Structural and thermodynamic characterization of allosteric transitions in human serum albumin with metadynamics simulations.

Human serum albumin (HSA) is the most prominent protein in blood plasma, responsible for the maintenance of blood viscosity and transport of endogenous and exogenous molecules. Fatty acids (FA) are the most common ligands of HSA and their binding can modify the protein's structure. The protein can assume two well-defined conformations, referred to as 'Neutral' and 'Basic'. The Neutral (N) state occurs at pH close to 7.0 and in the absence of bound FA. The Basic (B) state occurs at pH higher than 8.0 or when the protein is bound to long-chain FA. HSA's allosteric behaviour is dependent on the number on FA bound to the structure. However, the mechanism of this allosteric regulation is not clear. To understand how albumin changes its conformation, we compared a series of HSA structures deposited in the protein data bank to identify the minimum amount of FA bound to albumin, which is enough to drive the allosteric transition. Thereafter, non-biased molecular dynamics (MD) simulations were used to track protein's dynamics. Surprisingly, running an ensemble of relatively short MD simulations, we observed rapid transition from the B to the N state. These simulations revealed differences in the mobilities of the protein's subdomains, with one domain unable to fully complete its transition. To track the transition dynamics in full, we used these results to choose good geometrical collective variables for running metadynamics simulations. The metadynamics calculations showed that there was a low energy barrier for the transition from the B to the N state, while a higher energy barrier was observed for the N to the B transition. These calculations also offered valuable insights into the transition process.

Copper-Mediated Intramolecular Interrupted CuAAC Selanylation.

We, herein, describe a copper-mediated domino CuAAC intramolecular selanylation for the synthesis of unprecedented fused benzo[4,5][1,3]selenazolo[3,2-c][1,2,3]triazoles from 1,2-bis(2-azidoaryl)diselenides and terminal alkynes under microwave irradiation. This is the seminal method for the synthesis of these fused heterocycles, and it proceeds under mild conditions, tolerates several functional groups, and can be carried out using environmentally benign solvents such as dimethyl carbonate. This transformation has been successfully extended to TMS-protected alkynes and to bioactive alkynes. A plausible reaction mechanism is proposed based on several control experiments and previous reports.

One-pot synthesis of γ-lactams from ketoaziridines.

The remarkable biological activities of γ-lactams have stimulated the search for efficient synthetic methods to achieve these scaffolds. In this work, we have developed a simple one-pot diastereoselective synthesis of new γ-lactams from ketoaziridines with moderate to good yields via the Horner-Wadsworth-Emmons reaction, followed by an intramolecular ester-aziridine cyclization and its opening in situ. Preliminary efforts towards an enantioselective version of this method are also reported.

Resistance to a tyrosine kinase inhibitor mediated by changes to the conformation space of the kinase.

Gilteritinib is a highly selective and effective inhibitor of the FLT3/ITD mutated protein, and is used successfully in treating acute myeloid leukaemia (AML). Unfortunately, tumour cells gradually develop resistance to gilteritinib due to mutations in the molecular drug target. The atomistic details behind this observed resistance are not clear, since the protein structure of the complex is only available in the inactive state, while the drug binds better to the active state. To overcome this limitation, we used a computer-aided approach where we docked gilteritinib to the active site of FLT3/ITD and calculated the Gibbs free energy difference between the binding energies of the parental and mutant enzymes. These calculations agreed with experimental estimations for one mutation (F691L) but not the other (D698N). To further understand how these mutations operate, we used metadynamics simulations to study the conformational landscape of the activation process. Both mutants show a lower activation energy barrier which suggests that they are more likely to adopt an active state until inhibited, making the mutant enzymes more active. This suggests that a higher efficiency of tyrosine kinases contributes to resistance not only against type 2 but also against type 1 kinase inhibitors.

Synthesis of (Z)-ß-halo α,ß-unsaturated carbonyl systems via the combination of halotrimethylsilane and tetrafluoroboric acid.

