among different coronaviruses, any newly developed antiviral agents should better prepare us for potential future epidemics or pandemics. In this paper, we first describe the design and computational docking of a library of novel 188 first-generation peptidomimetic protease inhibitors using various electrophilic warheads with aza-peptide epoxides, α-ketoesters, and ß-diketones identified as the most effective. Second-generation designs, 192 compounds in total, focused on aza-peptide epoxides with drug-like properties, incorporating dipeptidyl backbones and heterocyclic ring motifs such as proline, indole, and pyrrole groups, yielding 8 hit candidates. These novel and specific inhibitors for SARS-CoV-2 Mpro can ultimately serve as valuable alternate and broad-spectrum antivirals against COVID-19.Communicated by Ramaswamy H. Sarma.

Design, synthesis, and in vitro evaluation of aza-peptide aldehydes and ketones as novel and selective protease inhibitors.

Aza-peptide aldehydes and ketones are a new class of reversible protease inhibitors that are specific for the proteasome and clan CD cysteine proteases. We designed and synthesised aza-Leu derivatives that were specific for the chymotrypsin-like active site of the proteasome, aza-Asp derivatives that were effective inhibitors of caspases-3 and -6, and aza-Asn derivatives that inhibited S. mansoni and I. ricinus legumains. The crystal structure of caspase-3 in complex with our caspase-specific aza-peptide methyl ketone inhibitor with an aza-Asp residue at P1 revealed a covalent linkage between the inhibitor carbonyl carbon and the active site cysteinyl sulphur. Aza-peptide aldehydes and ketones showed no cross-reactivity towards cathepsin B or chymotrypsin. The initial in vitro selectivity of these inhibitors makes them suitable candidates for further development into therapeutic agents to potentially treat multiple myeloma, neurodegenerative diseases, and parasitic infections.

Photoinduced interruption of interannular cooperativity for delivery of cationic guests in water.

The synergy among twelve carboxylates from two hexavalent baskets 16- assisted the encapsulation of one divalent diammonium guest 32+-62+ and the formation of ternary [3-6⊂12]10-. The reduction of basket's multivalency, by photoinduced α-decarboxylation of 16- to give 23-, intercepted the interannular cooperativity operating in the stabilization of capsulpex [3-6⊂12]10- to dramatically diminish the binding affinity towards diammonium guests. As a result, the cationic guests were released into bulk water with 23- assembling into nanoparticles. With numerous drugs carrying positive sites, the finding reported here could now be examined for their light-promoted spatiotemporal delivery.

Twist-Turn-Twist Motif Chaperoned Inside Molecular Baskets.

Two molecular baskets 16-, each with three (S)-glutamic acids at its rim, were found (NMR, ITC) to complex diammonium alkanes 22+-52+ (+H3N(CH2)nNH3+, n = 7-10) giving ternary [2-5⊂12]10- assemblies (K = 107-109 M-2). From the magnetic perturbation of proton nuclei (1H NMR, NICS), we deduced that each guest assumed a U shape within the binary complex, [2-5⊂1]4-. Two ammonium groups were bound in the "anionic nest" at the top of 16-, while the hydrocarbon chain resided in its nonpolar cavity. From detailed ITC analyses, we showed that the binary complex [2-5⊂1]4- forms first and then another 16- capped [2-5⊂1]4- to give [2-5⊂12]10-, via interactions of the carboxylates at the rims with ammoniums on the guest. Long-range NOEs revealed that U-shaped 22+ and 52+ coiled into highly strained twist-turn-twist formations, for the first time observed within an abiotic host while curiously resembling helix-turn-helix motif found in DNA binding proteins.

Photo-induced formation of organic nanoparticles possessing enhanced affinities for complexing nerve agent mimics.

Molecular baskets 16--36-, functionalized with α-amino acids at their rim, undergo photo-induced α-decarboxylations to give amphiphilic 43--63- assembling into nanoparticles. Nanoparticulate 43--63- possess greater affinities for complexing OPs (akin to sarin and cyclosarin) than monomeric 16--36-. With the ability of nanoparticles to function in urine, our study sets the stage for creating novel nanocarriers capable of spatiotemporal sequestration of nerve agents or pesticides in competitive chemical environments.

