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The synthesis, inhibitory activity and mode of action of oxazolidine-2,4-diones against porcine pancreatic elastase, here used as a model for human neutrophil elastase, are reported. The nature of N-substitution at the oxazolidine-2,4-dione scaffold has large effect on the inhibitory potency against elastase. N-Acyl and N-sulfonyloxazolidine-2,4-diones emerged as potent pseudo-irreversible inhibitors, displaying high second-order rate constants for PPE inactivation. The title compounds were also shown to be potent inhibitors of human neutrophil elastase (HNE) and proteinase-3, and weak inhibitors of human cathepsin G. The results herein presented show that the oxazolidine-2,4-diones represent a new promising class of serine protease inhibitors.

Cytochrome bc(1) is a validated drug target in malaria parasites. The spread of Plasmodium falciparum strains resistant to multiple antimalarials emphasizes the urgent need for new drugs. We screened in silico the ZINC and MOE databases, using ligand- and structure-based approaches, to identify new leads for development. The most active compound presented an IC(50) value against cultured P. falciparum of 2 μM and a docking pose consistent with its activity.

Chronic obstructive pulmonary disease (COPD) is a major increasing health problem and the World Health Organization (WHO) reports COPD as the fifth leading cause of death worldwide. COPD refers to a condition of inflammation and progressive weakening of the structure of the lung as well as irreversible narrowing of the airways. Current treatment is only palliative and no available drug halts the progression of the disease. Human neutrophil elastase (HNE) is a serine protease, which plays a major role in the COPD inflammatory process. The protease/anti-protease imbalance leads to an excess of extracellular HNE hydrolyzing elastin, the structural protein that confers elasticity to the lung tissue. Although HNE was identified as a therapeutic target for COPD more than 30 years ago, only Sivelestat (ONO-5046), an HNE inhibitor from Ono Pharmaceutical, has been approved for clinical use. Nevertheless, Sivelestat is only approved in Japan and its development in the USA was terminated in 2003. Other inhibitors in pre-clinical or phase I trials were discontinued for various reasons. Hence, there is an urgent need for low-molecular-weight synthetic elastase inhibitors and the present review discusses the recent advances on this field covering acylating agents, transition-state inhibitors, mechanism-based inhibitors, relevant natural products, and major patent disclosures.

Allopsoralens are angular psoralen derivatives presenting advantages over the parent compound because of monofunctional DNA-photobinding and consequent lower toxicity. Allopsoralen molecules with three different substituents and different protonation states were studied using the molecular dynamics technique. The location of these molecules when inside the lipid bilayer is of major importance because their photochemical properties can change with the environment. Also, the ability of psoralens to form photoadducts with unsaturated phospholipids depends on the preference of the molecules to locate themselves closer to the bilayer middle were the double bond functionality can be found. Herein we show that the allopsoralens tend to accumulate inside the lipid bilayer closer to the water interface when protonated or closer to the interface middle otherwise. Allopsoralens containing one amine terminated carbon chain tend to have different rotational and orientational behaviour and an orientation preference close to the ones shown by the lipids. The size and chemical nature of the substituent also affect the molecular mobility and capacity to interact with water molecules and the nitrogen or phosphorus atoms of the lipids.

The design, synthesis and evaluation of 3-methylene-substituted indolinones as falcipain inhibitors and antiplasmodial agents are described. These compounds react readily with thiols via an addition-elimination mechanism, indicating their potential as cysteine protease inhibitors. Several indolinones containing a Leu-i-amyl recognition moiety were found to be moderate inhibitors of the Plasmodium falciparum cysteine protease falcipain-2, but not of the related protease falcipain-3, and displayed antiplasmodial activity against the chloroquine-resistant P. falciparum W2 strain in the low micromolar range. Coupling a 7-chloroquinoline moiety to the 3-methylene-substituted indolinone scaffold led to a significant improvement in antiplasmodial activity.

