Interaction of a promising anticancer drug, lapatinib (LAP) with the major transport protein in human blood circulation, human serum albumin (HSA) was investigated using fluorescence and circular dichroism (CD) spectroscopy as well as molecular docking analysis. LAP-HSA complex formation was evident from the involvement of static quenching mechanism, as revealed by the fluorescence quenching data analysis. The binding constant, Ka value in the range of 1.49-1.01×10(5)M(-1), obtained at three different temperatures was suggestive of the intermediate binding affinity between LAP and HSA. Thermodynamic analysis of the binding data (∆H=-9.75kJmol(-1) and ∆S=+65.21Jmol(-1)K(-1)) suggested involvement of both hydrophobic interactions and hydrogen bonding in LAP-HSA interaction, which were in line with the molecular docking results. LAP binding to HSA led to the secondary and the tertiary structural alterations in the protein as evident from the far-UV and the near-UV CD spectral analysis, respectively. Microenvironmental perturbation around Trp and Tyr residues in HSA upon LAP binding was confirmed from the three-dimensional fluorescence spectral results. LAP binding to HSA improved the thermal stability of the protein. LAP was found to bind preferentially to the site III in subdomain IB on HSA, as probed by the competitive drug displacement results and supported by the molecular docking results. The effect of metal ions on the binding constant between LAP and HSA was also investigated and the results showed a decrease in the binding constant in the presence of these metal ions.
In the presence of guest 2,4'-bpy molecules or under acidic conditions, three compounds, [Cd(4,4'-bpy)(2)(H(2)O)(2)](ClO(4))(2).(2,4'-bpy)(2).H(2)O (1), [Zn(4,4'-bpy)(2)(H(2)O)(2)](ClO(4))(2).(2,4'-bpy)(2).H(2)O (2), and [Cu(4,4'-bpy)(2)(H(2)O)(2)](ClO(4))(4).(4,4'-H(2)bpy) (3), were obtained from the reactions of the metal salts and 4,4'-bpy in an EtOH-H(2)O mixture. 1 has a 2-D square-grid network structure, crystallizing in the monoclinic space group P2/n, with a = 13.231(3) Å, b = 11.669(2) Å, c = 15.019(3) Å, beta = 112.82(3) degrees, Z = 2; 2 is isomorphous with 1, crystallizing in the monoclinic space group P2/n, with a = 13.150(3) Å, b = 11.368(2) Å, c = 14.745(3) Å, beta = 110.60(3) degrees, Z = 2. The square grids superpose on each other into a channel structure, in which each layer consists of two pairs of shared edges, perfectly square-planar with an M(II) ion and a 4,4'-bpy at each corner and side, respectively. The square cavity has dimensions of 11.669(2) x 11.788(2) and 11.368(2) x 11.488(2) Å for 1 and 2, respectively. Every two guest 2,4'-bpy molecules are clathrated in each hydrophobic host cavity and are further stabilized by pi-pi stacking and hydrogen bonding interactions. The NMR spectra clearly confirm that both 1 and 2 contain 4,4'-bpy and 2,4'-bpy molecules in a 1:1 ratio, which have stacking interaction with each other in the solution. 3 crystallizes in the orthorhombic space group Ibam, with a = 11.1283(5) Å, b = 15.5927(8) Å, c = 22.3178(11) Å, Z = 4. 3 is made up of two-dimensional square [Cu(4)(4,4'-bpy)(4)] grids, where the square cavity has dimensions of 11.13 x 11.16 Å. Each [4,4'-H(2)bpy](2+) cation is clathrated in a square cavity and stacks with one pair of opposite edges of the host square cavity in an offset fashion with the face-to-face distance of ca. 3.95 Å. Within each cavity, the [4,4'-H(2)bpy](2+) cation forms twin three-center hydrogen bonds with two pairs of ClO(4)(-) anions. The results suggest that the guest 2,4'-bpy molecules and protonated [4,4'-H(2)bpy](2+) cations present in the reaction systems serve as structure-directing templates in the formation of the crystal structures and exclude self-inclusion of the networks having larger square cavities.