Light-Triggered Transformation of Molecular Baskets into Organic Nanoparticles.

Discovering novel and functional photoresponsive materials is of interest for improving controlled release of molecules and scavenging toxic compounds for cleaning our environment or designing chemosensors. In this study, we report on the photoinduced decarboxylation of basket 16- , containing three glutamic acids at its rim. This concave compound is, in an aqueous environment (30 mm phosphate buffer at pH 7.0), monomeric (1 H NMR DOSY, DLS) with glutamic acid residues randomly oriented about its rim (1 H NMR and MM-OPLS3). The irradiation (300 nm) of 16- leads to the exclusive removal of its α-carboxylates to give amphiphilic 23- possessing γ-carboxylates. The photochemical transformation is a consecutive reaction with mono- and bis-decarboxylated products observed with 1 H NMR spectroscopy and ESI mass spectrometry. Amphiphilic 23- is a preorganized molecule (MM-OPLS3) that, in water, aggregates into organic nanoparticles (ca. 50-200 nm in diameter; DLS, TEM and cryo-TEM) having a critical aggregation concentration of 12 µm (UV/Vis). As the transition of monomeric 16- into nanoparticulate 23- is triggered with light, we reasoned that stimuli-responsive formation of the soft material lends itself to nanotechnology applications such as controlled release or scavenging of targeted compounds.

A Stimuli-Responsive Molecular Capsule with Switchable Dynamics, Chirality, and Encapsulation Characteristics.

In this study, we report the preparation, conformational dynamics, and recognition characteristics of novel molecular capsule 1 comprising a bowl-shaped framework conjugated to a tris(2-pyridylmethyl)amine (TPA) lid. With the assistance of experiment (1H NMR spectroscopy) and theory (MM and DFT) we found that C3 symmetric 1 is poorly preorganized with three pyridines at the rim adopting a propeller-like orientation and undergoing P-to- M (or vice versa) stereoisomerization (Δ G⧧ < 8 kcal/mol, VT 1H NMR). Capsule 1 binds CH4, CH3Cl, CH2Cl2, CHCl3, and CCl4 with Ka < 7 M-1. Protonation of 1 with HCl, however, gives [1·H]-Cl, with the solid-state structure showing the TPA lid being "flattened" and the +N-H---Cl hydrogen-bonded group residing outside. Importantly, the P-to- M stereoisomerization would for [1·H]-Cl occur with Δ G⧧ = 11 kcal/mol (VT 1H NMR). Less dynamic and more preorganized [1·H]-Cl binds CH4, CH3Cl, CH2Cl2, CHCl3, and CCl4 guests with a greater affinity ( Ka = 100-400 M-1) than 1. The results of our studies suggest that the complexation of increasingly larger guests takes place in an induced-fit fashion, with [1·H]-Cl (a) elongating along its vertical axis and concurrently potentially (b) twisting pyridines from P into M (and vice versa) orientation. The addition of Et3N to [1·H]-Cl⊂CH2Cl2 causes deprotonation of the capsule and the release of CH2Cl2 with the process being fully reversed after the addition of HCl. Allosteric capsule 1 with unique structural and dynamic characteristics is expected to, in the future, assist the construction of complex molecular machines and smart functional materials.

Removal of Nerve Agent Simulants from Water Using Light-Responsive Molecular Baskets.

We found that molecular baskets 1-3, with amino acids at their rim, undergo photoinduced decarboxylations to give baskets 4-6 forming a solid precipitate in water. Furthermore, organophosphonates 7-9 (OP), akin in size and shape to G-type nerve agents, form inclusion complexes with baskets 1-3 (K = 6-2243 M-1). Light irradiation (300 nm) of an aqueous solution of 1-3⊂OP led to the formation of precipitate containing an OP compound thereby amounting to a novel strategy for light-induced sequestration of nerve agents or, perhaps, other targeted compounds. Importantly, the stability of basket⊂OP complexes in addition to functional groups at the basket's rim play a role in the efficiency (up to 98%) by which OPs are removed from water.