The first structure-activity relationship study of vinyl sulfones as caspase-3 inhibitors is reported. A series of 12 vinyl sulfones was synthesized and evaluated for two downstream caspases (caspases-3 and -7). Dipeptidyl derivatives were significantly superior to their counterparts containing only Asp at P(1), as caspase-3 inhibitors. Fmoc-Val-Asp-trans-CH=CH-SO(2)Me was the most potent inhibitor of caspase-3 in the series, with a IC(50) of 29 microM and a second-order rate constant of inactivation, k(inact)/K(i), of 1.5 M(-1) s(-1). Computational studies suggest that the second amino acid occupies position S(3) of the enzyme. In addition, Fmoc-Val-Asp-trans-CH=CH-SO(2)Ph was inactive for caspase-7 for the tested concentrations.

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(1H-Pyridin-4-ylidene)amines containing lipophilic side chains at the imine nitrogen atom were prepared as potential clopidol isosteres in the development of antimalarials. Their antiplasmodial activity was evaluated in vitro against the Plasmodium falciparum W2 (chloroquine-resistant) and FCR3 (atovaquone-resistant) strains. The most active of these derivatives, 4m, had an IC50 of 1 mu M against W2 and 3 mu M against FCR3. Molecular modeling studies suggest that (1H-pyridin-4-ylidene) amines may bind to the ubiquinol oxidation Q(o) site of cytochrome bc(1). (C) 2009 Elsevier Ltd. All rights reserved.. - Funda ao para a Ciencia e Tecnologia (FCT, Portugal) ; Doris Duke Charitable Foundation Distinguished Clinical Scientist [SFRH/BD/30689/2006]. - This work was supported by Funda ao para a Ciencia e Tecnologia (FCT, Portugal); T. R. acknowledges FCT for the Ph. D. grant SFRH/BD/30689/2006. P.J.R. is a Doris Duke Charitable Foundation Distinguished Clinical Scientist.

The promising photosensitizing properties of hypericin, a substituted phenanthroperylene quinone naturally found in Saint John's wort, has led to the proposal that it can be utilized in photodynamic therapy, Structurally modified derivatives are at the present time being investigated to generate a more effective hypericin photosensitizer. Neither the detailed mechanism behind the powerful action of hypericin, arising as a result of light excitation, nor the intracellular localization and transportation is still fully understood. In the present work, molecular dynamics simulations have been performed to study the properties and the permeability of hypericin and modifications thereof, substituted with one or four bromine atoms, in a dipalmitoylphosphatidylcholine lipid membrane. The molecules were found to accumulate in the most dense region of the lipids due to competing interactions with the hydrophobic lipid interior and the polar aqueous environment. This was confirmed by analyzing the radial distribution functions and by the density profiles of the system components. Calculated free energy profiles display large negative changes in free energy for the transport process of the molecules into the lipids, which also support this finding. Permeability coefficients show overall fastest diffusion in the membrane system for hypericin containing one bromine.. - Modelling and Simulation Research Center (ESEE) ; Swedish Research Council ; Faculty of Science and Technology at Orebro University ; National University of Ireland, Galway ; The Portuguese Fundacao para a Ciencia e a Tecnologia. - Financial Support from the Modelling and Simulation Research Center (ESEE), the Swedish Research Council, the Faculty of Science and Technology at Orebro University, and the National University of Ireland, Galway (LAE), is gratefully acknowledged. We also acknowledge generous grants of computing time at the National Supercomputing Center (NSC) in Linkoping. The Portuguese Fundacao para a Ciencia e a Tecnologia is also acknowledged for financial support.

A new class of inhibitors 4-oxo-beta-lactams (azetidine-2,4-diones), containing the required structural elements for molecular recognition, inhibit porcine pancreatic elastase (PPE) but show a dramatically lower reactivity toward hydroxide compared with the analogous inhibitors 3-oxo-beta-sultams. Inhibition is the result of acylation of the active site serine and electron-withdrawing substituents at the N-(4-aryl) position in 3,3-diethyl- N-aryl derivatives increasing the rate of enzyme acylation and generating a Hammett rho-value of 0.65. Compared with a rho-value of 0.96 for the rates of alkaline hydrolysis of the same series, this is indicative of an earlier transition state for the enzyme-catalyzed reaction. Docking studies indicate favorable noncovalent interactions of the inhibitor with the enzyme. Compound 2i, the most potent inhibitor against PPE, emerged as a very potent HLE inhibitor, with a second-order rate for enzyme inactivation of approximately 5 x 10 (5) M (-1) s (-1).