The title compound, 2C14H14N4O·H2O, comprises a neutral mol-ecule containing a central pyrazol-3-one ring flanked by an N-bound phenyl group and a C-bound 5-methyl-1H-pyrazol-3-yl group (at positions adjacent to the carbonyl substituent), its zwitterionic tautomer, whereby the N-bound proton of the central ring is now resident on the pendant ring, and a water mol-ecule of crystallization. Besides systematic variations in geometric parameters, the two independent organic mol-ecules have broadly similar conformations, as seen in the dihedral angle between the five-membered rings [9.72 (9)° for the neutral mol-ecule and 3.32 (9)° for the zwitterionic tautomer] and in the dihedral angles between the central and pendant five-membered rings [28.19 (8) and 20.96 (8)° (neutral mol-ecule); 11.33 (9) and 11.81 (9)°]. In the crystal, pyrazolyl-N-H⋯O(carbon-yl) and pyrazolium-N-H⋯N(pyrazol-yl) hydrogen bonds between the independent organic mol-ecules give rise to non-symmetric nine-membered {⋯HNNH⋯NC3O} and {⋯HNN⋯HNC3O} synthons, which differ in the positions of the N-bound H atoms. These aggregates are connected into a supra-molecular layer in the bc plane by water-O-H⋯N(pyrazolide), water-O-H⋯O(carbon-yl) and pyrazolyl-N-H⋯O(water) hydrogen bonding. The layers are linked into a three-dimensional architecture by methyl-C-H⋯π(phen-yl) inter-actions. The different inter-actions, in particular the weaker contacts, formed by the organic mol-ecules are clearly evident in the calculated Hirshfeld surfaces, and the calculated electrostatic potentials differentiate the tautomers.
Binding studies between a multi-targeted anticancer drug, sunitinib (SU) and human serum albumin (HSA) were made using fluorescence, UV-vis absorption, circular dichroism (CD) and molecular docking analysis. Both fluorescence quenching data and UV-vis absorption results suggested formation of SU-HSA complex. Moderate binding affinity between SU and HSA was evident from the value of the binding constant (3.04×104M-1), obtained at 298K. Involvement of hydrophobic interactions and hydrogen bonds as the leading intermolecular forces in the formation of SU-HSA complex was predicted from the thermodynamic data of the binding reaction. These results were in good agreement with the molecular docking analysis. Microenvironmental perturbations around Tyr and Trp residues as well as secondary and tertiary structural changes in HSA upon SU binding were evident from the three-dimensional fluorescence and circular dichroism results. SU binding to HSA also improved the thermal stability of the protein. Competitive displacement results and molecular docking analysis revealed the binding locus of SU to HSA in subdomain IIA (Sudlow's site I). The influence of a few common ions on the binding constant of SU-HSA complex was also noticed.
Maltogenic amylase (MAG1) from Bacillus lehensis G1 displayed the highest hydrolysis activity on β-cyclodextrin (β-CD) to produce maltose as a main product and exhibited high transglycosylation activity on malto-oligosaccharides with polymerization degree of three and above. These substrate and product specificities of MAG1 were elucidated from structural point of view in this study. A three-dimensional structure of MAG1 was constructed using homology modeling. Docking of β-CD and malto-oligosaccharides was then performed in the MAG1 active site. An aromatic platform in the active site was identified which is responsible in substrate recognition especially in determining the enzyme's preference toward β-CD. Molecular dynamics (MD) simulation showed MAG1 structure is most stable when docked with β-CD and least stable when docked with maltose. The docking analysis and MD simulation showed that the main subsites for substrate stabilization in the active site are -2, -1, +1 and +2. A bulky residue, Trp359 at the +2 subsite was identified to cause steric interference to the bound linear malto-oligosaccharides thus prevented it to occupy subsite +3, which can only be reached by a highly bent glucose molecule such as β-CD. The resulted modes of binding from docking simulation show a good correlation with the experimentally determined hydrolysis pattern. The subsite structure generated from this study led to a possible mode of action that revealed how maltose was mainly produced during hydrolysis. Furthermore, maltose only occupies subsite +1 and +2, therefore could not be hydrolyzed or transglycosylated by the enzyme. This important knowledge has paved the way for a novel structure-based molecular design for modulation of its catalytic activities.
