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.

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 α-amino-1,3-dicarbonyl compounds via Ugi flow chemistry reaction: access to functionalized 1,2,3-triazoles.

The Ugi multicomponent reaction has been used as an important synthetic route to obtain compounds with potential biological activity. We present the rapid and efficient synthesis of [Formula: see text]-amino-1,3-dicarbonyl compounds in moderate to good yields via Ugi flow chemistry reactions performed with a continuous flow reactor. Such [Formula: see text]-amino-1,3-dicarbonyl compounds can act as precursors for the production of [Formula: see text]-amino acids via hydrolysis of the ethyl ester group as well as building blocks for the synthesis of novel compounds with the 1,2,3-triazole ring. The [Formula: see text]-amino acid derivatives of the Ugi flow chemistry reaction products were then used for dipeptide synthesis.

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.

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

In the title compound, C17H14N2O6, the conformation about the C=C double bond [1.345 (2) Å] is E, with the ketone moiety almost coplanar [C-C-C-C torsion angle = 9.5 (2)°] along with the phenyl ring [C-C-C-C = 5.9 (2)°]. The aromatic rings are almost perpendicular to each other [dihedral angle = 86.66 (7)°]. The 4-nitro moiety is approximately coplanar with the benzene ring to which it is attached [O-N-C-C = 4.2 (2)°], whereas the one in the ortho position is twisted [O-N-C-C = 138.28 (13)°]. The mol-ecules associate via C-H⋯O inter-actions, involving both O atoms from the 2-nitro group, to form a helical supra-molecular chain along [010]. Nitro-nitro N⋯O inter-actions [2.8461 (19) Å] connect the chains into layers that stack along [001].

1-[(Z)-2-Butyl-tellan-yl-1-chloro-ethen-yl]-cyclo-hex-1-ene.

The Te(II) atom in the title mol-ecule, C(12)H(19)ClTe, is coordinated in a V-shaped geometry by C atoms derived from the disparate organic substituents. A short intramolecular C-H⋯Cl contact occurs owing to the proximity of the ethene bond in the six-membered ring to the Cl atom. In the crystal, mol-ecules assemble into layers parallel to the ac plane, with the closest inter-actions between them being of the Te⋯Te type [3.9993 (16) Å].

1-Methyl-3,3-bis-(phenyl-sulfan-yl)piperidin-2-one.

The piperidone ring in the title compound, C(18)H(19)NOS(2), is in a distorted half-chair conformation, distorted towards a twisted boat, with the central methyl-ene C atom of the propyl backbone lying 0.606 (2) Šout of the plane defined by the other five atoms (r.m.s. deviation = 0.1197 Å). One of the S-bound phenyl rings is almost perpendicular to the least-squares plane through the piperidone ring, whereas the other is splayed [dihedral angles = 75.97 (6) and 44.21 (7)°, respectively]. The most prominent feature of the crystal packing is the formation of helical supra-molecular chains along the b axis sustained by C-H⋯O inter-actions. The chains are consolidated into a three-dimensional architecture via C-H⋯π inter-actions whereby one S-bound phenyl ring accepts two C-H⋯π contacts.

4,4-Dimethyl-2-[3-nitro-2-phenyl-1-(phenyl-sulfan-yl)prop-yl]-4,5-dihydro-1,3-oxazole.

In the title compound, C(20)H(22)N(2)O(3)S, the oxazoline ring is planar (r.m.s. deviation = 0.045 Å) and forms dihedral angles of 47.24 (8) and 10.11 (8)° with the S- and C-bound phenyl rings, respectively. The nitro group lies to the same side of the mol-ecule as the oxazoline ring but is orientated so as not to inter-act with the ring. Linear supra-molecular chains along [010] are formed via C-H⋯O and C-H⋯S contacts. Chains are consolidated into a three-dimensional architecture by C-H⋯π and van der Waals inter-actions.

3,3-Bis[(4-meth-oxy-phen-yl)sulfan-yl]-1-methyl-piperidin-2-one.

The piperidone ring in the title compound, C(20)H(23)NO(3)S(2), has a distorted half-chair conformation with the central methyl-ene atom of the propyl fragment lying 0.696 (1) Šout of the plane defined by the other five atoms (r.m.s. deviation = 0.071 Å). One of the S-bound phenyl rings is almost perpendicular to the mean plane through the piperidone ring, whereas the other is splayed [dihedral angles = 71.95 (6) and 38.42 (6)°]. In the crystal, C-H⋯O and C-H⋯π inter-actions lead to the formation of supra-molecular layers in the ab plane.

