Design, synthesis and biological evaluation of sugar-derived Ras inhibitors

The design and synthesis of novel Ras inhibitors with a bicyclic scaffold derived from the natural sugar D-arabinose are presented. Molecular modelling showed that these ligands can bind Ras by accommodating the aromatic moieties and the phenylhydroxylamino group in a cavity near the Switch II region of the protein. All the synthetic compounds were active in inhibiting nucleotide exchange on p21 human Ras in vitro, and two of them selectively inhibited Ras-dependent cell growth in vivo.     

Synthesis, characterization and biological activity of trans-platinum(II) and trans-platinum(IV) complexes with 4-hydroxymethylpyridine

The synthesis and chemical characterization of two new trans platinum complexes, trans-[PtCl(2)NH(3)(4-hydroxymethylpyridine)] (1) and trans-[PtCl(4)NH(3)(4-hydroxymethylpyridine)] (2) are described. Their ability to interact with 5'-GMP by themselves and in the presence of reducing agents in the case of trans-[PtCl(4)NH(3)(4-hydroxymethylpyridine)] were tested. Circular dichroism, electrophoretic mobility in agarose gel, and atomic force microscopy studies showed that the interaction of complex 1 with DNA is stronger than that of complex 2. Cytotoxicity tests against HL-60 tumor cells also showed higher activity for trans-[PtCl(2)NH(3)(4-hydroxymethylpyridine)] than for trans-[PtCl(4)NH(3)(4-hydroxymethylpyridine)]. Complex 1 presents similar behavior to cisplatin, but with a lower IC(50) at 24 h. Complex 1 also showed high apoptosis induction.     

Synthesis and biological evaluation of N-acylhydrazones as inhibitors of MurC and MurD ligases

The Mur ligases have an essential role in the intracellular biosynthesis of bacterial peptidoglycan, and they represent attractive targets for the design of novel antibacterials. A series of compounds with an N-acylhydrazone scaffold were synthesized and screened for inhibition of the MurC and MurD enzymes from Escherichia coli. Compounds with micromolar inhibitory activities against both MurC and MurD were identified, and some of them also showed antibacterial activity.     

Potent inhibitors of LXXLL-based protein-protein interactions

Protein-protein interactions between estrogen receptors, ERalpha and ERbeta, and their coactivators (CoAs) are an attractive target for drug intervention. This interaction is mediated by a small pentapeptide motif (LXXLL), termed the NR box. Based on this motif, a variety of cyclic and linear peptides were synthesized in order to gain a better understanding of the association of CoA proteins with the ER isoforms. Utilizing a time-resolved florescence-based coactivator interaction assay, we determined the abilities of these peptides to inhibit this interaction. Using molecular modeling and CD spectroscopy, we have examined the structural basis of their bioactivities with both hormone receptor isoforms. Either homocysteine or penicillamine was utilized as a substitute for cysteine in the disulfide-bridged peptides, while tertiary leucine and neopentyl glycine were used as the surrogates for the NR box leucines. The most potent disufide-bridged peptide (K(i)= 70 pM, with ERalpha) incorporates neopentyl glycine in the NR box, while the most active peptide in this series with ERbeta (K(i)=350 pM) incorporates tertiary leucine. Surprisingly, several linear peptides containing a single cysteine residue showed activities with low nanomolar K(i) values. Collectively, our results suggest a synthetic approach for designing potent and selective peptidomimetics for ERalpha and ERbeta interactions with CoA proteins effecting estrogen action.     

Structure‐Based Design of New KSP‐Eg5 Inhibitors Assisted by a Targeted Multicomponent Reaction

An integrated multidisciplinary approach that combined structure‐based drug design, multicomponent reaction synthetic approaches and functional characterization in enzymatic and cell assays led to the discovery of new kinesin spindle protein (KSP) inhibitors with antiproliferative activity. A focused library of new benzimidazoles obtained by a Ugi+Boc removal/cyclization reaction sequence generated low‐micromolar‐range KSP inhibitors as promising anticancer prototypes. The design and functional studies of the new chemotypes were assessed by computational modeling and molecular biology techniques. The most active compounds— 20 (IC₅₀=1.49 μM , EC₅₀=3.63 μM ) and 22 (IC₅₀=1.37 μM , EC₅₀=6.90 μM )—were synthesized with high efficiency by taking advantage of the multicomponent reactions.     

Synthesis and biological evaluation of bicyclic nucleosides as inhibitors of M. tuberculosis thymidylate kinase

Herein we describe the synthesis and conformational analysis of a series of bicyclic thymidine derivatives and their evaluation as inhibitors of thymidine monophosphate kinase from Mycobacterium tuberculosis (TMPKmt), based on previously discovered bicyclic sugar nucleosides. With a K(i) value of 2.3 microm, 1-[3-aminomethyl-3,5-dideoxy-2-O,6-N-(thiocarbonyl)-beta-D-ribofuranosyl]thymine emerged as the most potent TMPK inhibitor of this series. Moreover, this promising compound displays inhibitory potency against Mycobacteria cultures with an IC(99) value of 100 microg mL(-1), thus promoting TMPKmt for the first time as a validated target for further inhibitory design. Attempts to rationalise the observed structure-activity relationship (SAR) involving molecular modelling and conformational analysis are described.     