A series of 1,4-naphthoquinone derivatives diversely substituted at C-2, C-3, C-5 and C-8, prepared by reaction of amines, amino acids and alcohols with commercial 1,4-naphthoquinones, has been evaluated against papain and bovine spleen cathepsin B. These 1,4-naphthoquinone derivatives were found to be irreversible inhibitors for both cysteine proteases, with second-order rate constants, k(2), ranging from 0.67 to 35.4 M-1 s(-1) for papain, and from 0.54 to 8.03 M-1 s(-1) for cathepsin B. Some derivatives display a hyperbolic dependence of the first-order inactivation rate constant, k(obs) with the inhibitor concentration, indicative of a specific interaction process between enzyme and inhibitor. The chemical reactivity of the compounds towards cysteine as a model thiol is dependent on the naphthoquinone LUMO energy, whereas papain inactivation is not. The 1,4-naphthoquinone derivatives are inactive against the serine protease, porcine pancreatic elastase. (c) 2007 Elsevier Ltd. All rights reserved.

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5′-TpA in (AT)n sequences.

Molecular docking studies of two duplex DNA sequences as target fragments and allopsoralen as ligand were performed. The calculated interaction energies showed that the ligand can be docked into the minor groove as well as become intercalated. However, unlike psoralen, allopsoralen preferred binding mode for non-poly-TA sequences is minor groove binding. Calculated energies for intercalation between different base pairs suggest that the predicted sequence selectivity for allopsoralen is analogous to that observed for psoralen. Intercalation is favored in 5'-TpA sites in poly-TA sequences. (C) 2007 Elsevier B.V. All rights reserved.

The energetics of the phenolic O-H bond in the three hydroxybenzoic acid isomers and of the intramolecular hydrogen O-H- - -O-C bond in 2-hydroxybenzoic acid, 2-OHBA, were investigated by using a combination of experimental and theoretical methods. The standard molar enthalpies of formation of monoclinic 3- and 4-hydroxybenzoic acids, at 298.15 K, were determined as Delta(f)(3-OHBA, cr) = -593.9 +/- 2.0 kJ x mol(-1) and Delta(f)(4-OHBA, cr) = -597.2 +/- 1.4 kJ x mol(-1), by combustion calorimetry. Calvet drop-sublimation calorimetric measurements on monoclinic samples of 2-, 3-, and 4-OHBA, led to the following enthalpy of sublimation values at 298.15 K: Delta(sub)(2-OHBA) = 94.4 +/- 0.4 kJ x mol(-1), Delta(sub)(3-OHBA) = 118.3 +/- 1.1 kJ x mol(-1), and Delta(sub)(4-OHBA) = 117.0 +/- 0.5 kJ x mol(-1). From the obtained Delta(f)(cr) and Delta(sub) values and the previously reported enthalpy of formation of monoclinic 2-OHBA (-591.7 +/- 1.3 kJ x mol(-1)), it was possible to derive Delta(f)(2-OHBA, g) = -497.3 +/- 1.4 kJ x mol(-1), Delta(f)(3-OHBA, g) = -475.6 +/- 2.3 kJ x mol(-1), and Delta(f)(4-OHBA, cr) = -480.2 +/- 1.5 kJ x mol(-1). These values, together with the enthalpies of isodesmic and isogyric gas-phase reactions predicted by density functional theory (B3PW91/aug-cc-pVDZ, MPW1PW91/aug-cc-pVDZ, and MPW1PW91/aug-cc-pVTZ) and the CBS-QMPW1 methods, were used to derive the enthalpies of formation of the gaseous 2-, 3-, and 4-carboxyphenoxyl radicals as (2-HOOCC(6)H(4)O(*), g) = -322.5 +/- 3.0 kJ.mol(-1) Delta(f)(3-HOOCC(6)H(4)O(*), g) = -310.0 +/- 3.0 kJ x mol(-1), and Delta(f)(4-HOOCC(6)H(4)O(*), g) = -318.2 +/- 3.0 kJ x mol(-1). The O-H bond dissociation enthalpies in 2-OHBA, 3-OHBA, and 4-OHBA were 392.8 +/- 3.3, 383.6 +/- 3.8, and 380.0 +/- 3.4 kJ x mol(-1), respectively. Finally, by using the ortho-para method, it was found that the H- - -O intramolecular hydrogen bond in the 2-carboxyphenoxyl radical is 25.7 kJ x mol(-1), which is ca. 6-9 kJ x mol(-1) above the one estimated in its parent (2-OHBA), viz. 20.2 kJ x mol(-1) (theoretical) or 17.1 +/- 2.1 kJ x mol(-1) (experimental).