A convenient and broadly applicable method for the hydrohalogenation of ynones is described, by the combination of halotrimethylsilanes and tetrafluoroboric acid. Practically, one equivalent of HX (Brønsted acid) and BF3 (Lewis acid) is smoothly generated, which activates the carbonyl compounds. Through this protocol, 42 examples of (Z)-ß-halovinyl carbonyl compounds (Cl, Br and I) were obtained, in good yields and high stereoselectivity having 2-MeTHF as a solvent.

Ion-Pair Complexes of Pyrylium and Tetraarylborate as New Host-Guest Dyes: Photoinduced Electron Transfer Promoting Radical Polymerization.

Ultrafast transient absorption spectroscopy, NOESY-NMR, and EPR spectroscopy shed light on how π-π stacking interactions combined with electrostatic interactions can be used to form stable ion-pair complexes between pyrylium and tetraarylborate ions in which the interaction of the π-delocalized clouds promotes the observation of new radiative processes and also electron transfer processes excitation using visible light. The results exhibit a striking combination of properties, chemical stability and photophysical and photochemical events, that make these ion-pair complexes as a step toward the realization of chromophore/luminescent materials and also their use as a new monophotoinitiator system in radical polymerization reactions.

Organocatalyzed Asymmetric Vinylogous Addition of Oxazole-2(3H)-thiones to α,ß-Unsaturated Ketones: An Additive-Free Approach for Diversification of Heterocyclic Scaffold.

A straightforward organocatalyzed asymmetric addition of oxazole-2(3H)-thiones to α,ß-unsaturated ketones is described. This additive-free Michael reaction in the presence of chiral cinchonine-derived primary amines as catalysts has proven to be highly effective for a wide range of cyclic and acyclic enones, leading to the Michael adducts in very good yields and excellent enantioselectivities. The absolute configuration (R) of compound 5j was unambiguously assigned by X-ray diffraction analysis. Furthermore, experimental and theoretical studies were performed and a mechanism is presented and discussed for this novel reaction.

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations.

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

Molecular Structures of Isomeric Ortho, Meta, and Para Bromo-Substituted α-Methylsulfonyl-α-diethoxyphosphoryl Acetophenones by X-ray and DFT Molecular Orbital Calculations.

The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.

Triterpenoids as novel natural inhibitors of human cathepsin L.

Cathepsins L (catL) and B play an important role in tumor progression and have been considered promising therapeutic targets in the development of novel anticancer agents. Using a bioactivity-guided fractionation, a series of triterpenoids was identified as a new class of competitive inhibitors towards cathepsin L with affinity values in micromolar range. Among the 14 compounds evaluated, the most promising were 3-epiursolic acid (3), 3-(hydroxyimino)oleanolic acid (9), and 3-(hydroxyimino)masticadienoic acid (13) with IC50 values of 6.5, 2.4, and 2.6 µM on catL, respectively. Most of the evaluated triterpenoids do not inhibit cathepsin B. Thus, the evaluated compounds exhibit a great potential to help in the design of new inhibitors with enhanced potency and affinity towards catL. Docking studies were performed in order to gain insight on the binding mode and SAR of these compounds.

Synthesis, molecular and crystal structure analysis of 1-(4-Methylbenzenesulfonyl)indole-3-carbaldehyde and DFT investigation of its rotational conformers.

Two independent molecules that differ in terms of rotation about the central S-N bond comprise the asymmetric unit of the title compound 1. The molecules have a V-shape with the dihedral angles between the fused ring system and benzene ring being 79.08(6)° and 72.83(5)°, respectively. The packing is mostly driven by p···p interactions occurring between the tolyl ring of one molecule and the C6 ring of the indole fused ring system of the other. DFT and IRC calculations for these and related 1-(arylsulfonyl)indole molecules showed that the rotational barrier about the S-N bond between conformers is within the 2.5-5.5 kcal/mol range. Crystal data for C16H13NO3S (1): Mr = 299.33, space group Pna21, a = 19.6152(4) Å, b = 11.2736(4) Å, c = 12.6334(3) Å, V = 2793.67(13) Å3, Z = 8, Z' = 2, R = 0.034.