(5R)-3-(2-Chloro-acet-yl)-4-methyl-5-phenyl-1,3,4-oxadiazinan-2-one.

The 1,3,4-oxadiazinan-2-one ring in the title compound, C(12)H(13)ClN(2)O(3), is in a distorted half-chair conformation. The phenyl and chloro-acetyl groups occupy axial and equatorial positions, respectively, and lie to the opposite side of the mol-ecule to the N-bound methyl substituent. Mol-ecules are consolidated in the crystal structure by C-H⋯O inter-actions.

1-[(Z)-1-Bromo-2-(butyl-dichloro-λ-tellan-yl)ethen-yl]cyclo-hex-1-ene.

The Te(IV) atom in the title compound, [Te(C(4)H(9))(C(8)H(10)Br)Cl(2)] or C(12)H(19)BrCl(2)Te, is in a distorted ψ-trigonal-bipyramidal geometry, with the lone pair of electrons projected to occupy a position in the equatorial plane, and with the Cl atoms being mutually trans [172.48 (4)°]. Close intra-molecular [Te⋯Br = 3.3444 (18) Å] and inter-molecular [Te⋯Cl = 3.675 (3) Å] inter-actions are observed. The latter lead to centrosymmetric dimers which assemble into layers in the bc plane. The primary connections between layers are of the type C-H⋯Cl.

(4R,4aS,4bS,7R,10aR)-4-Hy-droxy-4a,7-dimethyl-2-(propan-2-yl)-1,4,4a,4b,5,6,7,8,10,10a-deca-hydro-phenanthren-1-one.

In the title compound, C(19)H(28)O(2), the A ring adopts a chair conformation, and each of the B and C rings adopts a distorted half-chair conformation with the methine C atom in the CH(2)C(H)C(=O) residue, common to both rings, lying 0.6397 (19) and 0.6328 (18) Šout of the approximate plane defined by the remaining five C atoms (r.m.s. deviations = 0.0791 and 0.0901 Šfor rings B and C, respectively). Helical supra-molecular chains along the a axis mediated by hy-droxy-carbonyl O-H⋯O hydrogen bonds feature in the crystal packing.

(4aS,4bR,7R,10aS)-3,7-Dimethyl-10a-(propan-2-yl)-1,4,4a,4b,5,6,7,8,10,10a-deca-hydro-phenanthrene-1,4-dione.

In the title compound, C(19)H(26)O(2), the A ring adopts a chair conformation, whereas the B and C rings both adopt distorted half-chair conformations with the quaternary C atom common to both rings lying 0.577 (3) and 0.648 (3) Šout of the approximate plane defined by the remaining five C atoms (r.m.s. deviations = 0.1386 and 0.1156 Å) for the B and C rings, respectively. Mol-ecules are assembled in the crystal through C-H⋯O inter-actions involving both carbonyl O atoms, which lead to supra-molecular chains aligned along the b axis.

(4R*,4aS*,4bS*,5R*,10aR*)-4-Hy-droxy-4a,5-dimethyl-2-(propan-2-yl)-1,4,4a,4b,5,6,7,8,10,10a-deca-hydro-phenan-thren-1-one.

In the title compound, C(19)H(28)O(2), the A ring adopts a chair conformation. Both the B and C rings adopt envelope conformations with the C atoms common to both rings and adjacent to the carbonyl and hydroxyl groups, respectively, lying 0.604 (3) and 0.634 (3) Šout of the mean planes defined by the remaining five C atoms of rings B and C, respectively (r.m.s. deviations = 0.0100 and 0.0157 Å, respectively). The formation of linear supra-molecular C(7) chains along the a axis mediated by hy-droxy-O-H⋯O(carbon-yl) hydrogen bonds is the most prominent feature of the crystal packing.

(R)-2-Phen-oxy-1-(4-phenyl-2-sulfan-ylidene-1,3-oxazolidin-3-yl)ethanone.