Effective novel peptide inhibitors which targeted the domain III of the dengue envelope (E) protein by blocking dengue virus (DENV) entry into target cells, were identified. The binding affinities of these peptides towards E-protein were evaluated by using a combination of docking and explicit solvent molecular dynamics (MD) simulation methods. The interactions of these complexes were further investigated by using the Molecular Mechanics-Poisson Boltzmann Surface Area (MMPBSA) and Molecular Mechanics Generalized Born Surface Area (MMGBSA) methods. Free energy calculations of the peptides interacting with the E-protein demonstrated that van der Waals (vdW) and electrostatic interactions were the main driving forces stabilizing the complexes. Interestingly, calculated binding free energies showed good agreement with the experimental dissociation constant (Kd) values. Our results also demonstrated that specific residues might play a crucial role in the effective binding interactions. Thus, this study has demonstrated that a combination of docking and molecular dynamics simulations can accelerate the identification process of peptides as potential inhibitors of dengue virus entry into host cells.
In the title compound, C26H22N2O2, the dihedral angles between the 1-methyl-indole units (A and B) and the benzoic acid moiety (C) are A/B = 64.87 (7), A/C = 80.92 (8) and B/C = 75.05 (8)°. An intra-molecular C-H⋯O inter-action arising from the methyne group helps to establish the conformation. In the crystal, R22(8) carb-oxy-lic acid inversion dimers linked by pairs of O-H⋯O hydrogen bonds are observed. A Hirshfeld surface analysis shows that the greatest contributions are from H⋯H, C⋯H/H⋯C and O⋯H/H⋯O contacts (percentage values = 54.6%, 29.6% and 10.1%, respectively).
The asymmetric unit of the title compound, C24H14F4O2, comprises of one and a half mol-ecules; the half-mol-ecule is completed by crystallographic inversion symmetry. In the crystal, mol-ecules are linked into a three-dimensional network by C-H⋯F and C-H⋯O hydrogen bonds. Some of the C-H⋯F links are unusually short (< 2.20 Å). Hirshfeld surface analyses (dnorm surfaces and two-dimensional fingerprint plots) for the title compound are presented and discussed.
In the title chalcone derivative, C16H11ClF2O2, the enone group adopts an E conformation. The dihedral angle between the benzene rings is 0.47 (9)° and an intra-molecular C-H⋯F hydrogen bond closes an S(6) ring. In the crystal, mol-ecules are linked into a three-dimensional network by C-H⋯O hydrogen bonds and aromatic π-π stacking inter-actions are also observed [centroid-centroid separation = 3.5629 (18) Å]. The inter-molecular inter-actions in the crystal structure were qu-anti-fied and analysed using Hirshfeld surface analysis.
In the title mol-ecular salt, C6H10N3O(+)·C7H5O3(-), the cation is protonated at the N atom lying between the amine and methyl substituents and the dihedral angle between the carboxyl group and its attached ring in the anion is 4.0 (2)°. The anion features an intra-molecular O-H⋯O hydrogen bond, which closes an S(6) ring. The cation and anion are linked by two N-H⋯O hydrogen bonds [R2(2)(8) motif] to generate an ion pair in which the dihedral angle between the aromatic rings is 8.34 (9)°. Crystal symmetry relates two ion pairs bridged by further N-H⋯O hydrogen bonds into a tetra-meric DDAA array. The tetra-mers are linked by pairs of C-H⋯O hydrogen bonds to generate [100] chains. Hirshfeld surface and fingerprint plot analyses are presented.