The synthesis of phosphonate derivatives of N-phenyl- and N-benzyl-gamma- and delta-sultams, and their application in the Wittig-Horner reaction with N-Boc-L-phenylalanine aldehyde to afford E- and Z-isomers, are described. These compounds were further processed to provide five dipeptide vinyl sultams, which were found to be inactive against papain at concentrations up to 50 microM. In contrast, vinyl sultams demonstrated weak activity against recombinant falcipain-2 and Plasmodium falciparum W2.

The energetics of the phenol O–H bond in methanol and the water O–H bond in liquid water were investigated by microsolvation modelling and statistical mechanics Monte Carlo simulations. The microsolvation approach was based on density functional theory calculations. Optimised structures for clusters of phenol and the phenoxy radical with one and two methanol molecules are reported. By analysing the differential solvation of phenol and the phenoxy radical in methanol, we predict that the phenol O–H homolytic bond dissociation enthalpy in solution is 24.3±11 kJ/mol above the gas-phase value. The analysis of the water O–H bond dissociation by microsolvation was based on optimised structures of OH•–(H2O)1−6 and –(H2O)1−7 clusters. Microsolvation modelling and statistical mechanics simulations predict that the HO–H bond dissociation enthalpies in the gas phase and in liquid water are very similar. Our results stress the importance of estimating the differences between the solvation enthalpies of the radical species and the parent molecule and the limitations of local models based on microsolvation.

Human neutrophil elastase (HNE) plays an important role in the Chronic Obstructive Pulmonary Disease (COPD) inflammatory process. Over the last few decades HNE inhibitors have been evaluated as potential drug candidates; nevertheless their development was discontinued for various reasons and only sivelestat has been approved for clinical use in Acute Respiratory Distress Syndrome (ARDS). Hence, there is an urgent need for new chemotypes that allow efficient and selective HNE inhibition. With the aim of searching for a new HNE inhibitor we carried out a structure-based virtual screening of the Molecular Operating Environment (MOE) database of drug-like compounds. A commercial library of 653 214 drug-like compounds from different suppliers was docked into the HNE enzyme active site and 28 compounds were selected for purchase and tested. Four new HNE inhibitors in the low micromolar range were identified, displaying selectivity towards HNE when compared with other neutrophil serine proteases. Moreover, the inhibitors 19 and 27 exhibited a non-cytotoxic profile. Compound 19 has shown to be stable toward human plasma and pooled rat microsomal activity whereas ester 27 revealed stability issues toward hydrolytic enzymes. Compounds 19 and 27 appear to be promising leads for further development of HNE inhibitors. This study confirms the extra value of using structure-based chemoinformatic protocols and has successfully identified novel distinct chemotypes for development as new agents against HNE.

The O–H and S–H homolytic bond dissociation enthalpies of a set of disubstituted phenols and thiophenols (NH2, OH, CH3, Cl, CF3, and NO2) have been computed by a density functional theory procedure with the 6-311++G(d,p) basis set. A very good agreement between our results and available experimental ones is observed. The effect of substituents on structure, charges and BDEs are investigated and their correlation with Hammett parameters is studied. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Monte Carlo simulations and thermodynamic perturbation theory calculations have been carried out to analyze the differential hydration of phenol (PhOH) and phenoxy radical (PhO•). The hydration enthalpy of phenol predicted by different phenol−water interaction models is in good agreement with experimental data. On the basis of the difference in the hydration enthalpy of phenol and phenoxy radical, we find that the O−H bond dissociation enthalpy in water is above the recommended experimental value for the gas phase by ca. 7 kcal/mol. This result is in agreement with photoacoustic calorimetry measurements for phenol in other polar solvents. Thermodynamic perturbation theory results for the relative hydration Gibbs energy of phenol and phenoxy radical are also reported. The structure of the solutions suggests that the differential solvation of phenol and phenoxy radical can be related to the strong character of phenol as a hydrogen bond donor in comparison with the role played by phenoxy radical as a hydroge...