Tommi Nyrönen

BODIL: a molecular modeling environment for structure-function analysis and drug design.

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html

A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods.

A panel of 92 catechol-O-methyltransferase (COMT) inhibitors was used to examine the molecular interactions affecting their biological activity. COMT inhibitors are used as therapeutic agents in the treatment of Parkinsons disease, but there are limitations in the currently marketed compounds due to adverse side effects. This study combined molecular docking methods with three-dimensional structure-activity relationships (3D QSAR) to analyse possible interactions between COMT and its inhibitors, and to incite the design of new inhibitors. Comparative molecular field analysis (CoMFA) and GRID/GOLPE models were made by using bioactive conformations from docking experiments, which yielded q2 values of 0.594 and 0.636, respectively. The docking results, the COMT X-ray structure, and the 3D QSAR models are in agreement with each other. The models suggest that an interaction between the inhibitors catechol oxygens and the Mg2+ ion in the COMT active site is important. Both hydrogen bonding with Lys144, Asn170 and Glu199, and hydrophobic contacts with Trp38, Pro174 and Leu198 influence inhibitor binding. Docking suggests that a large R1 substituent of the catechol ring can form hydrophobic contacts with side chains of Val173, Leu198, Met201 and Val203 on the COMT surface. Our models propose that increasing steric volume of e.g. the diethylamine tail of entacapone is favourable for COMT inhibitory activity.

“RKKH” Peptides from the Snake Venom Metalloproteinase ofBothrops jararaca Bind Near the Metal Ion-dependent Adhesion Site of the Human Integrin α2 I-domain

Integrin α1β1and α2β1 are the major cellular receptors for collagen, and collagens bind to these integrins at the inserted I-domain in their α subunit. We have previously shown that a cyclic peptide derived from the metalloproteinase domain of the snake venom protein jararhagin blocks the collagen-binding function of the α2 I-domain. Here, we have optimized the structure of the peptide and identified the site where the peptide binds to the α2 I-domain. The peptide sequence Arg-Lys-Lys-His is critical for recognition by the I-domain, and five negatively charged residues surrounding the “metal ion-dependent adhesion site” (MIDAS) of the I-domain, when mutated, show significantly impaired binding of the peptide. Removal of helix αC, located along one side of the MIDAS and suggested to be involved in collagen-binding in these I-domains, does not affect peptide binding. This study supports the notion that the metalloproteinase initially binds to the α2 I-domain at a location distant from the active site of the protease, thus blocking collagen binding to the adhesion molecule in the vicinity of the MIDAS, while at the same time leaving the active site free to degrade nearby proteins, the closest being the β1 subunit of the α2β1cell-surface integrin itself.

Comparing the quality and predictiveness between 3D QSAR models obtained from manual and automated alignment.

A set of 113 flexible cyclic urea inhibitors of human immunodeficiency virus protease (HIV-1 PR) was used to compare the quality and predictive power of CoMFA and CoMSIA models for manually or automatically aligned inhibitor set. Inhibitors that were aligned automatically with molecular docking were in agreement with information obtained from existing X-ray structures. Both alignment methods produced statistically significant CoMFA and CoMSIA models, with the best q(2) value being 0.649 and the best predictive r(2) being 0.754. The manual alignment gave statistically higher values, whereas the automated alignment gave more robust models for predicting the activities of an external inhibitor set. Both models utilized similar amino acids in the HIV-1 PR active site, supporting the idea that hydrogen bonds form between an inhibitor and the backbone carbonyl oxygens of Gly48 and Gly48 and also the backbone NH group of Asp30, Gly48, Asp29, and Gly48 of the enzyme. These results suggest that an automated inhibitor alignment can yield predictive 3D QSAR models that are well comparable to manual methods. Thus, an automated alignment method in creating 3D QSAR models is encouragable when a well-characterized structure of the target protein is available.

A linear open-chain piperazine-pyridine ligand and its meso-helical Co complex

Abstract An oligomeric ligand (HPPy) 2 P, N , N ′-bis[2-(6-( N -( N ′-(2-hydroxyethyl)piperazinyl)methyl)]piperazine, was designed to resemble structurally open-chain aza-crowns. Owing to the all- trans configuration of piperazine and pyridine free electron pairs, it should adopt a near linear overall structure in solvent. Theoretical calculations at ab initio level confirm the overall linear structure of free ligand. The crystal structure of the complex [(HPPy) 2 P][Co(NO 3 ) 2 ] 2 shows a contraction from ∼3 to 2 nm structure. Each coordination site creates either a Δ or Δ configuration around the metal ion, thus causing a ligand with an even number of coordination centres to be meso -helical. The complex (C 30 H 48 N 12 O 14 Co 2 ) crystallizes in the monoclinic space group P 2 1 / n (No. 14) with the cell dimensions a = 11.673(4), b = 13.212(8), c = 12.561(7) A , β = 90.33(1)°, V = 1937(2) A 3 and Z = 2 . The structure is refined to a final agreement factor R ( F 0 2 ) = 0.0576 using 2121 reflections with l >4 σ ( l ). The molecule is centrosymmetric with two identical coordination centres, in which the regular octahedral geometry is tetragonally distorted.