Weak ligand binding: data processing and electron density calculation methods

P. Kolenko1,2, M. Malý1,2, J. Dušková1, T. Kovaľ1, T. Skálová1, L. H. Østergaard3, J. Dohnálek1

1 Institute of Biotechnology CAS, v.v.i., Biocev, 252 50 Vestec, Czech Republic

2 Dept. of Solid State Physics, FNSPE, CTU, Břehová 7, 115 19 Prague 1, Czech Republic

3 Dept. of Agile Protein Screening, Novozymes A/S, Krogshoejvej 36, Bagsvaerd, Denmark

petr.kolenko@ibt.cas.cz

 

Analysis of interactions between macromolecules and small molecule ligands represents one of the leading courses to develop new drugs. A number of libraries containing from tens to thousands of small molecule fragments have been already used to screen potential binding sites [1]. These observations were later used for the design of a larger ligand composed of chemically linked fragments that would be of a biological importance. One of the problematic issues is weak (or partial) binding of a fragment that may lead to potential loss of information in calculated electron density.

We collected a medium resolution test dataset of an FAD-dependent enzyme that binds a ligand with partial occupancy. At first, we have analyzed the influence of diffraction limit estimation. After the careful diffraction data processing, we have tested several methods of electron density calculation (e.g. composite omit map, feature-enhanced map, polder map, etc.) [2-3]. Comparative analysis of the calculated electron densities was performed.

We show that weak reflections may significantly increase the quality of observed electron density for the ligand, and also an importance of various electron density calculation approaches in the validation of ligand binding. We have demonstrated that careful analysis of the data may lead from initial unobserved ligand binding to final determination and validation of partial occupancy ligand binding.

 

This publication was supported by the ERDF fund (CZ.02.1.01/0.0/0.0/16_013/0001776) and by the Grant Agency of the Czech Technical University in Prague, grant No. SGS16/246/OHK4/3T/14.

 

1. Congreve, M., Chessari, G., Tisi, D. and Woodhead, A.J., J. Med. Chem., 2008, 51, 3661–3680.

2. Adams, P. D. et al., Acta Cryst., 2010, D66, 213-221.

3. Winn, M. D. et al., Acta. Cryst., 2011, D67, 235-242.