Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors.

A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.

Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method.

We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in trans configuration and the corresponding 484 (222) dipeptides. To mimic the environment in a protein chain, the N- and C-termini of the studied systems were capped with acetyl and N-methylamide groups, respectively. We systematically varied the main chain dihedral angles (ϕ, ψ) by 40° steps and all side chain angles by 90° or 120° steps. We optimized the molecular geometries with the GFN2-xTB semiempirical (SQM) method and performed single point density functional theory calculations at the BP86-D3/DGauss-DZVP//COSMO-RS level in water, 1-octanol, N,N-dimethylformamide, and n-hexane. For each restrained (nonequilibrium) structure, we also calculated energy gradients (in water) and natural atomic charges. The exhaustive and unprecedented QM-based sampling enabled us to construct Ramachandran plots of quantum mechanical (QM(BP86-D3)//COSMO-RS) energies calculated on SQM structures, for all 506 (484 dipeptides and 22 amino acids) studied systems. We showed how the character of an amino acid side chain influences the conformational space of single amino acids and dipeptides. With clustering techniques, we were able to identify unique minima of amino acids and dipeptides (i.e., minima on the GFN2-xTB potential energy surfaces) and analyze the distribution of their BP86-D3//COSMO-RS conformational energies in all four solvents. We also derived an empirical formula for the number of unique minima based on the overall number of rotatable bonds within each peptide. The final peptide conformer data set (PeptideCs) comprises over 400 million structures, all of them annotated with QM(BP86-D3)//COSMO-RS energies. Thanks to its completeness and unbiased nature, the PeptideCs can serve, inter alia, as a data set for the validation of new methods for predicting the energy landscapes of protein structures. This data set may also prove to be useful in the development and reparameterization of biomolecular force fields. The data set is deposited at Figshare (10.25452/figshare.plus.19607172) and can be accessed using a simple web interface at http://peptidecs.uochb.cas.cz.

Closed Shell Iron(IV) Oxo Complex with an Fe-O Triple Bond: Computational Design, Synthesis, and Reactivity.

Iron(IV)-oxo intermediates in nature contain two unpaired electrons in the Fe-O antibonding orbitals, which are thought to contribute to their high reactivity. To challenge this hypothesis, we designed and synthesized closed-shell singlet iron(IV) oxo complex [(quinisox)Fe(O)]+ (1+ ; quinisox-H=(N-(2-(2-isoxazoline-3-yl)phenyl)quinoline-8-carboxamide). We identified the quinisox ligand by DFT computational screening out of over 450 candidates. After the ligand synthesis, we detected 1+ in the gas phase and confirmed its spin state by visible and infrared photodissociation spectroscopy (IRPD). The Fe-O stretching frequency in 1+ is 960.5 cm-1 , consistent with an Fe-O triple bond, which was also confirmed by multireference calculations. The unprecedented bond strength is accompanied by high gas-phase reactivity of 1+ in oxygen atom transfer (OAT) and in proton-coupled electron transfer reactions. This challenges the current view of the spin-state driven reactivity of the Fe-O complexes.

Chemoselectivity in the Oxidation of Cycloalkenes with a Non-Heme Iron(IV)-Oxo-Chloride Complex: Epoxidation vs. Hydroxylation Selectivity.

We report and analyze chemoselectivity in the gas phase reactions of cycloalkenes (cyclohexene, cycloheptene, cis-cyclooctene, 1,4-cyclohexadiene) with a non-heme iron(IV)-oxo complex [(PyTACN)Fe(O)(Cl)]+, which models the active species in iron-dependent halogenases. Unlike in the halogenases, we did not observe any chlorination of the substrate. However, we observed two other reaction pathways: allylic hydrogen atom transfer (HAT) and alkene epoxidation. The HAT is clearly preferred in the case of 1,4-cyclohexadiene, both pathways have comparable reaction rates in reaction with cyclohexene, and epoxidation is strongly favored in reactions with cycloheptene and cis-cyclooctene. This preference for epoxidation differs from the reactivity of iron(IV)-oxo complexes in the condensed phase, where HAT usually prevails. To understand the observed selectivity, we analyze effects of the substrate, spin state, and solvation. Our DFT and CASPT2 calculations suggest that all the reactions occur on the quintet potential energy surface. The DFT-calculated energies of the transition states for the epoxidation and hydroxylation pathways explain the observed chemoselectivity. The SMD implicit solvation model predicts the relative increase of the epoxidation barriers with solvent polarity, which explains the clear preference of HAT in the condensed phase.

Characterized cis-FeV(O)(OH) intermediate mimics enzymatic oxidations in the gas phase.

