540 Chemie und zugeordnete Wissenschaften
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Reliable prediction of the isotropic hyperfine coupling constant, a\(_{iso}\), is still a difficult task for ab initio calculations. Strong dependence on the method used for its calculation is found. Within a truncated multi-referencc ansatz a\(_{iso}\) is strongly affected by the size ofthe reference space and the nurober of terms in the truncated Cl expansion. In the present paperdifferent effects of the neglected Cl space are discussed. Modified B\(_K\) and A\(_K\) methods are used to estimate the contributions ofthe neglected configurations. lt can be shown that a combination of both methods is able to recover about 90-9 S% of the total error in a\(_{iso}\)· Furthermore, it was found that to obtain about 90% of the B\(_K\) correction only about I 0-20% ofthe configurations within H0 have to be corrected.
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
The concepts of aromaticity and antiaromaticity have a long history, and countless demonstrations of these phenomena have been made with molecules based on elements from the p, d, and f blocks of the periodic table. In contrast, the limited oxidation‐state flexibility of the s‐block metals has long stood in the way of their participation in sophisticated π‐bonding arrangements, and truly antiaromatic systems containing s‐block metals are altogether absent or remain poorly defined. Using spectroscopic, structural, and computational techniques, we present herein the synthesis and authentication of a heterocyclic compound containing the alkaline earth metal beryllium that exhibits significant antiaromaticity, and detail its chemical reduction and Lewis‐base‐coordination chemistry.
The facile synthesis and detailed investigation of a class of highly potent protease inhibitors based on 1,4-naphthoquinones with a dipeptidic recognition motif (HN-l-Phe-l-Leu-OR) in the 2-position and an electron-withdrawing group (EWG) in the 3-position is presented. One of the compound representatives, namely the acid with EWG = CN and with R = H proved to be a highly potent rhodesain inhibitor with nanomolar affinity. The respective benzyl ester (R = Bn) was found to be hydrolyzed by the target enzyme itself yielding the free acid. Detailed kinetic and mass spectrometry studies revealed a reversible covalent binding mode. Theoretical calculations with different density functionals (DFT) as well as wavefunction-based approaches were performed to elucidate the mode of action.
Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the S\(_N\)Ar addition/elimination reactions. Such building blocks have only rarely been employed for the design of enzyme inhibitors. Herein, we demonstrate the combination of a peptidic recognition sequence with such electrophilic (het)arenes to generate highly active inhibitors of disease-relevant proteases. We further elucidate an unexpected mode of action for the trypanosomal protease rhodesain using NMR spectroscopy and mass spectrometry, enzyme kinetics and various types of simulations. After hydrolysis of an ester function in the recognition sequence of a weakly active prodrug inhibitor, the liberated carboxylic acid represents a highly potent inhibitor of rhodesain (K\(_i\) = 4.0 nM). The simulations indicate that, after the cleavage of the ester, the carboxylic acid leaves the active site and re-binds to the enzyme in an orientation that allows the formation of a very stable π-complex between the catalytic dyad (Cys-25/His-162) of rhodesain and the electrophilic aromatic moiety. The reversible inhibition mode results because the S\(_N\)Ar reaction, which is found in an alkaline solvent containing a low molecular weight thiol, is hindered within the enzyme due to the presence of the positively charged imidazolium ring of His-162. Comparisons between measured and calculated NMR shifts support this interpretation
We have investigated theoretically the importance of the O(\(^3\)P)+CH(a\(^4\sum^-\)) and the O(\(^3\)P)+CH(X\(^2\Pi\)) channels in the collinear chemi-ionization reaction O+CH->HCO\(^+\) +e\(^-\). We have found that both channels may lead to chemi-ionization via favorable Franck-Condon overlaps with the states ofthe ionic species.
The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable \(^{19}\)F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the \(^{19}\)F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of \(^{19}\)F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.
The development of ligands capable of effectively stabilizing highly reactive main‐group species has led to the experimental realization of a variety of systems with fascinating properties. In this work, we computationally investigate the electronic, structural, energetic, and bonding features of proximity‐enforced group 13–15 homodimers stabilized by a rigid expanded pincer ligand based on the 1,8‐naphthyridine (napy) core. We show that the redox‐active naphthyridine diimine (NDI) ligand enables a wide variety of structural motifs and element‐element interaction modes, the latter ranging from isolated, element‐centered lone pairs (e.g., E = Si, Ge) to cases where through‐space π bonds (E = Pb), element‐element multiple bonds (E = P, As) and biradical ground states (E = N) are observed. Our results hint at the feasibility of NDI‐E2 species as viable synthetic targets, highlighting the versatility and potential applications of napy‐based ligands in main‐group chemistry.
Reliable prediction of the isotropic hyperfine coupling constant A\(_{iso}\) is still a difficult task for ab initio calculations. Strang dependence on the method employed for its ca1culation has been found. Within a CI ansatz A\(_{iso}\) is considerably affected by the excitation classes taken into account within the CI calculation. In the present work the influence of various excitation classes on A\(_{iso}\) is examined. Calculations including all single, double, triple and a large part of the quadruple excitations are performed and the individual effects of the excitation classes are studied. It is found that the surprisingly good agreement found for S-CI treatments is due to large error cancellations. The importance of higher than double excitations arises from their indirect influence on the single excitations.
Multi-reference configuration interaction calculations employing various orbital transformations are undertaken to obtain the isotropic hyperfine coupling constant a\(_{iso\) in nitrogen and a\(_{iso\) (H) in the CH molecule. The natural orbital (NO) basis is found to be more effective than the simple RHF-MO basis; the most obvious is a basis of spin natural orbitals (SNO). It is found that a\(_{iso\) is approached from opposite sides in the NO and 2s shell SNO basis if the CI expansion is increased. Both results are within a few percent of the full CI Iimit for the nitrogen atorn (in the given AO basis) and the experimental value for Hin the CH radical. Various features ofthe SNO are discussed.