Two Sides of Quantum-Based Modeling of Enzyme-Catalyzed Reactions: Mechanistic and Electronic Structure Aspects of the Hydrolysis by Glutamate Carboxypeptidase

We report the results of a computational study of the hydrolysis reaction mechanism of N-acetyl-l-aspartyl-l-glutamate (NAAG) catalyzed by glutamate carboxypeptidase II. Analysis of both mechanistic and electronic structure aspects of this multistep reaction is in the focus of this work. In these simulations, model systems are constructed using the relevant crystal structure of the mutated inactive enzyme. After selection of reaction coordinates, the Gibbs energy profiles of elementary steps of the reaction are computed using molecular dynamics simulations with ab initio type QM/MM potentials (QM/MM MD). Energies and forces in the large QM subsystem are estimated in the DFT(PBE0-D3/6-31G**) approximation. The established mechanism includes four elementary steps with the activation energy barriers not exceeding 7 kcal/mol. The models explain the role of point mutations in the enzyme observed in the experimental kinetic studies; namely, the Tyr552Ile substitution disturbs the “oxyanion hole”, and the Glu424Gln replacement increases the distance of the nucleophilic attack. Both issues diminish the substrate activation in the enzyme active site. To quantify the substrate activation, we apply the QTAIM-based approaches and the NBO analysis of dynamic features of the corresponding enzyme-substrate complexes. Analysis of the 2D Laplacian of electron density maps allows one to define structures with the electron density deconcentration on the substrate carbon atom, i.e., at the electrophilic site of reactants. The similar electronic structure element in the NBO approach is a lone vacancy on the carbonyl carbon atom in the reactive species. The electronic structure patterns revealed in the NBO and QTAIM-based analyses consistently clarify the reactivity issues in this system.

Dimethyl 4,5-dichlorophthalate

While endeavoring to synthesize new chlorinated ligands for ruthenium-based metathesis catalysts, the title compound dimethyl 4,5-dichlorophthalate, C10H8Cl2O4, was prepared from commercially available 4,5-dichlorophthalic acid in ∼77% yield. The title molecule, which also finds utility as a precursor molecule for the synthesis of drugs used in the treatment of Alzheimer's disease, shows one carbonyl-containing methyl ester moiety lying nearly co-planar with the chlorine-derivatized aromatic ring while the second methyl ester shows a significant deviation of 101.05 (12)° from the least-squares plane of the aromatic ring. Within the crystal, structural integrity is maintained by the concerted effects of electrostatic interactions involving the electron-deficient carbonyl carbon atom and the electron-rich aromatic ring along the a-axis direction and C—H...O hydrogen bonds between neighboring molecules parallel to b.

Durable Modification of Wood by Benzoylation—Proof of Covalent Bonding by Solution State NMR and DOSY NMR Quick-Test

A convenient, broadly applicable and durable wood protection was recently published by Kaufmann and Namyslo. This procedure efficiently allows for esterification of wood hydroxyl groups with (1H-benzotriazolyl)-activated functionalized benzoic acids. The result of such wood-modifying reactions is usually monitored by an increase in mass of the wood material (weight percent gain value, WPG) and by infrared spectroscopy (IR). However, diagnostic IR bands suffer from overlap with naturally occurring ester groups, mainly in the hemicellulose part of unmodified wood. In contrast to known NMR spectroscopy approaches that use the non-commonly available solid state techniques, herein we present solution state NMR proof of the covalent attachment of our organic precursors to wood. The finding is based on a time-efficient, non-uniformly sampled (NUS) solution state 1H,13C-HMBC experiment that only needs a tenth of the regular recording time. The appropriate NMR sample of thoroughly dissolved modified wood was prepared by a mild and non-destructive method. The 2D-HMBC shows a specific cross-signal caused by spin–spin coupling over three bonds from the ester carbonyl carbon atom to the α‑protons of the esterified wood hydroxyl groups. This specific coupling pathway requires a covalent bonding as a conditio sine qua non. An even more rapid test to monitor the covalent bonding was achieved with an up-to-date diffusion-ordered spectroscopy sequence (Oneshot—DOSY) based on 1H or 19F as the sensitive nucleus. The control experiment in a series of DOSY spectra gave a by far higher D value of (1.22 ± 0.06)∙10−10 m2∙s−1, which is in accordance with fast diffusion of the “free” and thus rapidly moving small precursor molecule provided as its methyl ester. In the case of a covalent attachment to wood, a significantly smaller D value of (0.12 ± 0.01)∙10−10 m2∙s−1 was obtained.

Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling

Boronic acids are prospective compounds in inhibition of metallo-β-lactamases as they form covalent adducts with the catalytic hydroxide anion in the enzymatic active site upon binding. We compare this chemical reaction in the active site of the New Delhi metallo-β-lactamase (NDM-1) with the hydrolysis of the antibacterial drug imipenem. The nucleophilic attack occurs with the energy barrier of 14 kcal/mol for imipenem and simultaneously upon binding a boronic acid inhibitor. A boron atom of an inhibitor exhibits stronger electrophilic properties than the carbonyl carbon atom of imipenem in a solution that is quantified by atomic Fukui indices. Upon forming the prereaction complex between NDM-1 and inhibitor, the lone electron pair of the nucleophile interacts with the vacant p-orbital of boron that facilitates the chemical reaction. We analyze a set of boronic acid compounds with the benzo[b]thiophene core complexed with the NDM-1 and propose quantitative structure-sroperty relationship (QSPR) equations that can predict IC50 values from the calculated descriptors of electron density. These relations are applied to classify other boronic acids with the same core found in the database of chemical compounds, PubChem, and proposed ourselves. We demonstrate that the IC50 values for all considered benzo[b]thiophene-containing boronic acid inhibitors are 30–70 μM.

Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations

<p>We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed after binding into the active site the carbonyl group of this inhibitor is accommodated into the oxyanion hole formed by the NH main chain groups of residues 143 to 145. The P1-P3 groups of the inhibitor establish similar interaction with the enzyme to those of equivalent groups in the natural peptide substrate, while the hydroxymethyl moiety of the inhibitor partly mimics the interactions established by the P1’ group of the peptide in the active site. Regarding the formation of the covalent complex, the reaction is initiated after the proton transfer from Cys145 to His41. Formation of the covalent hemithioacetal complex takes place by means of the nucleophilic attack of the Sg atom of Cys145 on the electron deficient carbonyl carbon atom and a proton transfer from the catalytic His41 to the carbonyl oxygen atom mediated by the hydroxyl group. Our findings can be used as a guide to propose modifications of the inhibitor in order to increase its affinity by the 3CL protease.</p>

Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations

<p>We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed after binding into the active site the carbonyl group of this inhibitor is accommodated into the oxyanion hole formed by the NH main chain groups of residues 143 to 145. The P1-P3 groups of the inhibitor establish similar interaction with the enzyme to those of equivalent groups in the natural peptide substrate, while the hydroxymethyl moiety of the inhibitor partly mimics the interactions established by the P1’ group of the peptide in the active site. Regarding the formation of the covalent complex, the reaction is initiated after the proton transfer from Cys145 to His41. Formation of the covalent hemithioacetal complex takes place by means of the nucleophilic attack of the Sg atom of Cys145 on the electron deficient carbonyl carbon atom and a proton transfer from the catalytic His41 to the carbonyl oxygen atom mediated by the hydroxyl group. Our findings can be used as a guide to propose modifications of the inhibitor in order to increase its affinity by the 3CL protease.</p>

Reaction of an Al/P-based frustrated Lewis pair with benzophenone: formation of adducts and aluminium alcoholates via β-hydride elimination

Treatment of the Al/P-based frustrated Lewis pair (FLP) Mes2P–C(AltBu2)=C(H)-Ph (1) with benzophenone afforded the simple 1:1 adduct (4) with a O=CPh2 molecule coordinated to the aluminum atom by an Al←O donor-acceptor bond. Steric repulsion may prevent an interaction between the electrophilic carbonyl carbon atom and the Lewis-basic phosphorus atom. 4 is unstable in solution at room temperature, the coordination to aluminium increases the polarisation of the carbonyl group and favours its reduction. As suggested by quantum chemical calculations, a C–H bond of a tBu group approaches the electrophilic center and facilitates β-hydride elimination with the release of isobutene and the formation of an Al–OCHPh2 ligation. An intact O=CPh2 molecule completes the coordination sphere of the metal atom (5). The second tBu group at aluminium reacts similarly by the selective formation of an Al(OCHPh2)2 moiety (6). The thermodynamics of adduct formation and the mechanism of the hydride shift have been evaluated by quantum chemical DFT calculations.

Crystal and Molecular Structure of 1,1-Bis(methylthio)-5-(4-chlorophenyl)-1,4-pentadien-3-one

The 1,1-bis(methylthio)-5-(4-chlorophenyl)-1,4-pentadien-3-one compound crystallizes in the space group C2/c with unit cell parameters a=25.5763 Å, b=8.08863 Å, c=14.1452 Å, and β=108.6∘. The structure was solved by direct methods and refined to an R-factor of 0.0593. Due to the steric interaction between the two methyl groups, one of the methylthio groups is in cis conformation with C11–C10 double bond and the other is in trans conformation. The cinnamoyl group on the carbonyl carbon atom effects more delocalization of the electrons within the molecule so that the structure is highly conjugated and planar.