Scientific Report 2008

Molecular Biology

Computational Structural Proteomics for Drug Discovery

R. Abagyan, G. Bottegoni, A. Grigoryan, J. Kovacs, I. Kufareva, G. Nicola, S.-J. Park, K. Reynolds, M. Rueda

We focus on developing and implementing new mathematical and computational methods to improve structure prediction and docking methods for structure-based drug design.

De Novo Discovery of Drug Leads

Our improved structure-based methods led to the discovery of new drug leads and inhibitors in collaborative studies with many scientists (Table 1).

Table 1. New drug leads and inhibitors.
Lead or inhibitor	Condition affected	Collaborators
Androgen receptor antagonist (Fig. 1)	Cancer	X.K. Zhang, Burnham Institute, La Jolla, California P. Sexton, A. Christopoulos, Monash University, Victoria, Australia J. Dalton, Ohio State University, Columbus, Ohio
α1-Antitrypsin polymerization blocker	α1-Antitrypsin deficiency, emphysema	D.A. Lomas, University of Cambridge, Cambridge, England
Serotonin N-acetyltransferase inhibitor	Sleep and mood disorders	P.A. Cole, Johns Hopkins School of Medicine, Baltimore, Maryland
Enoyl reductase inhibitor	Malaria	D.A. Fidock, Albert Einstein College of Medicine, Bronx, New York J.C. Sacchettini, Texas A&M University, College Station, Texas
Telomeric G-quadruplex	Cancer	K.Y. Wong, Hong Kong Polytechnic University, Hong Kong, China
Melanin-concentrating hormone receptor 1	Obesity	F. Monsma, Schering Plough Research Institute, Kenilworth, New Jersey A. Orry, C. Cavasotto, MolSoft L.L.C., La Jolla, California
Ubiquitin-like poxvirus proteinase I7L	Smallpox	V. Katritch, D. Hruby, SIGA Technologies, Inc., Corvallis, Oregon

Fig. 1. A novel androgen receptor antagonist repurposed from an antipsychotic drug.

Advanced Applications of Molecular Modeling and Docking

In collaborations with A.G. Kazantsev, Harvard Medical School, Charlestown, Massachusetts, we built structural models of inhibition of sirtuin 2. This foundation may be helpful in the further development of sirtuin 2 inhibitors for the treatment of Parkinson's disease.

We used the multiple receptor conformation approach to elucidate the structural mechanism of inhibition of the 3-phosphoinositide-dependent protein kinase-1 by 3-hydroxyanthranilic acid, a tryptophan metabolite. We found that 3-hydroxyanthranilic acid inhibited activation of the transcription factor NF-κB upon engagement of T-cell receptors by specifically targeting the kinase. Our docking models helped rationalize this interaction, which appears to play a key role in natural regulation of NF-κB activity.

Collaboration with M. Yeager, Department of Cell Biology, led to the development of techniques and models for complex multisubunit transmembrane proteins. The detailed atomic models of the gap junction channel and several other membrane proteins have been assigned to low-resolution electron density and refined by using the internal coordinate mechanics protocols. We also used the internal coordinate mechanics protocols in collaboration with J. Gertsch, ETH Zurich, Zürich, Switzerland, to develop models of supramolecular aggregates of cannabinomimetics. J. Fernandez-Recio and colleagues, University of Zaragoza, Zaragoza, Spain, collaborated with us to improve the prediction for transient protein-protein complexes. Finally, in collaboration with L.J. Miller, Mayo Clinic Scottsdale, Scottsdale, Arizona; P.C. Lam, MolSoft; and P.M. Sexton and A. Christopoulos, University of Monash; we designed a series of protocols designed for predicting realistic atomic models of a ternary complex of the secretin peptide and 2 domains of its receptor, a family B G protein—coupled receptor.

Challenges In Structure-Based Docking and Screening

Receptor flexibility is a critical issue in structure-based virtual screening methods. Most of the docking protocols rely on a fixed conformation of the receptor or on prior knowledge of multiple conformations representing the variation of the pocket. We have developed an induced-fit docking protocol called SCARE (SCan Alanines and Refines) that requires only a single initial pocket conformation for ligand docking and no prior knowledge about the location of the binding site.

To overcome the error of binding pose and binding score of ligands with single fixed receptors, we have introduced multiple receptor conformation, which will improve the docking calculation overall and account for receptor flexibility. We used this approach to screen large ligand databases against p38α kinase and the nuclear receptor peroxisome proliferator—activated receptor γ and found dramatic improvement in database enrichment factors against both receptors.

