Eliška Procházková

Highly Selective Phosphatidylinositol 4-Kinase IIIβ Inhibitors and Structural Insight into Their Mode of Action

Phosphatidylinositol 4-kinase IIIβ is a cellular lipid kinase pivotal to pathogenesis of various RNA viruses. These viruses hijack the enzyme in order to modify the structure of intracellular membranes and use them for the construction of functional replication machinery. Selective inhibitors of this enzyme are potential broad-spectrum antiviral agents, as inhibition of this enzyme results in the arrest of replication of PI4K IIIβ-dependent viruses. Herein, we report a detailed study of novel selective inhibitors of PI4K IIIβ, which exert antiviral activity against a panel of single-stranded positive-sense RNA viruses. Our crystallographic data show that the inhibitors occupy the binding site for the adenine ring of the ATP molecule and therefore prevent the phosphorylation reaction.

Microwave-assisted hydrolysis of phosphonate diesters: an efficient protocol for the preparation of phosphonic acids

A new highly efficient method for the hydrolysis of acyclic nucleoside phosphonate diesters (or generally of any organophosphonates) to the corresponding phosphonic acids has been developed. This novel methodology employs inexpensive hydrochloric acid in equimolar amounts to the number of ester groups present in the molecule and thus, avoids using trimethylsilyl halogenides, the standard reagents for these types of transformations. Moreover, simple and easy work-up of the reaction mixture affords very clean products in high yields (usually 77–93%). Another advantage of the described hydrolysis of phosphonate diesters is the fact that the course of the reaction can be instantly monitored through pressure changes in the reaction vessel. This ‘green’ method has also been successfully used for the preparation of otherwise synthetically difficult to access (phosphonomethoxy)ethyl (PME) derivatives of guanine (PMEG) and hypoxanthine (PMEHx), and furthermore, the method gains access to important novel acyclic nucleoside phosphonates derived from 2-chlorohypoxanthine and from xanthine (e.g. PMEX).

Resolution of Organic Polymorphic Crystals by Raman Spectroscopy

Depending on crystallization conditions, many organic compounds can form crystals of different structure. Their proper characterization is important, for example, in the pharmaceutical industry. While the X-ray diffractometry established as a standard method, alternative techniques are desirable for broader application flexibility and economic reasons. In the present study, Raman spectroscopy combined with the density functional calculations is suggested as a complementary method to the X-ray and other higher resolution techniques. The potential to discriminate structural differences in polymorphic crystalline forms is documented on three model compounds of industrial importance. Methacrylamide, piracetam, and 2-thiobarbituric acid were crystallized under various conditions, and their Raman spectra were recorded using 532 and 1064 nm laser excitations. X-ray diffractometry and nuclear magnetic resonance spectroscopy were used as complementary techniques to verify sample composition and structure. To interpret the observed differences in Raman frequencies and intensities, three computational strategies were explored based on single molecule, a cluster model, and a plane-wave periodic boundary conditions calculation. The single-molecule modeling was found inadequate, whereas the plane-wave approach provides the most realistic spectra. For all compounds, the differences in the Raman spectra of polymorphic forms could be unambiguously assigned to the simulations. The modeling revealed that the spectral differences were caused by the molecular structure itself as well as by crystal packing. The relative importance of these factors significantly varied across the investigated samples. Owing to its simplicity, Raman spectroscopy appears to be a promising technique capable of reliable discriminating between organic crystal polymorphic states.

A switchable intramolecular hydrogen bond in polysubstituted 5-nitrosopyrimidines.

The formation of strong intramolecular hydrogen bonds was observed in a series of 2-amino-5-nitrosopyrimidines with alkylamino and arylamino substituents at positions 4 and 6. Mixtures of two rotamers differing in the orientation of the nitroso group were observed in the NMR spectra of the compounds where two distinct intramolecular hydrogen bonds could be formed. The ratio of the two rotamers depends strongly on the character of the substituents at positions 4 and 6 and can be finely tuned over a broad range of conformation ratios. The experimental results were supported by DFT calculations, which also made it possible to explain the apparent contradiction in the experimental dependence of the rotamer ratio on the Hammett constants for the arylamino substituents. The UV/vis spectra of the compounds also significantly depend on the nature of the substituents; however, the orientation of the nitroso group does not have any influence on the position of the absorption bands in the spectra.

Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates as Inhibitors of Plasmodium falciparum and Human 6-Oxopurine Phosphoribosyltransferases.

Acyclic nucleoside phosphonates (ANPs) are a promising class of antimalarial therapeutic drug leads that exhibit a wide variety of Ki values for Plasmodium falciparum (Pf) and human hypoxanthine‐guanine‐(xanthine) phosphoribosyltransferases [HG(X)PRTs]. A novel series of ANPs, analogues of previously reported 2‐(phosphonoethoxy)ethyl (PEE) and (R,S)‐3‐hydroxy‐2‐(phosphonomethoxy)propyl (HPMP) derivatives, were designed and synthesized to evaluate their ability to act as inhibitors of these enzymes and to extend our ongoing antimalarial structure–activity relationship studies. In this series, (S)‐3‐hydroxy‐2‐(phosphonoethoxy)propyl (HPEP), (S)‐2‐(phosphonomethoxy)propanoic acid (CPME), or (S)‐2‐(phosphonoethoxy)propanoic acid (CPEE) are the acyclic moieties. Of this group, (S)‐3‐hydroxy‐2‐(phosphonoethoxy)propylguanine (HPEPG) exhibits the highest potency for PfHGXPRT, with a Ki value of 0.1 μM and a Ki value for human HGPRT of 0.6 μM. The crystal structures of HPEPG and HPEPHx (where Hx=hypoxanthine) in complex with human HGPRT were obtained, showing specific interactions with active site residues. Prodrugs for the HPEP and CPEE analogues were synthesized and tested for in vitro antimalarial activity. The lowest IC50 value (22 μM) in a chloroquine‐resistant strain was observed for the bis‐amidate prodrug of HPEPG.

