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Boronic acids (BAs) are a prominent functionality extensively used to design biologically active compounds and functional biomaterials. Boronic acids open shell can lead to unspecific reactivity of BAs with endogenous nucleophiles and to undesired off-target effects. Here, diazaborines are presented as a new class of boron-based warheads for serine proteases inhibition, in which the boron function is stabilized in the form of an aromatic boron-based heterocycle. In this study, diazaborines were readily synthesized in a single step in yields up to 96%, without any chromatographic operation and were shown to reversibly inhibit human neutrophil elastase (HNE) serine protease with IC50 values in the low μM range. Diazaborines were also selective toward HNE, as no inhibition was observed against a panel of five closely related serine proteases. Synthetic and theoretical studies performed on this system suggest that, similar to BAs, the reaction mechanism involves the formation of a reversible covalent bond between the diazaborine boron center and the catalytic serine oxygen. Finally, different from BAs, diazaborines were shown to be very stable in pH 7.4 phosphate buffer and human plasma.

Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the most common genetic disorder affecting the mitochondrial fatty acid β-oxidation pathway. The mature and functional form of human MCAD (hMCAD) is a homotetramer assembled as a dimer of dimers (monomers A/B and C/D). Each monomer binds a FAD cofactor, necessary for the enzyme's activity. The most frequent mutation in MCADD results from the substitution of a lysine with a glutamate in position 304 of mature hMCAD (p.K329E in the precursor protein). Here, we combined in vitro and in silico approaches to assess the impact of the p.K329E mutation on the protein's structure and function. Our in silico results demonstrated for the first time that the p.K329E mutation, despite lying at the dimer-dimer interface and being deeply buried inside the tetrameric core, seems to affect the tetramer surface, especially the β-domain that forms part of the catalytic pocket wall. Additionally, the molecular dynamics data indicate a stronger impact of the mutation on the protein's motions in dimer A/B, while dimer C/D remains similar to the wild type. For dimer A/B, severe disruptions in the architecture of the pockets and in the FAD and octanoyl-CoA binding affinities were also observed. The presence of unaffected pockets (C/D) in the in silico studies may explain the decreased enzymatic activity determined for the variant protein (46% residual activity). Moreover, the in silico structural changes observed for the p.K329E variant protein provide an explanation for the structural instability observed experimentally, namely, the disturbed oligomeric profile, thermal stability, and conformational flexibility, with respect to the wild-type.

The transport of molecules across biological membranes are critical for most cellular processes. Membrane permeability is also a key determinant for drug absorption, distribution, and elimination. Diffusion, that is, the migration of matter down a concentration gradient, is a simple mechanism by which both endogenous and drug molecules can enter (or exit) cells. This paper describes a simple and engaging physical chemistry undergraduate laboratory experiment for health and life sciences students studying diffusion of drug and dye molecules in solution. In this experiment, the diffusion of amitriptyline hydrochloride, ranitidine hydrochloride, and tartrazine across a cellulose dialysis membrane is evaluated using an innovative macro and microscale approach. Compound concentration in solution as a function of time is obtained both from conductivity measurements of 25 mL solutions and from absorbance measurements of 100 μL samples taken in a 96-well microplate. By using solutions of different concentrations,...

Human neutrophil elastase (HNE) is an attractive target for treating chronic and acute inflammatory lung diseases. An optimization campaign of the kojic acid scaffold to develop new potent HNE inhibitors is reported. O3-Pivaloyl derivatives were shown to be the most potent inhibitors with IC5o values down to 80 nM. These compounds presented excellent selectivity and cytotoxicity profiles with suitable ligand efficiency.

The human leukocyte elastase (HLE), a neutrophil serine protease of the chymotrypsin superfamily, is a major therapeutic target for a number of inflammatory diseases, such as chronic obstructive pulmonary disease (COPD). In this work, we present a comparative explicit water molecular dynamics (MD) study on the free and inhibitor-bound HLE. Knowledge of the flexibility and conformational changes induced by this irreversible inhibitor, whether in a prebound stage or covalently bound at the enzyme binding site, encases fundamental biological interest and is particularly relevant to ongoing structure-based drug design studies. Our results suggest that HLE operates by an induced-fit mechanism with direct intervention of a surface loop which is open toward the solvent in the free enzyme and closed while in the presence of the ligand. MM-PBSA free energy calculations furthermore elucidate the energetic contributions to the distinct conformations adopted by this loop. Additionally, a survey of the major contributions to the inhibitor binding free energies was attained. Our findings enforce the need to account for HLE flexibility, whether through the use of MD-generated ensembles of HLE conformations as targets for molecular docking or via sophisticated flexible-docking algorithms. We anticipate that inclusion of the observed HLE dynamic behavior into future drug design methodologies will have a relevant impact in the development of novel, more efficient, inhibitors.

Multidrug resistance related to the increased expression of P-glycoprotein (P-gp) by cancer cells is the major contributor for the failure of chemotherapeutic treatments. Starting from pharmacophores and data already published and in macrocyclic diterpenes isolated from Euphorbia species, a comprehensive study of pharmacophore definitions of features was performed in order to obtain a new improved four-point pharmacophore able to detect literature and in-house modulators and simultaneously specific enough to avoid the detection of most nonactive molecules in a universe of 152 (literature), 74 (in-house), and 46 (inactive) molecules. This pharmacophore detects 84.2% of the molecules described in the literature, along with 100% detection of in-house isolated compounds and 19.5% of false positives. The importance of the hydrophobic and electron acceptor moieties as essential features for recognition of different molecules by the P-gp drug-binding site is clarified. The best combination of acceptor, donor, hydrophobic, and aromatic characteristics that contribute for the increased selectivity shown by the described pharmacophore is evaluated, and the protonation state of the molecules is also addressed.