FeV(O)(OH) species have long been proposed to play a key role in a wide range of biomimetic and enzymatic oxidations, including as intermediates in arene dihydroxylation catalyzed by Rieske oxygenases. However, the inability to accumulate these intermediates in solution has thus far prevented their spectroscopic and chemical characterization. Thus, we use gas-phase ion spectroscopy and reactivity analysis to characterize the highly reactive [FeV(O)(OH)(5tips3tpa)]2+ (32+) complex. The results show that 32+ hydroxylates C-H bonds via a rebound mechanism involving two different ligands at the Fe center and dihydroxylates olefins and arenes. Hence, this study provides a direct evidence of FeV(O)(OH) species in non-heme iron catalysis. Furthermore, the reactivity of 32+ accounts for the unique behavior of Rieske oxygenases. The use of gas-phase ion characterization allows us to address issues related to highly reactive intermediates that other methods are unable to solve in the context of catalysis and enzymology.

Trapping Iron(III)-Oxo Species at the Boundary of the "Oxo Wall": Insights into the Nature of the Fe(III)-O Bond.

Terminal non-heme iron(IV)-oxo compounds are among the most powerful and best studied oxidants of strong C-H bonds. In contrast to the increasing number of such complexes (>80 thus far), corresponding one-electron-reduced derivatives are much rarer and presumably less stable, and only two iron(III)-oxo complexes have been characterized to date, both of which are stabilized by hydrogen-bonding interactions. Herein we have employed gas-phase techniques to generate and identify a series of terminal iron(III)-oxo complexes, all without built-in hydrogen bonding. Some of these complexes exhibit ∼70 cm-1 decrease in ν(Fe-O) frequencies expected for a half-order decrease in bond order upon one-electron reduction to an S = 5/2 center, while others have ν(Fe-O) frequencies essentially unchanged from those of their parent iron(IV)-oxo complexes. The latter result suggests that the added electron does not occupy a d orbital with Fe═O antibonding character, requiring an S = 3/2 spin assignment for the nascent FeIII-O- species. In the latter cases, water is found to hydrogen bond to the FeIII-O- unit, resulting in a change from quartet to sextet spin state. Reactivity studies also demonstrate the extraordinary basicity of these iron(III)-oxo complexes. Our observations show that metal-oxo species at the boundary of the "Oxo Wall" are accessible, and the data provide a lead to detect iron(III)-oxo intermediates in biological and biomimetic reactions.

Nucleophilic versus Electrophilic Reactivity of Bioinspired Superoxido Nickel(II) Complexes.

The formation and detailed spectroscopic characterization of the first biuret-containing monoanionic superoxido-NiII intermediate [LNiO2 ]- as the Li salt [2; L=MeN[C(=O)NAr)2 ; Ar=2,6-iPr2 C6 H3 )] is reported. It results from oxidation of the corresponding [Li(thf)3 ]2 [LNiII Br2 ] complex M with excess H2 O2 in the presence of Et3 N. The [LNiO2 ]- core of 2 shows an unprecedented nucleophilic reactivity in the oxidative deformylation of aldehydes, in stark contrast to the electrophilic character of the previously reported neutral Nacnac-containing superoxido-NiII complex 1, [L'NiO2 ] (L'=CH(CMeNAr)2 ). According to density-functional theory (DFT) calculations, the remarkably different behaviour of 1 versus 2 can be attributed to their different charges and a two-state reactivity, in which a doublet ground state and a nearby spin-polarized doublet excited-state both contribute in 1 but not in 2. The unexpected nucleophilicity of the superoxido-NiII core of 2 suggests that such a reactivity may also play a role in catalytic cycles of Ni-containing oxygenases and oxidases.

Detection of Indistinct Fe-N Stretching Bands in Iron(V) Nitrides by Photodissociation Spectroscopy.

We report for the first time infrared spectra of three non-heme pseudo-octahedral iron(V) nitride complexes with assigned Fe-N stretching vibrations. The intensities of the Fe-N bands in two of the complexes are extremely weak. Their detection was enabled by the high resolution and sensitivity of the experiments performed at 3 K for isolated complexes in the gas phase. Multireference CASPT2 calculations revealed that the Fe-N bond in the ground doublet state is influenced by two low-lying excited doublet states. In particular, configuration interaction between the ground and the second excited state leads to avoided crossing of their potential energy surfaces along the Fe-N coordinate, which thus affects the ground-state Fe-N stretching frequency and intensity. Therefore, DFT calculated Fe-N stretching frequency strongly depends on the amount of Hartree-Fock exchange potential. As a result, by tuning the amount of Hartree-Fock exchange potential in the B3LYP functional, it was possible to obtain theoretical spectra perfectly consistent with the experimental data. The theory shows that the intensity of the Fe-N stretching vibration can almost vanish due to strong coupling with other stretching modes of the ligands.

Spin-State-Controlled Photodissociation of Iron(III) Azide to an Iron(V) Nitride Complex.

The generation of iron(V) nitride complexes, which are targets of biomimetic chemistry, is reported. Temperature-dependent ion spectroscopy shows that this reaction is governed by the spin-state population of their iron(III) azide precursors and can be tuned by temperature. The complex [(MePy2 TACN)Fe(N3 )]2+ (MePy2 TACN=N-methyl-N,N-bis(2-picolyl)-1,4,7-triazacyclononane) exists as a mixture of sextet and doublet spin states at 300 K, whereas only the doublet state is populated at 3 K. Photofragmentation of the sextet state complex leads to the reduction of the iron center. The doublet state complex photodissociates to the desired iron(V) nitride complex. To generalize these findings, we show results for complexes with cyclam-based ligands.

