Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide

The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (M^pro) is a promising target for COVID-19 treatment. Here, we report an irreversible SARS-CoV-2 M^pro inhibitor possessing chlorofluoroacetamide (CFA) as a warhead for the covalent modification of M^pro. Ugi multicomponent reaction using chlorofluoroacetic acid enabled the rapid synthesis of dipeptidic CFA derivatives that identified 18 as a potent inhibitor of SARS-CoV-2 M^pro. Among the four stereoisomers, (R,R)-18 exhibited a markedly higher inhibitory activity against M^pro than the other isomers. Reaction kinetics and computational docking studies suggest that the R configuration of the CFA warhead is crucial for the rapid covalent inhibition of M^pro. Our findings highlight the prominent influence of the CFA chirality on the covalent modification of proteinous cysteines and provide the basis for improving the potency and selectivity of CFA-based covalent inhibitors.

Chlorofluoroacetamide (CFA) was used as the warhead for covalent targeting of SARS-CoV-2 M^pro. The chirality at CFA showed marked influence on inhibitory activity, suggesting stereospecific activation of CFA for cysteine modification in the protein.     

Unique Participation of Unprotected Internucleotidic Phosphodiester Residues on Unexpected Cleavage Reaction of the Si?O Bond of the Diisopropylsilandiyl Group Used as a Linker for the Solid‐Phase Synthesis of 5′‐Terminal Guanylated Oligodeoxynucleotides

In connection with the synthesis of guanosine‐capped oligodeoxynucleotides on polymer supports, we found an unprecedented Si O bond cleavage reaction, which occurred when polymer‐linked oligodeoxynucleotides having unprotected internucleotidic phosphate groups were allowed to react with the guanosine 5′‐phosphorimidazolide derivative 18 in the presence of 4‐nitro‐6‐(trifluoromethyl)‐1H‐benzotriazol‐1‐ol (Ntbt‐OH) as an effective activator in pyridine. This side reaction was confirmed by the fact that the liquid‐phase reaction of DMTrTpT O Si(iPr₂)OEt 42 with a simpler model compound, methyl phosphorimidazolide 34 , in the presence of Ntbt‐OH gave DMTrTpT 43 . It turned out that the side reaction hardly occurs without unprotected internucleotidic phosphate groups on oligodeoxynucleotides. The detailed study of this side reaction disclosed that Ntbt‐OH directly attacks the Si‐atom to release oligonucleotides from the resin. It is likely that Ntbt‐OH serves as a very strong nucleophile in pyridine, especially to the Si‐atom of the linker.     

Synthesis and functionalities of poly(N-vinylalkylamide). IV. Synthesis and free radical polymerization of N-vinylisobutyramide and thermosensitive properties of the polymer

Pyrolysis of (N-α-isopropoxyethyl)isobutyramide, which was obtained by the reaction of isobutyramide, 2-propanol, and acetaldehyde in the presence of conc. sulfuric acid, produced N-vinylisobutyramide (NVIBA). The free radical polymerization of NVIBA was carried out in various solvents in the presence of a radical initiator. It was found that the polymerizability of NVIBA is similar to that of N-vinylacetamide. The resulting polyNVIBA showed a lower critical solution temperature (LCST) sharply at 39°C. Thermosensitive properties of polyNVIBA were investigated in comparison with poly(N-isopropylacrylamide). © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 1763–1768, 1997     

Preparation and anticoagulant surface properties of glucoside- or sulfated glucoside-bearing polymer grafted poly(ethylene) films

Poly(GEMA) or poly(GEMA)-sulfate grafted surfaces were prepared for the purpose of developing biomaterials with anticoagulant surfaces. Their functionalities were investigated as anticoagulant activity, proteins and cells adhesion activity, and complement activation activity. These results revealed that the adhesion of blood cells onto a GEMA-sulfate grafted surface was due to protein adsorption and that complement activation onto a GEMA-sulfate grafted surface was larger than that on a GEMA grafted surface. A GEMA-sulfate grafted surface, however, exhibited good anticoagulant activity. These functions seemed to be due to the specific functionality of the SO₃ groups in a GEMA-sulfate.     