Norbornane-based nucleoside and nucleotide analogues locked in North conformation

We report on the synthesis of novel conformationally locked nucleoside and nucleotide derivatives, which are structurally closely related to clinically used antivirals such as didanosine and abacavir. As a suitable conformationally rigid substitute of the sugar/pseudosugar ring allowing a permanent stabilization of the nucleoside in North conformation we employed bicyclo[2.2.1]heptane (norbornane) substituted in the bridgehead position with a hydroxymethyl group and in the C-3 position with a nucleobase. Prepared nucleoside derivatives were also converted into appropriate phosphoramidate prodrugs (ProTides) in order to increase delivery of the compounds in the cells. All target compounds were evaluated in a broad antiviral and cytostatic assay panel.

Uncovering Key Structural Features of an Enantioselective Peptide-Catalyzed Acylation Utilizing Advanced NMR Techniques

We report on a detailed NMR spectroscopic study of the catalyst-substrate interaction of a highly enantioselective oligopeptide catalyst that is used for the kinetic resolution of trans-cycloalkane-1,2-diols via monoacylation. The extraordinary selectivity has been rationalized by molecular dynamics as well as density functional theory (DFT) computations. Herein we describe the conformational analysis of the organocatalyst studied by a combination of nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC)-based methods that resulted in an ensemble of four final conformers. To corroborate the proposed mechanism, we also investigated the catalyst in mixtures with both trans-cyclohexane-1,2-diol enantiomers separately, using advanced NMR methods such as T1 relaxation time and diffusion-ordered spectroscopy (DOSY) measurements to probe molecular aggregation. We determined intramolecular distance changes within the catalyst after diol addition from quantitative NOE data. Finally, we developed a pure shift EASY ROESY experiment using PSYCHE homodecoupling to directly observe intermolecular NOE contacts between the trans-1,2-diol and the cyclohexyl moiety of the catalyst hidden by spectral overlap in conventional spectra. All experimental NMR data support the results proposed by earlier computations including the proposed key role of dispersion interaction.

From norbornane-based nucleotide analogs locked in South conformation to novel inhibitors of feline herpes virus

A synthetic route toward a series of unique cyclic nucleoside phosphonates locked in South conformation is described. The desired conformation is stabilized by a substitution of the sugar moiety by bicyclo[2.2.1]heptane (norbornane) bearing a purine or pyrimidine nucleobase in the bridgehead position. Although the final phosphonate derivatives are devoid of any significant antiviral activity probably due to the unfavorable conformational properties, several intermediates and their analogs exhibit surprising activity against feline herpes virus. Since these compounds do not possess an appropriate hydroxymethyl function allowing phosphorylation and subsequent incorporation into the polynucleotide chain, it seems to be likely that these compounds act by a novel unknown mechanism of action and may represent a new possible alternative for nucleoside and nucleotide therapeutics of this widely spread feline infection. A number of derivatives exerted also a significant antiviral activity against Coxsackievirus B3 and B4.

Tunable Push–Pull Interactions in 5-Nitrosopyrimidines

The effect of push-pull interactions in a series of variously substituted 5-nitrosopyrimidines on the strength of intramolecular hydrogen bonds, the height of rotational barriers around formally single bonds, UV-vis spectra and electrochemical behavior is explored. Intramolecular charge transfer (ICT) leads to a shift of electron density from electron-donating substituents, which is readily observable by NMR spectroscopy. The 5-nitroso group is able to form strong intramolecular hydrogen bonds with neighboring amino substituents. As a result, two rotamers with reversed orientation of the 5-nitroso group are observed for compounds with two different hydrogen-bond donors in neighboring positions. The barriers of interconversion between the two rotamers are strongly influenced by ICT, whereas the ratio of such rotamers depends primarily on the character of the hydrogen-bond donors. The ICT also significantly affects the position of UV-vis absorption maxima, which can be tuned in a broad range of 100 nm by the selection of appropriate substituents. Finally, ICT influences oxidation potential of the 5-nitrosopyrimidines and the stability of the resulting nitroso radical cations, the structures of which are determined by EPR spectroscopy.

Purine analogs as phosphatidylinositol 4-kinase IIIβ inhibitors

Abstract We report on an extensive structure–activity relationship study of novel PI4K IIIβ inhibitors. The purine derivative of the potent screening hit T-00127-HEV1 has served as a suitable starting point for a thorough investigation of positions 8 and 2. While position 8 of the purine scaffold can only bear a small substituent to maintain the inhibitory activity, position 2 is opened for extensive modification and can accommodate even substituted phenyl rings without the loss of PI4K IIIβ inhibitory activity. These empirical observations nicely correlate with the results of our docking study, which suggests that position 2 directs towards solution and can provide the necessary space for the interaction with remote residues of the enzyme, whereas the cavity around position 8 is strictly limited. The obtained compounds have also been subjected to antiviral screening against a panel of (+)ssRNA viruses.