The mol-ecular structure of the title chalcone derivative, C15H10FNO3, is nearly planar and the mol-ecule adopts a trans configuration with respect to the C=C double bond. The nitro group is nearly coplanar with the attached benzene ring, which is nearly parallel to the second benzene ring. In the crystal, mol-ecules are connected by pairs of weak inter-molecular C-H⋯O hydrogen bonds into inversion dimers. The dimers are further linked by another C-H⋯O hydrogen bond and a C-H⋯F hydrogen bond into sheets parallel to (104). π-π inter-actions occur between the sheets, with a centroid-centroid distance of 3.8860 (11) Å. Hirshfeld surface analysis was used to investigate and qu-antify the inter-molecular inter-actions.
The title aza-stilbene derivative, C14H13NO2 {systematic name: (E)-2-[(4-meth-oxy-benzyl-idene)amino]-phenol}, is a product of the condensation reaction between 4-meth-oxy-benzaldehyde and 2-amino-phenol. The mol-ecule adopts an E conformation with respect to the azomethine C=N bond and is almost planar, the dihedral angle between the two substituted benzene rings being 3.29 (4)°. The meth-oxy group is coplanar with the benzene ring to which it is attached, the Cmeth-yl-O-C-C torsion angle being -1.14 (12)°. There is an intra-molecular O-H⋯N hydrogen bond generating an S(5) ring motif. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming zigzag chains along [10-1]. The chains are linked via C-H⋯π inter-actions, forming a three-dimensional structure.
The mol-ecule of the title Schiff base compound, C14H14N2O2, displays an E conformation with respect the imine C=N double bond. The mol-ecule is approximately planar, with the dihedral angle formed by the planes of the pyridine and benzene rings being 5.72 (6)°. There is an intra-molecular hydrogen bond involving the phenolic H and imine N atoms.
In the title di-thio-carbazate compound, C17H19N3S2, the central CN2S2 residue is essentially planar (r.m.s. deviation = 0.0288 Å) and forms dihedral angles of 9.77 (8) and 77.47 (7)° with the substituted-pyridyl and p-tolyl rings, respectively, indicating a highly twisted mol-ecule; the dihedral angle between the rings is 85.56 (8)°. The configuration about the C=N bond is Z, which allows for the formation of an intra-molecular N-H⋯N(pyrid-yl) hydrogen bond. The packing features tolyl-methyl-C-H⋯N(imine), pyridyl-C-H⋯π(tol-yl) and π-π inter-actions [between pyridyl rings with a distance = 3.7946 (13) Å], which generates jagged supra-molecular layers that stack along the b axis with no directional inter-actions between them.
In the title compound, C13H15NO4, the oxopyrrolidin-3-yl ring has an envelope conformation, with the C atom bearing the acetate group being the flap. The acetate and phenyl groups are inclined with respect to the central ring, forming dihedral angles of 50.20 (12) and 87.40 (9)°, respectively, with the least-squares plane through the ring. The dihedral angle between the acetate group and the phenyl ring is 63.22 (8)°, indicating a twisted conformation in the mol-ecule. In the crystal, supra-molecular chains along the b axis are formed by (hy-droxy)O-H⋯O(ring carbon-yl) hydrogen bonds. The chains are consolidated into the three-dimensional architecture by C-H⋯O inter-actions.
In the title thio-semicarbazone compound, C18H18ClN3S, the CN3S residue is almost planar (r.m.s. deviation = 0.0031 Å) and forms dihedral angles of 65.99 (7) and 34.60 (10)° with the phenyl and chloro-benzene rings, respectively; the dihedral angle between the aromatic rings is 85.13 (8)°. The conformation about the C=N bond is Z, and that about the C=C bonds is E. The imine N and ethyl N atoms are syn and are linked by an eth-yl-imine N-H⋯N hydrogen bond. This H atom also forms an inter-molecular hydrogen bond to the thione S atom, resulting in a supra-molecular helical chain propagating along the b axis. The chains are consolidated into a three-dimensional architecture by phenyl-C-H⋯Cl contacts and weak π-π inter-actions between centrosymmetrically related chloro-benzene rings [inter-centroid distance = 3.9127 (15) Å].