Graft copolymers having hydrophobic backbone and hydrophilic branches. XI. Preparation and thermosensitive properties of polystyrene microspheres having poly (N-isopropylacrylamide) branches on their surfaces

Thermosensitive microspheres with 0.4–1.2 μm diameter consisting of a polystyrene core and poly(N-isopropylacrylamide) (polyNIPAAm) branches on their surfaces were prepared by the free radical polymerization of a polyNIPAAm macromonomer and styrene in ethanol. Electron spectroscopy for chemical analysis (ESCA) of the microsphere surface suggested that polyNIPAAm chains were favorably located on the surface of the microspheres. The morphology of the microspheres was observed by transmission electron micrograph (TEM) and the particle size of was estimated by submicron particle analyzer. The molecular weight of the polyNIPAAm macromonomer, the ratio of the macromonomer and styrene, and the polymerization temperature affected the particle size. Thermosensitive properties of polyNIPAAm-coated polystyrene microspheres were evaluated by the turbidity of their dispersion solutions and the hydrodynamic size of the miocrospheres. The transmittance in dispersion solutions changed clearly, similar to oligoNIPAAm and polyNIPAAm macromonomers. In addition, the particle size of microspheres decreased with rising temperature. These results were explained by the thermosensitivity of polyNIPAAm branches on the microsphere surface. © 1996 John Wiley & Sons, Inc.     

Enhanced nucleophilicity of ambiphilic silylene and silylenoid bearing 8-(dimethylamino)-1-naphthyl group

Some new aspects of intramolecularly amine-coordinated silylenes, ammonium silaylide, and amine-coordinated magnesium (chloro)silylenoids are summarized. The divalent silicon species bearing the 8-(dimethylamino)-1-naphthyl group, generated by the thermal degradation of a pseudo-pentacoordinated ethoxy- or fluoro-disilane, behaves as a nucleophilic ammonium silaylide as well as the amine-coordinated silylene, whose electrophilic character is weakened in comparison with that of free silylenes in some reactions in the presence of trapping agents such as 1,3-diene, diphenyl acetylene (in the absence or presence of water), and phenylacetylene, and in the absence of any trapping agent. The amine-coordinated silylenoid also behaves as an ambiphile, but the reaction courses are different from those observed with the amine-coordinated silylene and silaylide. A novel amino-group migration from naphthyl carbon to silicon has been observed in both species.     

Polymorphism of phenylpyruvic acid studied by IR, Raman and solid state C NMR spectroscopy

Polymorphs I and II of phenylpyruvic acid are obtained as mixtures of both crystal forms or relatively pure crystals, from different solvents. Polymorph I is more stable than polymorph II at room temperature. Spectral characteristics of these polymorphs are discussed on the basis of IR, Raman and solid state ¹³C NMR spectra. Also, the assignment of the IR features observed in the 1600–1700 cm⁻¹ region is re-investigated by referring to the spectra of heavy-atom substituted derivatives. It is suggested that the C=O stretching band is split by the crystal field for both polymorphs.     

High repetition rate femtosecond WDM pulse generation using direct space-to-time pulse shapers and arrayed waveguide gratings

For the application of high repetition rate wavelength division multiplexed (WDM) pulse train generation from a femtosecond modelocked fiber laser, the direct space-to-time pulse shaper and a properly designed arrayed waveguide grating (AWG) are equivalent. The analogy between the bulk optics and integrated configuration is explored for this application. The critical design parameters of the AWG are the free spectral range and the pathlength difference between adjacent guides in the array.     

Size-Exclusion Effect and Protein Repellency of Concentrated Polymer Brushes Prepared by Surface-Initiated Living Radical Polymerization

The adsorption of proteins on poly(2-hydroxyethyl methacrylate) (PHEMA) brushes was systematically investigated from the viewpoint of the size-exclusion effect of the concentrated brushes. By use of surface-initiated atom transfer radical polymerization, well-defined, concentrated PHEMA brushes were successfully grafted on the inner surface of the silica monolithic column with meso pores of ca. 80 nm as well as a silicon wafer and a quartz crystal microbalance (QCM) chip. By eluting low-polydispersity pullulans with different molecular weight through the modified monolithic column, the concentrated PHEMA brush was characterized and demonstrated to sharply exclude solute molecules with the critical molecular size (size-exclusion limit) comparable to the distance between the nearest-neighboring graft points d. The elution behaviors of proteins with different sizes were studied with this PHEMA-grafted column: the protein sufficiently larger than the critical size was perfectly excluded from the brush layer and separated only in the size-exclusion mode by the meso pores without affinity interaction with the brush surface. Then, the irreversible adsorption of proteins on PHEMA brushes was investigated using QCM by varying graft densities (σ = 0.007, 0.06, and 0.7 chains/nm²) and protein sizes (effective diameter = 2–13 nm). A good correlation between the protein size and the graft density was observed: proteins larger than d caused no significant irreversible adsorption on the PHEMA brushes. Thus, we experimentally substantiated the postulated size-exclusion effect of the concentrated brushes and confirmed that this effect plays an important role for suppressing protein adsorption.