Crystal structure of ethyl 2-[(4-bromo-phen-yl)amino]-3,4-di-methyl-pent-3-enoate.

In the title compound, C15H20BrNO2, there are two independent mol-ecules (A and B) comprising the asymmetric unit and these adopt very similar conformations. In A, the dihedral angle between the CO2 and MeC=CMe2 groups is 80.7 (3)°, and these make dihedral angles of 3.5 (3) and 84.09 (16)°, respectively, with the bromo-benzene ring. The equivalent dihedral angles for mol-ecule B are 78.4 (3), 2.1 (3) and 78.37 (12)°, respectively. The most prominent inter-actions in the crystal packing are amine-N-H⋯O(carbon-yl) hydrogen bonds between the two independent mol-ecules, resulting in non-centrosymmetric ten-membered {⋯OC2NH}2 synthons. Statistical disorder is noted for each of the terminal methyl groups of the ethyl residues.

Crystal structure of (3E)-3-[(4-nitro-phen-oxy)-meth-yl]-4-phenyl-but-3-en-2-one.

In the title compound, C17H15NO4, the conformation about the C=C double bond [1.348 (2) Å] is E with the ketone group almost co-planar [C-C-C-C torsion angle = 7.2 (2)°] but the phenyl group twisted away [C-C-C-C = 160.93 (17)°]. The terminal aromatic rings are almost perpendicular to each other [dihedral angle = 81.61 (9)°] giving the mol-ecule an overall U-shape. The crystal packing feature benzene-C-H⋯O(ketone) contacts that lead to supra-molecular helical chains along the b axis. These are connected by π-π inter-actions between benzene and phenyl rings [inter-centroid distance = 3.6648 (14) Å], resulting in the formation of a supra-molecular layer in the bc plane.

Spectroscopic and theoretical studies of some 3-(4'-substituted phenylsulfanyl)-1-methyl-2-piperidones.

The analysis of the IR carbonyl bands of some 3-(4'-substituted phenylsulfanyl)-1-methyl-2-piperidones 1-6 bearing substituents: NO2 (compound 1), Br (compound 2), Cl (compound 3), H (compound 4) Me (compound 5) and OMe (compound 6) supported by B3LYP/6-31+G(d,p) and PCM calculations along with NBO analysis (for compound 4) and X-ray diffraction (for 2) indicated the existence of two stable conformations, i.e., axial (ax) and equatorial (eq), the former corresponding to the most stable and the least polar one in the gas phase calculations. The sum of the energy contributions of the orbital interactions (NBO analysis) and the electrostatic interactions correlate well with the populations and the νCO frequencies of the ax and eq conformers found in the gas phase. Unusually, in solution of the non-polar solvents n-C6H14 and CCl4, the more intense higher IR carbonyl frequency can be ascribed to the ax conformer, while the less intense lower IR doublet component to the eq one. The same νCO frequency trend also holds in polar solvents, that is ν(CO)(eq)< ν(CO)(ax). However, a reversal of the ax/eq intensity ratio occurs going from non-polar to polar solvents, with the ax conformer component that progressively decreases with respect to the eq one in CHCl3 and CH2Cl2, and is no longer detectable in the most polar solvent CH3CN. The PCM method applied to compound 4 supports these findings. In fact, it predicts the progressive increase of the eq/ax population ratio as the relative permittivity of the solvent increases. Moreover, it indicates that the computed ν(CO) frequencies of the ax and eq conformers do not change in the non-polar solvents n-C6H14 and CCl4, while the ν(CO) frequencies of the eq conformer become progressively lower than that of the ax one going from CHCl3 to CH2Cl2 and to CH3CN, in agreement with the experimental IR values. The analysis of the geometries of the ax and eq conformers shows that the carbonyl oxygen atom of the eq conformer is free for solvation, while the O[CO]…H[o-Ph] hydrogen bond that takes place in the ax conformer partially hinders the approach of the solvent molecules to the carbonyl oxygen atom. Therefore, the larger solvation that occurs in the carbonyl oxygen atom of the eq conformer is responsible for the observed and calculated decrease of the corresponding frequency. The X-ray single crystal analysis of 2 indicates that this compound adopts the most polar eq geometry in the solid. In fact, in order to obtain the largest energy gain, the molecules are arranged in the crystal in a helical fashion due to dipole moment coupling along with C-H…O and C-H…π(Ph) hydrogen bonds.