Generation, Spectroscopic, and Chemical Characterization of an Octahedral Iron(V)-Nitrido Species with a Neutral Ligand Platform.

Iron complex [FeIII(N3)(MePy2tacn)](PF6)2 (1), containing a neutral triazacyclononane-based pentadentate ligand, and a terminally bound azide ligand has been prepared and spectroscopically and structurally characterized. Structural details, magnetic susceptibility data, and Mössbauer spectra demonstrate that 1 has a low-spin (S = 1/2) ferric center. X-ray diffraction analysis of 1 reveals remarkably short Fe-N (1.859 Å) and long FeN-N2 (1.246 Å) distances, while the FT-IR spectra show an unusually low N-N stretching frequency (2019 cm-1), suggesting that the FeN-N2 bond is particularly weak. Photolysis of 1 at 470 or 530 nm caused N2 elimination and generation of a nitrido species that on the basis of Mössbauer, magnetic susceptibility, EPR, and X-ray absorption in conjunction with density functional theory computational analyses is formulated as [FeV(N)(MePy2tacn)]2+ (2). Results indicate that 2 is a low-spin (S = 1/2) iron(V) species, which exhibits a short Fe-N distance (1.64 Å), as deduced from extended X-ray absorption fine structure analysis. Compound 2 is only stable at cryogenic (liquid N2) temperatures, and frozen solutions as well as solid samples decompose rapidly upon warming, producing N2. However, the high-valent compound could be generated in the gas phase, and its reactivity against olefins, sulfides, and substrates with weak C-H bonds studied. Compound 2 proved to be a powerful two-electron oxidant that can add the nitrido ligand to olefin and sulfide sites as well as oxidize cyclohexadiene substrates to benzene in a formal H2-transfer process. In summary, compound 2 constitutes the first case of an octahedral FeV(N) species prepared within a neutral ligand framework and adds to the few examples of FeV species that could be spectroscopically and chemically characterized.

Reactivity of Copper(III)-Oxo Complexes in the Gas Phase.

An efficient way to generate [(L)CuO]+ complexes with a number of monodentate and bidentate ligands (L) from their [(L)Cu(ClO3 )]+ precursors by electrospray ionization was herein explored. Further, we studied [(L)CuO]+ with L=9,10-phenanthraquinone, 1,10-phenanthroline, and acetonitrile in detail. The signature of these terminal copper-oxo complexes was found to be elimination of the oxygen atom upon collisional activation. We investigated and compared their reactions with water, ethane, ethylene, and 1,4-cyclohexadiene. The [(MeCN)CuO]+ complex oxidized water and performed C-H activation and hydroxylation of ethane. The complexes with bidentate ligands did not react with water and oxidized only larger hydrocarbons. All the investigated complexes showed comparable reactivities in the oxygen-transfer reaction with ethylene.

Chasing the Evasive Fe═O Stretch and the Spin State of the Iron(IV)-Oxo Complexes by Photodissociation Spectroscopy.

We demonstrate the application of infrared photodissocation spectroscopy for determination of the Fe═O stretching frequencies of high-valent iron(IV)-oxo complexes [(L)Fe(O)(X)]2+/+ (L = TMC, N4Py, PyTACN, and X = CH3CN, CF3SO3, ClO4, CF3COO, NO3, N3). We show that the values determined by resonance Raman spectroscopy in acetonitrile solutions are on average 9 cm-1 red-shifted with respect to unbiased gas-phase values. Furthermore, we show the assignment of the spin state of the complexes based on the vibrational modes of a coordinated anion and compare reactivities of various iron(IV)-oxo complexes generated as dications or monocations (bearing an anionic ligand). The coordinated anions can drastically affect the reactivity of the complex and should be taken into account when comparing reactivities of complexes bearing different ligands. Comparison of reactivities of [(PyTACN)Fe(O)(X)]+ generated in different spin states and bearing different anionic ligands X revealed that the nature of anion influences the reactivity more than the spin state. The triflate and perchlorate ligands tend to stabilize the quintet state of [(PyTACN)Fe(O)(X)]+, whereas trifluoroacetate and nitrate stabilize the triplet state of the complex.

Spectroscopic Characterization and Reactivity of Triplet and Quintet Iron(IV) Oxo Complexes in the Gas Phase.

Closely structurally related triplet and quintet iron(IV) oxo complexes with a tetradentate aminopyridine ligand were generated in the gas phase, spectroscopically characterized, and their reactivities in hydrogen-transfer and oxygen-transfer reactions were compared. The spin states were unambiguously assigned based on helium tagging infrared photodissociation (IRPD) spectra of the mass-selected iron complexes. It is shown that the stretching vibrations of the nitrate counterion can be used as a spectral marker of the central iron spin state.