Two independent mol-ecules, A and B, comprise the asymmetric unit of the title compound, C20H21N3OSe. While the benzene ring directly bound to the central triazole ring is inclined to the same extent in both mol-ecules [dihedral angles = 40.41 (12) (mol-ecule A) and 44.14 (12)° (B)], greater differences are apparent in the dihedral angles between the Se-bound rings, i.e. 74.28 (12) (mol-ecule A) and 89.91 (11)° (B). Close intra-molecular Se⋯N inter-actions of 2.9311 (18) (mol-ecule A) and 2.9482 (18) Å (B) are noted. In the crystal, supra-molecular chains along the a axis are formed via O-H⋯N hydrogen bonding. These are connected into layers via C-H⋯O and C-H⋯N inter-actions; these stack along (01-1) without directional inter-molecular inter-actions between them.
In the organic mol-ecule of the title hydrate, C11H15N3OS·H2O, {systematic name: 3-ethyl-1-{(E)-[1-(2-hy-droxy-phen-yl)ethyl-idene]amino}-thio-urea monohydrate}, a dihedral angle of 5.39 (2)° is formed between the hy-droxy-benzene ring and the non-H atoms comprising the side chain (r.m.s. deviation = 0.0625 Å), with the major deviation from planarity noted for the terminal ethyl group [the C-N-C-C torsion angle = -172.17 (13)°]. The N-H H atoms are syn and an intra-molecular hy-droxy-imine O-H⋯N hydrogen bond is noted. In the crystal, the N-bonded H atoms form hydrogen bonds to symmetry-related water mol-ecules, and the latter form donor inter-actions with the hy-droxy O atom and with a hy-droxy-benzene ring, forming a O-H⋯π inter-action. The hydrogen bonding leads to supra-molecular tubes aligned along the b axis. The tubes are connected into layers via C-H⋯O inter-actions, and these stack along the c axis with no directional inter-actions between them.
In the title compound, C25H26N2O2S2, the central CN2S2 atoms are almost coplanar (r.m.s. deviation = 0.0058 Å). One phenyl ring clearly lies to one side of the central plane, while the other is oriented in the plane but splayed. Despite the different relative orientations, the phenyl rings form similar dihedral angles of 64.90 (3) and 70.06 (3)° with the central plane, and 63.28 (4)° with each other. The benzene ring is twisted with respect to the central plane, forming a dihedral angle of 13.17 (7)°. The S2C=N, N-N and N-N=C bond lengths of 1.2919 (19), 1.4037 (17) and 1.2892 (19) Å, respectively, suggest limited conjugation over these atoms; the configuration about the N-N=C bond is E. An intra-molecular O-H⋯N hydrogen bond is noted. In the crystal, phen-yl-meth-oxy C-H⋯O and phen-yl-phenyl C-H⋯π inter-actions lead to supra-molecular double chains parallel to the b axis. These are connected into a layer via meth-yl-phenyl C-H⋯π inter-actions, and layers stack along the a axis, being connected by weak π-π inter-actions between phenyl rings [inter-centroid distance = 3.9915 (9) Å] so that a three-dimensional architecture ensues.
The title salt, C5H11N2S(+)·C7H4ClO2 (-), comprises a 2-amino-3-ethyl-4,5-di-hydro-1,3-thia-zol-3-ium cation in which the five-membered ring adopts an envelope conformation with the methyl-ene C adjacent to the S atom being the flap, and a planar 3-chloro-benzoate anion (r.m.s. deviation for the 10 non-H atoms = 0.021 Å). The most prominent feature of the crystal packing are N-H⋯O hydrogen bonds whereby the two amine H atoms bridge two carboxyl-ate O atoms resulting in the formation of a centrosymmetric 12-membered {⋯HNH⋯OCO}2 synthon involving two cations and two anions. These aggregates are linked by C-H⋯O inter-actions to form a supra-molecular chain along the a-axis direction.