Regioselective Synthesis of Phenols and Halophenols from Arylboronic Acids Using Solid Poly(N‐vinylpyrrolidone)/ Hydrogen Peroxide and Poly(4‐vinylpyridine)/Hydrogen Peroxide Complexes

Solid hydrogen peroxide complexes based on poly(N‐vinylpyrrolidone) and poly(4‐vinylpyridine) were prepared and used as solid hydroxylating reagents. These solid hydrogen peroxide equivalents are found to be much safer, convenient and efficient reagent systems for the ipso‐hydroxylation of arylboronic acids to the corresponding phenols in high yields at a faster rate. The versatility of the reagents has been further expanded for the one‐pot synthesis of halophenols. Density functional theory calculations were carried out on hydrogen peroxide complexes of N‐ethylpyrrolidone and 4‐ethylpyridine as models to get a better understanding of structure and behavior of hydrogen peroxide complexes of the polymers poly(N‐vinylpyrrolidone) and poly(4‐vinylpyridine) compared to aqueous hydrogen peroxide.     

Construction of an ab initio kinetic model for industrial ethane pyrolysis

The industrial steam cracking of ethane was simulated using an ab initio kinetic model. The reaction network consists of 20 species and 150 reversible elementary reactions. The thermodynamic and kinetic parameters were obtained from ab initio CBS‐QB3 and W1U calculations and agree well with available experimental data. Predicted C₂H₆, C₂H₄, and H₂ yields are within 5% of experimental data for the three sets of conditions tested. Though CH₄ yields and outlet temperatures are particularly sensitive to the accuracy of the kinetic parameters, they are simulated with an accuracy of better than 10%. Larger deviations for the C₃H₆ and C₂H₂ yields are attributed to the limited size of the reaction network. The effect of total pressure on the rate coefficients was evaluated using Quantum Rice‐Ramsberger‐Kassel theory with the Modified Strong‐Collision approximation, and was found to be relatively minor for the reaction conditions tested. This study hence demonstrates the feasibility of simulating complex radical reactions using a predictive kinetic model derived from state‐of‐the‐art quantum chemical calculations. © 2010 American Institute of Chemical Engineers AIChE J, 2011     

Structure/Enthalpy of Formation Relationships for Hydrocarbons Containing Benzene Rings

Simple protocols to convert molecular mechanics (MMX/PCMODEL), semiempirical PM3, and HF ab initio energies to accurate heats of formation for hydrocarbons with benzene rings are described. The data set consists of every hydrocarbon benzene derivative with an experimentally determined ΔH_f^o (g), and the ΔH_f^o (g)'s cover a range of -140 to +410 kJ/mol. The molecular structures are comprised of numerous structural types. Hierarchical sets of molecular structure parameters are defined to describe these molecules. The independent variables include atom types (level 1), group and ring terms (level 2), nonbonded atom interactions (level 3), and the calculated MMX, PM3 or ab initio HF energies, which contribute a final level 4 parameter for rectification of the ΔH_f^o (g) data. The additivity, level 1-3 parameters give an excellent correlation of the experimental ΔH_f^o (g)'s, average error = 3.4 kJ, and maximum error = 12.1 kJ. However, the correlations are further enhanced by addition of any level 4 parameter, with maximum improvement coming at the 6-31G*//STO-3G HF level of calculation.     

Naphthoxazepine inhibitors of HIV-1 integrase: synthesis and biological evaluation

Two sets of compounds derived from the fusion of a diversely annulated naphthoxazepinedione system with 1,3-thiazole and 1,3-oxazole are described. These compounds are close analogues of previously reported thiazolothiazepine inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN). Some of the new derivatives show potency similar to that of the reference compounds, thus gaining further insight into the structure-activity relationship of this class of IN inhibitors.     

Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach

The varied yet family‐specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH‐family‐specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low‐nanomolar inhibitor that is selective for GH family 47 inverting α‐mannosidases. Here we show, through quantum‐mechanical approaches, that kifunensine is restrained to a “ring‐flipped” ¹C₄ conformation with another accessible, but higher‐energy, region around the ^1,4B conformation. The conformations of kifunensine in complex with a range of GH47 enzymes—including an atomic‐level resolution (1 Å) structure of kifunensine with Caulobacter sp. CkGH47 reported herein and with GH family 38 and 92 α‐mannosidases—were mapped onto the kifunensine free‐energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymes but cannot mimic any conformational states relevant to the reaction coordinate of mannosidases from other families.     