Ethyl (2Z)-3-oxo-2-(3,4,5-tri-meth-oxy-benzyl-idene)butano-ate.

In the title compound, C16H20O6, the conformation about the C=C double bond [1.344 (2) Å] is Z. With respect to this bond, the ketone is almost coplanar [C-C-C-O torsion angle = -179.60 (10)°] and the ester is almost perpendicular [C-C-C-O = 78.42 (13)°]. The meth-oxy substituents of the central benzene ring are either almost coplanar [C-C-O-C = 3.54 (15) and 177.70 (9)°] or perpendicular [C-C-O-C = 80.08 12)° for the central substituent]. In the crystal, the three-dimensional architecture features C-H⋯O and π-π [inter-centroid distance = 3.6283 (6) Å] inter-actions.

(±)-(4aR,5R,8S,8aR)-8-(tert-Butyl-dimethyl-sil-yloxy)-2,5,8a-trimethyl-4a,5,8,8a-tetra-hydro-naphthalene-1,4-dione.

In the title compound, C19H30O3Si, both rings adopt a half-boat conformation. Overall, the mol-ecule approximates a U-shape as the cyclo-2-ene-1,4-dione and butyl-dimethyl-sil-yloxy substituents lie to the same side of the central cyclo-hexene ring; the methyl substituent lies to the other side of the mol-ecule. In the crystal, linear supra-molecular chains along the b axis are sustained by C-H⋯O inter-actions.

3,3-Bis(4-bromo-phenyl-sulfan-yl)-1-methyl-piperidin-2-one.

In the title compound, C18H17Br2NOS2, the conformation of the piperidin-2-one ring is based on a half-chair with the methyl-ene C atom diagonally opposite the N atom being 0.649 (3) Šabove the plane of the remaining five atoms (r.m.s. deviation = 0.1205 Å). The S atoms occupy axial and bis-ectional positions, and the dihedral angle between the benzene rings of 59.95 (11)° indicates a splayed disposition. Helical supra-molecular chains along the b axis sustained by C-H⋯O inter-actions is the major feature of the crystal packing. The chains are connected into a three-dimensional architecture by C-H⋯Br and C-H⋯π inter-actions.

Rh(III)-Catalyzed C-2 Alkylation of Indoles followed by a Post-Synthetic Modification via the Ugi Reaction.

Indole derivatives substituted at the C-2 position have shown important biological activities. Due to these properties, several methods have been described for the preparation of structurally diverse indoles. In this work, we have synthesized highly functionalized indole derivatives via Rh(III)-catalyzed C-2 alkylation with nitroolefins. Under the optimized condition, 23 examples were prepared with 39-80 % yield. Moreover, the nitro compounds were reduced and submitted to the Ugi four-component reaction, furnishing a series of new indole-peptidomimetics in moderate to good overall yields.

4,5-seco-guaiane and a nine-membered sesquiterpene lactone from Holostylis reniformis.

Root extracts of Holostylis reniformis (Aristolochiaceae) yielded three new natural sesquiterpenes, a sesquiterpene with an unusual carbon skeleton, 4,5-seco-guaiane (7-epi-11-hydroxychabrolidione A, 1), a nine-membered lactone with new carbon skeleton (holostylactone, 2), and a new megastigmane [(6S,7E)-6,9-dihydroxy-10-(2'-hydroxy-ethoxy)-4,7-megastigmadien-3-one, 3], together with bulnesol and sitosterol-3-O-β-D-glucopyranoside. The structures of these compounds were determined by spectroscopic analyses and B3LYP/STO-3G** theoretical studies.