Aspirin blocks binding of photosensitizer SnET2 into human serum albumin: implications for photodynamic therapy.

Tin etiopurpurin dichloride (SnET2) is one of the photosensitizers under investigation to be used in photodynamic therapy of prostate cancer. The drug is delivered intravenously, transported in vivo by liposomes and plasma proteins and localized within the prostate. SnET2 exists in two tautomeric forms (I - closed ring, II - open ring) with I converting spontaneously into the more energetically stable form II at physiological pH. Up to approximately 50% of the drug can be carried by serum albumin, although this association can increase photo-bleaching and diminish the drug efficiency. Molecular modeling and force field calculations indicate that Sudlow Site I in human serum albumin (HSA) is the most probable binding site for both forms of SnET2, with the porphyrin moiety nestling between domains IIA and IB, and the esterolytic side group oriented toward domain IIIA of HSA. Other drugs, including aspirin, bind to the same part of HSA. SnET2 does not bind to HSA when pre-incubated with aspirin, which confirms that its place of binding to this protein must be located near Lys199. This observation could be exploited to improve photo-efficiency of SnET2 by finding drugs that could compete with the photosensitizer for binding into Sudlow Site I of HSA.

Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.

Flash-freezing is a technique that is commonly used nowadays to collect diffraction data for X-ray structural analysis. It can affect both the crystal and molecular structure and the molecule's surface, as well as the internal cavities. X-ray structural data often serve as a template for the protein receptor in docking calculations. Thus, the size and shape of the binding site determines which small molecules could be found as potential ligands in silico, especially during high-throughput rigid docking. Data were analyzed for wild soybean lipoxygenase-3 (MW 97 kDa) at 293 and 93 K and compared with the results from studies of its molecular complexes with known inhibitors, structures published by others for a derivative of the same enzyme (98 K) or a topologically close isozyme lipoxygenase-1 (at ambient temperature and 100 K). Analysis of these data allows the following conclusions. (i) Very small changes in the relative orientation of the molecules in the crystal can cause major changes in the crystal reciprocal lattice. (ii) The volume of the internal cavities can ;shrink' by several percent upon freezing even when the unit-cell and the protein molecular volume show changes of only 1-2%. (iii) Using a receptor structure determined based on cryogenic data as a target for computational screening requires flexible docking to enable the expansion of the binding-site cavity and sampling of the alternative conformations of the crucial residues.

Indole- and carbazole-substituted pyridinium iodide salts: a rare case of conformational isomerism in crystals.

A series of indole- and carbazole-substituted pyridinium iodide salts has been synthesized and characterized. X-ray analysis revealed that the iodide salt of the indole-substituted cation (E)-4-(1H-indol-3-ylvinyl)-N-methylpyridinium (IMPE(+)), C(16)H(15)N(2)(+) x I(-), (I), has two polymorphic modifications, (Ia) and (Ib), and a hemihydrate structure, C(16)H(15)N(2)(+) x I(-) x 0.5H(2)O, (II). Until now, only one crystal modification has been identified for the (E)-4-(9-ethyl-9H-carbazol-3-ylvinyl)-N-methylpyridinium (ECMPE(+)) iodide salt, C(22)H(21)N(2)(+) x I(-), (III). Crystals of (Ia) and (Ib) comprise stacks of antiparallel cations with iodide anions located in the channels between the stacks. Due to the presence of the water molecules, the packing in (II) is quite different to that found in (Ia) and (Ib), and positional disorder involving a statistical superposition of two rotamers of IMPE(+), with different orientations of the indole fragment, was found. Crystals of (III) contain two independent ECMPE(+) rotamers with different orientations of their carbazole substituents. The cations are packed in stacks, with the iodide anions located in the channels between the stacks. In (III), the iodide was found to be disordered over two sites, with occupancies of 0.83 and 0.17.

Conformational polymorphs of 22-cyano-N-methyl-5-phenylpent-2-en-4-ynamide.

Although the two polymorphic modifications, (I) and (II), of the title compound, C(13)H(10)N(2)O, crystallize in the same space group (P2(1)/c), their asymmetric units have Z' values of 1 and 2, respectively. These are conformational polymorphs, since the molecules in phases (I) and (II) adopt different rotations of the phenyl ring with respect the central 2-cyanocarboxyaminoprop-2-enyl fragment. Calculations of crystal packing using Cerius(2) [Molecular Simulations (1999). 9685 Scranton Road, San Diego, CA 92121, USA] have shown that (I) is more stable than (II), by 1.3 kcal mol(-1) for the crystallographically determined structures and by 1.56 kcal mol(-1) for the optimized structures (1 kcal mol(-1) = 4.184 kJ mol(-1)). This difference is mainly attributed to the different strengths of the hydrogen bonding in the two forms.