Synthesis of N-heteroaryl retinals and their artificial bacteriorhodopsins

N-Heteroaryl retinals derived from indole, 1-indolizine and 3-indolizine (10 a-c) have been synthesized after their UV/Vis red-shifted absorption properties had been predicted by time-dependent density functional theory (TD-DFT) computations. The three new analogues form artificial pigments upon recombination with bacterioopsin: indolyl retinal 10 a undergoes fast and efficient reconstitution to form a species with a UV/Vis absorbance maximum similar to that of wild-type bacteriorhodopsin, whilst the indolizinyl retinals 10 b and 10 c also reconstitute in significant proportion to give noticeably red-shifted, although unstable, pigments. Significant changes in the pK(a) values of these artificial bacteriorhodopsins are interpreted as arising from nonoptimal binding-site occupancy by the chromophore due to steric constraints.     

Synthesis and biological activity of a novel inhibitor of dihydroceramide desaturase

A novel mechanism-based dihydroceramide desaturase inhibitor (XM462) in which the substrate C5 methylene group is replaced by a sulfur atom is reported. Dihydroceramide desaturase inhibition occurred both in vitro and in cultured cells with IC(50) values of 8.2 and 0.78 microM, respectively, at a substrate concentration of 10 microM. In vitro experiments showed that XM462 produced a mixed-type inhibition (K(i)=2 microM, alpha=0.83). LC-MS analyses showed that accumulation of endogenous dihydroceramides occurred in cells upon treatment with XM462 in serum-free medium, whereas ceramides built up in controls. In addition, XM462 was found to be metabolised to its 1-glucosyl and 1-phosphocholine derivatives, and to the products of N-deacylation and reacylation with palmitoyl and stearoyl groups. In Jurkat A3 cells cultured in serum-free medium, viability, as the percentage of trypan blue unstained cells in total cells, was reduced upon XM462 treatment (5 microM, 24 h), but not in controls. The interest of this compound is discussed.     

Synthesis and evaluation of TAC-based inhibitors of papain as mimics of cystatin B

An approach for mimicking protein-protein interactions by using a discontinuous epitope to construct a mimic that is about one tenth of the size of a natural inhibitor of papain, namely, cystatin B, is described. The discontinuous epitope of cystatin B, which is involved in the interaction with papain, was mimicked by synthesis of a tripodal molecular construct by using the triazacyclophane (TAC) scaffold. The mimic contains three peptide arms: one that mimics the N terminus, one that mimics the C terminus, and one that mimics the beta-hairpin loop structure of cystatin B. These peptide sequences were assembled on the TAC scaffold. The resulting cystatin mimic, CysTACtin 9, showed excellent inhibition of papain with a K(i) of 12 nM, which approaches the inhibitory potency of cystatin B (K(i)=0.12 nM). Experiments with molecular constructs that contained one or two arms or a mixture of the nonscaffolded peptides showed that both scaffolding and the presence of the three peptide arms are crucial for a successful mimic.     

Theoretical estimation of the apparent rate constants for ozone decomposition in gas and aqueous phases using ab initio calculations

An ab initio study, using the coupled cluster calculations (CCSD) method was conducted to investigate the kinetics of the ozone degradation in gas and aqueous phases considering the reaction of ozone with the hydroperoxyl radical. Two potential transition state paths, oxygen and hydrogen transfer, are studied and compared. It was revealed by the ab initio quantum chemical calculations that the calculated overall rate constant in the gas phase differs by approximately an order of magnitude from measured values. However, the calculated selectivity (branching fraction), which was measured directly with isotope studies of hydrogen atom transfer, is almost exactly equal to the experimental value at 298.15 K. The sensitivity analysis showed that adding the reaction between ozone and hydroperoxyl radical to the kinetic model accelerates the decomposition process by more than four times in the aqueous phase (pH = 7–8.5), and for an order of magnitude change in the rate constant of this reaction, the decomposition half-life changes by 20–45 %. This result might affect our understanding of atmospheric ozone chemistry.     

Synthesis of stable analogues of geranylgeranyl diphosphate possessing a (Z,E,E)-geranylgeranyl side chain, docking analysis, and biological assays for prenyl protein transferase inhibition

Herein, we report the synthesis of novel stable analogues of geranylgeranyl diphosphate (GGPP), in which the "natural" all-trans geranylgeranyl portion has been replaced by a (Z,E,E)-geranylgeranyl chain. The change in configuration and consequent change in the relative position of the polar portion with the lipophilic side chain did not improve the properties of the E,E,E analogues in their inhibition of geranylgeranyl protein transferase I (GGTase I). However, a significant level of GGTase I inhibition and selectivity for GGTase I over farnesyl transferase (FTase) was maintained the unsubstituted phosphonoacetamidoxy derivative 4 a. This has shed light on the relative importance of the configuration at the C2=C3 double bond among GGPP derivatives. Moreover, the biological activities of all the compounds reported herein, in particular the preferential FTase inhibitory activity shown by compound 6, were in good agreement with the results of docking analysis.