Maciej Geller

Water properties inside nanoscopic hydrophobic pocket studied by computer simulations

The structure and dynamics of water in the vicinity of the hemispherical hydrophobic pocket of 8 A radius were examined via molecular dynamics simulations in NVT ensemble. Density, hydrogen bonding properties, and residence times of water molecules were projected on two-dimensional planes providing a spatial description of water behavior. We found that the average water density is significantly depleted relative to bulk value. A detailed analysis of pocket occupancy revealed fluctuations between states of completely empty pocket and a pocket filled with a bulklike fluid, which seem to result from collective behavior of water molecules. Free energy differences accompanying these fluctuations are rather small, suggesting that the given pocket radius is close to the critical one for transition between gas and liquid phases in the considered system. We show that the situation is different in the case of a simple Lennard-Jones fluid. These results indicate that changing the surface curvature from flat to concave may lead to qualitative difference in water behavior in its vicinity. We think that our studies may also put some light on binding site desolvation process which is necessary to understand to make correct predictions of binding energies.

Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: Crystallographic refinement of 2 A data.

The structure of a complex between a hexapeptide‐based inhibitor, MVT‐101, and the chemically synthesized (Aba 67,95,167,195; Aba: l‐α‐amino‐n‐butyric acid) protease from the human immunodeficiency virus (HIV‐1), reported previously at 2.3 Å has now been refined to a crystallographic R factor of 15.4% at 2.0 Å resolution. Root mean square deviations from ideality are 0.18 Å for bond lengths and 2.4° for the angles. The inhibitor can be fitted to the difference electron density map in two alternative orientations. Drastic differences are observed for positions and interactions at P3/S3 and P3′/S3′ subsites of the two orientations due to different crystallographic environments.

ANALYSIS OF THE STRUCTURE OF HIV-1 PROTEASE COMPLEXED WITH A HEXAPEPTIDE INHIBITOR. PART II: MOLECULAR DYNAMIC STUDIES OF THE ACTIVE SITE REGION

Six models of the catalytic site of HIV‐1 protease complexed with a reduced peptide inhibitor, MVT‐101, were investigated. These studies focused on the details of protonation of the active site, its total net charge and hydrogen bonding pattern, which was consistent with both the observed coplanar configuration of the acidic groups of the catalytic aspartates (Asp‐25 and Asp‐125) and the observed binding mode of the inhibitor. Molecular dynamic simulations using AMBER 4.0 indicated that the active site should be neutral. The planarity of the aspartate dyad may be due to the formation of two hydrogen bonds: one between the inner Oδ1oxygen atoms of the two catalytic aspartates and another between the Oδ2atom of Asp‐125 and the nitrogen atom of the reduced peptide bond of the bound inhibitor. This would require two additional protonations, either of both aspartates, or of one Asp and the amido nitrogen atom of Nle‐204. Our results favor the Asp‐inhibitor protonation but the other one is not excluded. Implications of these findings for the mechanism of enzymatic catalysis are discussed. Dynamic properties of the hydrogen bond network in the active site and an analysis of the interaction energy between the inhibitor and the protease are presented.

Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease

The mechanism of the first steps of the reaction catalyzed by HIV-1 protease was studied through molecular dynamics simulations. The potential energy surface in the active site was generated using the approximate valence bond method. The approximate valence bond (AVB) method was parameterized based on density functional calculations. The surrounding protein and explicit water environment was modeled with conventional, classical force field. The calculations were performed based on HIV-1 protease complexed with the MVT-101 inhibitor that was modified to a model substrate. The protonation state of the catalytic aspartates was determined theoretically. Possible reaction mechanisms involving the lytic water molecule are accounted for in this study. The modeled steps include the dissociation of the lytic water molecule and proton transfer onto Asp-125, the nucleophilic attack followed by a proton transfer onto peptide nitrogen. The simulations show that in the active site most preferable energetically are structures consisting of ionized or polarized molecular fragments that are not accounted for in conventional molecular dynamics. The mobility of the lytic water molecule, the dynamics of the hydrogen bond network, and the conformation of the aspartates in the active center were analyzed.

