Structure-Based Ligand Design

With the use of Molecular Dynamics simulations coupled to the Linear Interaction Energy (LIE) Method properties of ligand binding can be deduced. This method has been successfully used in a variety of biological systems, including COX-1, HIV-1 reverse transcriptase and Plasmepsin Plm II and IV.

List of Publications

Sund J, Lind C, Åqvist J., (2014) J Phys Chem B.  "Binding Site Preorganization and Ligand Discrimination in the Purine Riboswitch".

Shamsudin Khan Y, Gutiérrez-de-Terán H, Boukharta L, Åqvist J. (2014). J Chem Inf Model. 54, 1488-1499. "Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX‐1 Inhibitors"

Boukharta L, Gutiérrez-de-Terán H, Åqvist J. (2014) PLoS Comput Biol. 10, 1-11. "Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors". Open Access.

Wallin G, Nervall M, Carlsson J and Åqvist J; Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method J. Chem. Theory Comput.5, 380, (2009)

Nervall, M., Hanspers, P., Carlsson, J., Boukharta, L., Åqvist, J. Predicting binding modes from free energy calculations. J. Med. Chem.51, 2657, (2008)

Carlsson, J., Boukharta, L., Aqvist, J. Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. J. Med. Chem.51, 2648, (2008)

Ersmark, K., Nervall, M., Guiterrez de Teran, H., Hamelink, E., Janka, L.K., Clemente, J.C., Dunn, B.M., Gogoll, A., Samuelsson, B., Åqvist, J., Hallberg, A. Macrocyclic Inhibitors of the Malarial Aspartic Proteases Plasmepsin Plm II and IV. Bioorg, Med. Chem.14, 2197, (2006)

Guiterrez de Teran, H., Nervall, M., Ersmark, K., Liu, P., Janka, L.K., Dunn, B., Hallberg, A., Åqvist, J. Inhibitor Binding to the Plasmepsin IV Aspartic Protease from Plasmodium falciparum. Biochemistry45, 10529, (2006)

Guiterrez-de-Teran, H., Nervall, M., Dunn, B.M., Clemente, J.C., Åqvist, J. Computational Analysis of Plasmepsin IV Bound to an Allophenylnorstatine Inhibitor. FEBS Lett.580, 5910, (2006)

Lovmar, M., Nilsson, K., Vimberg, V., Tenson, T., Nervall, M., Ehrenberg, M. The Molecular Mechanism of Peptide-Mediated Erythromycin Resistance. J. Biol. Chem.281, 6742, (2006)

Ersmark, K., Nervall, M., Hamelink, E., Janka, L.K., Clemente, J.C., Dunn, B.M., Blackman, M.J., Samuelsson, B., Åqvist, J., Hallberg, A. Synthesis of Malarial Plasmepsin Inhibitors and Prediction of Binding Modes by Molecular Dynamics Simulations. J. Med. Chem.48, 6090, (2005)

Ersmark, K., Bjelic, S., Feierberg, I., Hamerlink, E., Hackett, F., Blackman, M.J., Hultén J., Samuelsson, B., Åqvist, J., Hallberg, A. Potent Inhibitors of the P. falciparum Enzymes Plasmepsin I and II Devoid of Cathepsin D Inhibitory Activity. J. Med. Chem.47, 110, (2004)

Ersmark, K., Feierberg, I., Bjelic, S., Hultén J., Samuelsson, B., Åqvist, J., Hallberg, A. C2-Symmetric Inhibitors of Plasmodium falciparum Plasmepsin II: Synthesis and Theoretical Predictions. Bioorg. Med. Chem.11, 3723, (2003)