Tommy Liljefors

Antileishmanial chalcones : Statistical design, synthesis, and three-dimensional quantitative structure-activity relationship analysis

A large number of substituted chalcones have been synthesized and tested for antileishmanial and lymphocyte-suppressing activities. A subset of the chalcones was designed by using statistical methods. 3D-QSAR analyses using 67 (antileishmanial activity) and 63 (lymphocyte-suppressing activity) of the compounds for the training sets and 9 compounds as an external validation set were performed by using the GRID/GOLPE methodology. The Smart Region Definition procedure with subsequent region selection as implemented in GOLPE reduced the number of variables to approximately 1300 yielding 3D-QSAR models of high quality (lymphocyte-suppressing model, R2 = 0. 90, Q2 = 0.80; antileishmanial model, R2 = 0.73, Q2 = 0.63). The coefficient plots indicate that steric interactions between the chalcones and the target are of major importance for the potencies of the compounds. A comparison of the coefficient plots for the antileishmanial effect and the lymphocyte-suppressing activity discloses significant differences which should make it possible to design chalcones having a high antileishmanial activity without suppressing the proliferation of lymphocytes.

Conformational energy penalties of protein-bound ligands

The conformational energies required for ligands to adopt their bioactive conformations were calculated for 33 ligand–protein complexes including 28 different ligands. In order to monitor the force field dependence of the results, two force fields, MM3 and AMBER, were employed for the calculations. Conformational analyses were performed in vacuo and in aqueous solution by using the generalized Born/solvent accessible surface (GB/SA) solvation model. The protein-bound conformations were relaxed by using flat-bottomed Cartesian constraints. For about 70% of the ligand–protein complexes studied, the conformational energies of the bioactive conformations were calculated to be ≤3 kcal/mol. It is demonstrated that the aqueous conformational ensemble for the unbound ligand must be used as a reference state in this type of calculations. The calculations for the ligand–protein complexes with conformational energy penalties of the ligand calculated to be larger than 3 kcal/mol suffer from uncertainties in the interpretation of the experimental data or limitations of the computational methods. For example, in the case of long-chain flexible ligands (e.g. fatty acids), it is demonstrated that several conformations may be found which are very similar to the conformation determined by X-ray crystallography and which display significantly lower conformational energy penalties for binding than obtained by using the experimental conformation. For strongly polar molecules, e.g. amino acids, the results indicate that further developments of the force fields and of the dielectric continuum solvation model are required for reliable calculations on the conformational properties of this type of compounds.

Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 Ligand-binding Core

Glutamate is the principal excitatory neurotransmitter within the mammalian CNS, playing an important role in many different functions in the brain such as learning and memory. In this study, a combination of molecular biology, X-ray structure determinations, as well as electrophysiology and binding experiments, has been used to increase our knowledge concerning the ionotropic glutamate receptor GluR2 at the molecular level. Five high-resolution X-ray structures of the ligand-binding domain of GluR2 (S1S2J) complexed with the three agonists (S)-2-amino-3-[3-hydroxy-5-(2-methyl-2H-tetrazol-5-yl)isoxazol-4-yl]propionic acid (2-Me-Tet-AMPA), (S)-2-amino-3-(3-carboxy-5-methylisoxazol-4-yl)propionic acid (ACPA), and (S)-2-amino-3-(4-bromo-3-hydroxy-isoxazol-5-yl)propionic acid (Br-HIBO), as well as of a mutant thereof (S1S2J-Y702F) in complex with ACPA and Br-HIBO, have been determined. The structures reveal that AMPA agonists with an isoxazole moiety adopt different binding modes in the receptor, dependent on the substituents of the isoxazole. Br-HIBO displays selectivity among different AMPA receptor subunits, and the design and structure determination of the S1S2J-Y702F mutant in complex with Br-HIBO and ACPA have allowed us to explain the molecular mechanism behind this selectivity and to identify key residues for ligand recognition. The agonists induce the same degree of domain closure as AMPA, except for Br-HIBO, which shows a slightly lower degree of domain closure. An excellent correlation between domain closure and efficacy has been obtained from electrophysiology experiments undertaken on non-desensitising GluR2i(Q)-L483Y receptors expressed in oocytes, providing strong evidence that receptor activation occurs as a result of domain closure. The structural results, combined with the functional studies on the full-length receptor, form a powerful platform for the design of new selective agonists.

A Comparison of Conformational Energies Calculated by Several Molecular Mechanics Methods

Several commonly used molecular mechanics force fields have been tested for accuracy in conformational energy calculations. Differences in performance between the force fields are discussed for different classes of structures. MMFF93 and force fields based on the MM2 or MM3 functional form are found to perform significantly better than other force fields in the test, with average conformational energy errors around 0.5 kcal/mol. CFF91 also reaches this accuracy for the subset in which fully determined parameters are used, but it doubles the overall error due to use of estimated parameters. Harmonic force fields generally have average errors exceeding 1 kcal/mol. Factors influencing accuracy are identified and discussed.

Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data

A general set of procedures for automated parameterization of molecular mechanics force fields is presented. The current implementation for MacroModel force fields can easily be adapted to other programs running under Unix. Several variants of numerical Newton–Raphson and simplex methodologies are used to fit simultaneously both experimental and quantum mechanical data. In a sample parameterization of ethane, 24 different modes of combining various sources of reference data are compared. The best cost/performance ratio for generating quantum mechanical source data was obtained with the B3LYP/6‐31G* method. The best optimization strategy consists of initial subset optimizations with a modified simplex method, followed by Newton–Raphson optimization using Lagrange multipliers. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1146–1166, 1998

GABA-A Receptor Ligands and their Therapeutic Potentials

The GABA(A) receptor system is implicated in a number of neurological diseases, making GABA(A) receptor ligands interesting as potential therapeutic agents. Only a few different classes of structures are currently known as ligands for the GABA recognition site on the GABA(A) receptor complex, reflecting the very strict structural requirements for GABA(A) receptor recognition and activation. Within the series of compounds showing agonist activity at the GABA(A) receptor site that have been developed, most of the ligands are structurally derived from the GABA(A) agonists muscimol, THIP or isoguvacine. Using recombinant GABA(A) receptors, functional selectivity has been shown for a number of compounds such as the GABA(A)agonists imidazole-4-acetic acid and THIP, showing highly subunit-dependent potency and maximal response. In the light of the interest in partial GABA(A) receptor agonists as potential therapeutics, structure-activity studies of a number of analogues of 4-PIOL, a low-efficacy partial GABA(A) agonist, have been performed. In this connection, a series of GABA(A) ligands has been developed showing pharmacological profiles from moderately potent low-efficacy partial GABA(A) agonist activity to potent and selective antagonist effect. Only little information about direct acting GABA(A) receptor agonists in clinical studies is available. Results from clinical studies on the effect of the GABA(A) agonist THIP on human sleep pattern shows that the functional consequences of a direct acting agonist are different from those seen after administration of GABA(A) receptor modulators.

Chain-elongated analogues of a pheromone component of the turnip moth, Agrotis segetum. A structure–activity study using molecular mechanics

Chain-elongated analogues of (Z)-dec-5-enyl acetate, a pheromone component of the turnip moth, Agrotis segetum, have been studied. The conformational energies required for the analogues to mimic spatial relationships in the parent molecule, assumed to be crucial for the receptor interaction, were calculated by molecular mechanics (MM2). The calculated energies show a striking correlation with measured single-cell electrophysiological activities. The results indicate that an elongated alkyl chain is conformationally rearranged when the analogue is bound to the receptor, and that the biological activity is determined by the corresponding conformational energy.

Structure-activity relationships for chain-shortened analogs of (Z)-5-decenyl acetate, a pheromone component of the turnip moth, Agrotis segetum.

Structure-activity relationships for chain-shortened analogs of (Z)-5-decenyl acetate, a pheromone component of the turnip moth,Agrotis segetum, have been studied by electrophysiological single-sensillum technique and interpreted in terms of a previously reported receptor-interaction model. The results indicate that the terminal methyl group, as well as the acetate group, interacts with highly complementary receptor sites. The terminal alkyl chain is suggested to interact with a hydrophobic “pocket” extending over the two methylene groups closest to the terminal methyl group. The amounts of stimulus actually released from the odor source have been studied. The results demonstrate the necessity to take differences of volatility into account in comparisons of electrophysiological data for compounds of different chain lengths. It is shown that relative vapor pressures may to a good approximation be employed to estimate correction factors.

Effects of double-bond configuration on interaction between a moth sex pheromone component and its receptor : A receptor-interaction model based on molecular mechanics.

The dependence of the electrophysiological activity on the change of double-bond configuration of (Z)-5-decenyl acetate, a pheromone component of the turnip moth,Agrotis segetum, and a dienic analog, (E)-2,(Z)-5-decadienyl acetate, have been investigated by single-cell measurements and molecular mechanics calculations (MM2). A previously reported model for the interaction between a moth sex pheromone component and its receptor has been refined. This new model gives an essentially quantitative correlation between the measured activities and the calculated conformational energies for a biologically active conformation defined by the model. Previously obtained structure-activity results for chain-elongated analogs of (Z)-5-decenyl acetate are significantly improved by the refined model. The effect of a change of the double-bond configuration on the substrate-receptor interaction is not additive but depends on the conformational properties of the entire molecule.

On the relationship between the potential barrier and the activation energy for the internal rotation of a methyl group

Abstract The absolute rate theory expression for the rate of the internal rotation of a methyl group, or a similar internal rotor, hindered by a three-fold barrier, is developed. This expression is used to derive the activation energy and activation enthalpy for the process. Numerical calculations are performed using two assumptions regarding the form of the potential for two typical methyl barrier heights at three temperatures. The Arrhenius activation energies ( E a ) are found to be nearly temperature independent in the range 200–333 K and only 2–4% lower than the barrier height values ( V 3 ). The effect of tunneling is estimated to be about 2–3%.