Hydration of the tautomeric forms of 2-oxopyrimidine: A Monte Carlo simulation

Abstract The hydration of both tautomeric forms of 2-oxopyrimidine has been investigated using the Monte Carlo method for a cluster consisting of 50 water molecules at T = 300 K. The structure of the first hydration shell in both tautomers is discussed. Local minima of the interaction energy between n = 1, 2, 3, 4, 5 or 10 water molecules and 2-oxopyrimidine have been examined. The results clarify why water molecules in the first hydration shell are rarely located precisely at the minima corresponding to the interaction of one water molecule with the solute. The results also suggest that the hydration shifts the tautomeric equilibrium towards the lactam form.

Refinement of X-ray data on dual cosubstrate specificity of CK2 kinase by free energy calculations based on molecular dynamics simulation

Free energy differences of binding of adenosine triphosphate (ATP) and guanine triphosphate (GTP) to the protein kinase CK2 (casein kinase 2) were calculated, using molecular dynamics (MD) simulations and the thermodynamic cycle approach. Good agreement with experimental data was obtained. Simulations confirm observations based on crystallographic data that specifically interacting water molecules in the binding site region of CK2 kinase play a key role in its ability to use ATP or GTP as equally efficient phosphate donors. We point out that to obtain quantitatively reasonable results, it was necessary to modify original X‐ray data by assuming the presence of an additional water molecule in the CK2 binding site structure with GTP. Proteins 2005.

Solvation of the tautomeric forms of 2-oxopyrimidine in carbon tetrachloride solution: A Monte Carlo simulation

Abstract Solvation of both tautomeric forms of 2-oxopyrimidine by carbon tetrachloride has been investigated using the Monte Carlo method for a cluster consisting of 50 molecules at T =300 K. The results indicate that, in oposition to hydration, this solvation shifts the tautomeric equilibrium a little towards the lactim form, in agreement with experiment. The structure of the solvation shell in both tautomers closely resembles that of the pure solvent. Local minima of the interaction energy between n = 1, 2, 3, 4, 6 and 8 CCl 4 molecules and 2-oxopyrimidine have been examined. The results shed some light on the nature of the poor solubility of purines and pyrimidines in carbon tetrachloride.

Calculations of the conformational properties of acyclonucleosides: Part 2. Comparison of active and nonactive compounds

Abstract Two related molecules from the acyclic nucleoside family 9-(1,3-dihydroxy-2-propoxymethyl) guanine (DHPG) and 9-(1,5-dihydro-4-hydroxymethyl-3-oxapentyl-2- [R])guanine (2′, 3′- secoG) have been compared by means of force field conformational analysis. They are respectively active and nonactive analogs of the antivirial compound 9-((2-hydroxyethoxy)methyl)guanine (ACG). As in the case of ACG many local minima are found for both molecules, indicating their great flexibility. For all three molecules conformations similar to those occurring in cyclic nucleosides have energies from 3 to 7 kcal mol −1 above the most stable minima.

Electroreduction mechanism of 2-thiopyrimidine derivatives: Part II. Correlation with electronic structure indices

Summary The experimentally observed changes in the electroreductionmechanism of 2-thiopyrimidine derivatives were interpretated on the basis of their electronic structure, calculated by the CNDO/2 and Huckel methods. For some of the examined compounds a linear correlation has been found between the experimental measurement of the electron acceptor properties of molecules (represented by a polarographic potential U 1/2 Red ) and the theoretical computation of the energy of the lowest unoccuppied molecular orbital (LUMO). For the same compounds it was also found that U 1/2 Red linearly correlates with the N 3 =C 4 bond order and the electronic charge distribution on N 3 and C 4 but not with other bond orders and charges. These results confirm the experimental data, indicating that the N 3 =C 4 bond is the electroactive centre of the molecules considered.

HIV-1 Protease and its Inhibitors

HIV-1 protease (HIV-1 PR), one of the three enzymes encoded by the viral genome and vital for its replication, is natural target for chemotherapy. The three-dimensional X-ray structure of the native form, and of its complexes with various inhibitors, provide a basis for understanding the physicochemical properties of the protease. Formation of the catalytically active homodimeric form of the protease, and of its complexes with inhibitors, may be determined by two physically different types of interactions: electrostatic and hydrophobic. Selected problems related to rational drug design will be discussed; rigidity and flexibility of the enzyme; analysis of electrostatic and hydrophobic interactions in the interface region; dissociative inhibition in the intertwining region; electrostatic field of the binding site; protonation state of the catalytic aspartates; location of internal water molecules; presentation of selected inhibitors. From a methodological point of view, HIV-1 PR is an exellent object for testing different theoretical methods applied to computer-aided drug design.