The central 1,3-oxazolidine-2-thione ring in the title compound, C(17)H(15)NO(3)S, is approximately planar with maximum deviations of 0.036 (4) and -0.041 (5) Šfor the O and methyl-ene-C atoms, respectively. The dihedral angles formed between this plane and the two benzene rings, which lie to the same side of the central plane, are 86.5 (2) [ring-bound benzene] and 50.6 (3)°. The ethan-1-one residue is also twisted out of the central plane, forming a O-C-N-C torsion angle of 151.5 (5)°. The dihedral angle formed by the benzene rings is 62.8 (2)° so that overall, the mol-ecule has a twisted U-shape. In the crystal, mol-ecules are linked into supra-molecular arrays two mol-ecules thick in the bc plane through C-H⋯O, C-H⋯S and C-H⋯π inter-actions.

Crystal structure, DNA binding studies, nucleolytic property and topoisomerase I inhibition of zinc complex with 1,10-phenanthroline and 3-methyl-picolinic acid.

Crystal structure analysis of the zinc complex establishes it as a distorted octahedral complex, bis(3-methylpicolinato-kappa(2) N,O)(2)(1,10-phenanthroline-kappa(2) N,N)-zinc(II) pentahydrate, [Zn(3-Me-pic)(2)(phen)]x5H(2)O. The trans-configuration of carbonyl oxygen atoms of the carboxylate moieties and orientation of the two planar picolinate ligands above and before the phen ligand plane seems to confer DNA sequence recognition to the complex. It cannot cleave DNA under hydrolytic condition but can slightly be activated by hydrogen peroxide or sodium ascorbate. Circular Dichroism and Fluorescence spectroscopic analysis of its interaction with various duplex polynucleotides reveals its binding mode as mainly intercalation. It shows distinct DNA sequence binding selectivity and the order of decreasing selectivity is ATAT > AATT > CGCG. Docking studies lead to the same conclusion on this sequence selectivity. It binds strongly with G-quadruplex with human tolemeric sequence 5'-AG(3)(T(2)AG(3))(3)-3', can inhibit topoisomerase I efficiently and is cytotoxic against MCF-7 cell line.

3-(1-Hydr-oxy-2-phenyl-prop-2-en-1-yl)phenol.

Two independent pseudo-enanti-omeric mol-ecules comprise the asymmetric unit in the title compound, C(15)H(14)O(2). While the central O-C-C-C residue approaches planarity [torsion angles = -15.8 (3) (mol-ecule a) and 15.4 (3)° (mol-ecule b)], the benzene rings are approximately orthogonal [the dihedral angles formed between the benzene rings are 62.89 (12) (mol-ecule a) and 80.15 (12)° (mol-ecule b)]. Two-dimensional arrays in the ab plane sustained by O-H⋯O hydrogen bonding are found in the crystal structure.

Ethyl (E)-2-methoxy-imino-2-(4-nitro-benzo-yl)acetate.

The title mol-ecule, C(12)H(12)N(2)O(6), features an E conformation about the oxime group. The methoxy-imino and ester residues are effectively coplanar with each other (r.m.s. deviation for the nine non-H atoms = 0.127 Å) and almost orthogonal [with dihedral angles of 99.44 (13) and -77.85 (13)°, respectively] to the carbonyl and nitro-phenyl groups which lie to either side of this central plane. The crystal structure is consolidated by C-H⋯O contacts.

Bis[(4-methyl-phen-yl)ethyn-yl] telluride.

The tellurium atom in the title bis-ethynyl telluride, Te(C(9)H(7))(2) or C(18)H(14)Te, is located on a crystallographic twofold axis, the C-Te-C angle being 92.23 (15)°. The dihedral angle between the rings is 87.27 (7)°. In the crystal structure, mol-ecules are connected in chains parallel to the b axis and mediated by C-H⋯π inter-actions.

1-Benzyl-2,5-dioxopyrrolidine-3,4-diyl diacetate.

The pyrrolidine-2,5-dione ring in the title compound, C(15)H(15)NO(6), is in a twisted conformation with the acetyl C atoms projecting to opposite sides of the ring. The acetyl groups lie to opposite sides of the five-membered ring. The benzene ring is roughly perpendicular to the heterocyclic ring, forming a dihedral angle of 76.57 (14)° with it. In the crystal, mol-ecules are connected through a network of C-H⋯O and C-H⋯π inter-actions.