A complicated path of salicylaldehyde through the Biginelli reaction: a case of unexpected spiroketalization

Cyclocondensation of salicylaldehydes with alkyl acetoacetates and 2-aminobenzothiazoles or 2-amino-5-methylthiazole under classical Biginelli reaction conditions gives rare hetarylamino substituted 2,2′-spirobischromanecarboxylate derivatives. The mechanism and observed stereoselectivity of the unexpected pseudo-four-component process are discussed.     

Design,structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease

Abstract  

Serine protease activity of the NS3 protein of Dengue virus is an important target of antiviral agents that interfere with the viral polyprotein precursor processing catalyzed by the NS3 protease (NS3pro), which is important for the viral replication and maturation. Recent studies showed that substrate-based peptidomimetics carrying an electrophilic warhead inhibit the NS2B-NS3pro cofactor-protease complex with inhibition constants in the low micromolar concentration range when basic amino acid residues occupy P₁ and P₂ positions of the inhibitor, and an aldehyde warhead is attached to the P₁. We have used computer-assisted combinatorial techniques to design, focus using the NS2B-NS3pro receptor 3D structure, and in silico screen a virtual library of more than 9,200 peptidomimetic analogs targeted around the template inhibitor Bz-Nle-Lys-Arg-Arg-H (Bz—benzoyl) that are composed mainly of unusual amino acid residues in all positions P₁–P₄. The most promising virtual hits were analyzed in terms of computed enzyme-inhibitor interactions and Adsorption, Distribution, Metabolism and Excretion (ADME) related physico-chemical properties. Our study can direct the interest of medicinal chemists working on a next generation of antiviral chemotherapeutics against the Dengue Fever towards the explored subset of the chemical space that is predicted to contain peptide aldehydes with NS3pro inhibition potencies in nanomolar range which display ADME-related properties comparable to the training set inhibitors.     

Ab Initio Calculations for FO3, FO 3 + , and FO 3 - Complexes Formed by Fluorine with Ozone

Complexes formed by fluorine with ozone, featuring neutral, positive, and negative species, as well as the decomposition reactions of the complexes are investigated with quantum chemical calculations, using the 6-311G* and the 6-311+G* basis sets, with the Moller-Plesset method. The most stable structures of the complexes are identified and the energies of the reactions of the complexes' formation and decomposition are obtained.     

Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> thymidine monophosphate kinase

Abstract  

Thymidine monophosphate kinase (TMPK_mt) is an essential enzyme for nucleotide metabolism in Mycobacterium tuberculosis, and thus an attractive target for novel antituberculosis agents. In this work, we have explored the chemical space around the 2′,3′-bicyclic thymidine nucleus by designing and in silico screening of a virtual focused library selected via structure based methods to identify more potent analogs endowed with favorable ADME-related properties. In all the library members we have exchanged the ribose ring of the template with a cyclopentane moiety that is less prone to enzymatic degradation. In addition, we have replaced the six-membered 2′,3′-ring by a number of five-membered and six-membered heterocyclic rings containing alternative proton donor and acceptor groups, to exploit the interaction with the carboxylate groups of Asp9 and Asp163 as well as with several cationic residues present in the vicinity of the TMPK_mt binding site. The three-dimensional structure of the TMPK_mt complexed with 5-hydroxymethyl-dUMP, an analog of dTMP, was employed to develop a QSAR model, to parameterize a scoring function specific for the TMPK_mt target and to select analogues which display the highest predicted binding to the target. As a result, we identified a small highly focused combinatorial subset of bicyclic thymidine analogues as virtual hits that are predicted to inhibit the mycobacterial TMPK in the submicromolar concentration range and to display favorable ADME-related properties.     

QSAR and Mechanistic studies on the genotoxic compounds including environmental effects

The effects of a proximate condensed environment as the solvent and cellular structured patterns (biopolymers, membranes, etc.) play an important role in determination of the courses of molecular processes in biology. We present here the background of methods developed for such an environmental effects estimation combining the continuum and discrete models. Their applications within theoretical studies into the mechanisms of carcinogenic action of alkylating N-nitrosocompounds are shown. The results given cover four different areas, namely the quantitative structure-activity relationship, mechanistic studies into their metabolic activation reactions, interactions of the ultimate carcinogens with DNA, and finally their genetic consequences.     

Molecular Interactions and Inclusion Phenomena in Substituted β-Cyclodextrins. Simple Inclusion Probes: H2O, C, CH4, C6H6, NH4 +, HCOO−

Using a simple molecular mechanics approach interaction energy profiles of simple probes (C, CH₄, C₆H₆, H₂O, NH₄ ⁺, and HCOO^-) passing through the center of the -CD ring cavity along the main molecular symmetry axis were first evaluated. Molecular Electrostatic Potential (MEP) values along the same path were also evaluated. The effect of the flexibility of the host -CD molecule together with solute-solvent (H₂O) interactions have been represented by averaging structures of MD calculations for -CD alone and -CD surrounded by 133 H₂O molecules. The effect of various substitutions of -CD has also been evaluated. Small symmetric hydrophobic probes (such as C, CH₄, C₆H₆) are predicted to form stable inclusion complexes with non-substituted and substituted -CDs, the probe position typically being near the cavity center. The stability of the inclusion complexes will increase with increasing size and aliphatic character of the probe. Small polar and charged probes (such as H₂O, NH₄ ⁺, HCOO^-) are predicted to prefer the interaction with the solvent (water) in the bulk phase rather than the formation of inclusion complexes with non-substituted and substituted -CDs. Guest–host interactions in the stable inclusion complexes with hydrophobic probes are almost entirely dominated by dispersion interactions. The MEP reaches magnitudes close to zero in the center of the non-substituted -CD ring cavity and in most of the studied substituted -CDs and shows maximum positive or negative values outside of the cavity, near the ring faces. Substitution of -CD by neutral substituents leads to enhanced binding of hydrophobic probes and significant changes in the MEP profile along the -CD symmetry axis.