The synthesis of cryptolepine derivatives containing basic side-chains at the C-11 position and their evaluations for antiplasmodial and cytotoxicity properties are reported. Propyl, butyl, and cycloalkyl diamine side chains significantly increased activity against chloroquine-resistant Plasmodium falciparum strains while reducing cytotoxicity when compared with the parent compound. Localization studies inside parasite blood stages by fluorescence microscopy showed that these derivatives accumulate inside the nucleus, indicating that the incorporation of a basic side chain is not sufficient enough to promote selective accumulation in the acidic digestive vacuole of the parasite. Most of the compounds within this series showed the ability to bind to a double-stranded DNA duplex as well to monomeric hematin, suggesting that these are possible targets associated with the observed antimalarial activity. Overall, these novel cryptolepine analogues with substantially improved antiplasmodial activity and selectivity index provide a promising starting point for development of potent and highly selective agents against drug-resistant malaria parasites.

Monte Carlo statistical mechanics simulations, density-functional theory calculations, time-resolved photoacoustic calorimetry, and isoperibol reaction-solution calorimetry experiments were carried out to investigate the solvation enthalpies and solvent effects on the energetics of the phenol O−H bond in benzene and acetonitrile. A good agreement between theoretical and experimental results is obtained for the solvation enthalpies of phenol in benzene and acetonitrile. The theoretical calculations also indicate that the differences between the solvation enthalpies of phenol (PhOH) and phenoxy radical (PhO•) in both benzene and acetonitrile are significantly smaller than previous estimations based on the ECW model. The results for the solvation enthalpies are used to obtain the O−H bond dissociation enthalpies in benzene and acetonitrile. For benzene and acetonitrile, the theoretical results of 89.4 ± 1.2 and 90.5 ± 1.7 kcal mol-1, respectively, are in good agreement with the experimental values (90.9 ± 1....

Time-resolved photoacoustic calorimetry (TR-PAC) and quantum chemistry calculations were used to investigate the energetics of sulfur-hydrogen bonds in thiophenol and four para-substituted thiophenols, 4-XC 6 H 4 SH (X = CH 3 , OCH 3 , Cl, and CF 3 ). The result obtained for the PhS-H gas-phase bond dissociation enthalpy, derived from the PAC experimental results in solution, is 349.4 ′ 4.5 kJ mol - 1 . This value is significantly higher than recent literature values but agrees with a value suggested some 20 years ago in a widely used review. The PAC result also concurs with the value computed at a high theory level, G3(MP2), 346.8 kJ mol - 1 . The data obtained for the substituted thiophenols support the idea that substituent effects are less pronounced on the S-H bond dissociation enthalpy than on the O-H bond dissociation enthalpy of the corresponding phenols.

The energetics of the C-Cl bond in 2-chloropropionic acid was investigated by using a combination of experimental and theoretical methods. The standard molar enthalpy of formation of liquid (S)-(-)-2-chloropropionic acid,at 298.15 K, was determined as Δ f H o m (C 3 H 5 O 2 Cl, 1) = -(534.6 ′ 1.1) kJ.mol - 1 , by rotating-bomb combustion calorimetry. The corresponding enthalpy of vaporization, Δ v a p H o m (C 3 H 5 O 2 Cl) = (64.9 ′ 0.5) kJ.mol - 1 , was also obtained from vapor pressure versus temperature measurements by the transpiration method, leading to Δ f H o m (C 3 H 5 O 2 Cl, g) = -(469.7 ′ 1.2) kJ.mol - 1 . This value, together with the enthalpy of the isodesmic and isogyric gas-phase reaction CH 3 CH(X)COOH(g) + C 2 H 5 (g) CH3CHCOOH(g) + C 2 H 5 X(g) (X = H, Cl) predicted by density functional theory calculations and other auxiliary data, was used to derive the enthalpy of formation of the gaseous 1-carboxyethyl radical as Δ f H o m [CH(CH 3 )COOH, g] = -(293 ′ 3) kJ.mol - 1 , from which DH°[H-CH(CH 3 )COOH] = 380.7 ′ 3.9 kJ.mol - 1 and DH°[Cl-CH(CH 3 )COOH] = 298.0 ′ 3.2 kJ.mol - 1 were obtained. These values are compared with the corresponding C-H and C-Cl bond dissociation enthalpies in XCH 2 COOH, XCH 3 , XC 2 H 5 , XCH 2 -Cl, XCH(CH 3 )Cl, XCH=CH 2 , and XC 6 H 5 (X = H, Cl). The order DH°(C-H) > DH°(C-Cl) is observed for the carboxylic acids and all other RX compounds. Comparison of DH°[X-CH(CH 3 )COOH] and DH°[X-CH 2 COOH] (X = H, Cl) indicates that the replacement of a hydrogen of the CH 2 group of XCH 2 COOH by a methyl group leads to a decrease of both the C-H and C-Cl bond dissociation enthalpy. It is finally concluded that the major qualitative trends exhibited by the C-Cl bond dissociation enthalpies for the series of compounds addressed in this work can be predicted based on Pauling's electrostatic-covalent model.

Structural, vibrational, and thermochemical properties of phenol−(H2O)1-6 and phenoxy radical−(H2O)1-4 complexes were calculated by using density functional theory. The insertion of a phenol molecu...