We also devised a method for evaluating the druggability (i.e., the potential to be targeted by a small-molecule drug) of protein targets at the level of structural proteomes. The method includes evaluating the structural feasibility of targeting the given protein with a small molecule (the presence of a sufficiently large and sufficiently buried binding pocket), predicting the target genomic instability and escape mutations (evolutionary conservation of the binding site across the genome of interest and related genomes), and predicting possible drug off-target activities and toxicities (the lack of homology with human proteins). This method has been applied to studies of the malarial proteome.

Publications

Bisson, W.H., Cheltsov, A.V., Bruey-Sedano, N., Lin, B., Chen, J., Goldberger, N., May, L.T., Christopoulos, A., Dalton, J.T., Sexton, P.M., Zhang, X.K., Abagyan, R. Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc. Natl. Acad. Sci. U. S. A. 104:11927, 2007.

Bottegoni, G., Kufareva, I., Totrov, M., Abagyan, R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J. Comput. Aided Mol. Des. 22:311, 2008.

Cavasotto, C.N., Orry, A.J., Murgolo, N.J., Czarniecki, M.F., Kocsi, S.A., Hawes, B.E., O'Neill, K.A., Hine, H., Burton, M.S., Voigt, J.H., Abagyan, R.A., Bayne, M.L., Monsma, F.J., Jr. Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J. Med. Chem. 51:581, 2008.

Chrencik, J.E., Brooun, A., Recht, M.I., Nicola, G., Davis, L.K., Abagyan, R., Widmer, H., Pasquale, E.B., Kuhn, P. Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J. Biol. Chem. 282:36505, 2007.

Dong, M., Lam, P.C., Gao, F., Hosohata, K., Pinon, D.I., Sexton, P.M., Abagyan, R., Miller, L.J. Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol. Pharmacol. 72:280, 2007.

Harikumar, K.G., Lam, P.C., Dong, M., Sexton, P.M., Abagyan, R.,Miller, L.J. Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. J. Biol. Chem. 282:32834, 2007.

Hayashi, T., Mo, J.H., Gong, X., Rossetto, C., Jang, A., Beck, L., Elliott, G.I., Kufareva, I., Abagyan, R., Broide, D.H., Lee, J., Raz, E. 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc. Natl. Acad. Sci. U. S. A. 104:18619, 2007.

Katritch, V., Byrd, C.M., Tseitin, V., Dai, D., Raush, E., Totrov, M., Abagyan, R., Jordan, R., Hruby, D.E. Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J. Comput. Aided Mol. Des. 21:549, 2007.

Kovacs, J.A., Baker, K.A., Altenberg, G.A., Abagyan, R., Yeager, M. Molecular modeling and mutagenesis of gap junction channels. Prog. Biophys. Mol. Biol. 94:15, 2007.

Kovacs, J.A., Yeager, M., Abagyan, R. Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys. J. 93:1950, 2007.

Lee, H.S., Choi, J., Kufareva, I., Abagyan, R., Filikov, A., Yang, Y., Yoon, S. Optimization of high throughput virtual screening by combining shape-matching and docking methods. J. Chem. Inf. Model. 48:489, 2008.

Ma, D.L., Lai, T.S., Chan, F.Y., Chung, W.H., Abagyan, R., Leung, Y.C., Wong, K.Y. Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking. ChemMedChem 3:881, 2008.

Mallya, M., Phillips, R.L., Saldanha, S.A., Gooptu, B., Brown, S.C., Termine, D.J., Shirvani, A.M., Wu, Y., Sifers, R.N., Abagyan, R., Lomas, D.A. Small molecules block the polymerization of Z α ₁-antitrypsin and increase the clearance of intracellular aggregates. J. Med. Chem. 50:5357, 2007.

Medina, M., Abagyan, R., Gómez-Moreno, C., Fernandez-Recio, J. Docking analysis of transient complexes: interaction of ferredoxin-NADP⁺ reductase with ferredoxin and flavodoxin. Proteins 72:848, 2008.

Nicola, G., Smith, C.A., Abagyan, R. New method for the assessment of all drug-like pockets across a structural genome. J. Comput. Biol. 15:231, 2008.

Nicola, G., Smith, C.A., Lucumi, E., Kuo, M.R., Karagyozov, L., Fidock, D.A., Sacchettini, J.C., Abagyan, R. Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening. Biochem. Biophys. Res. Commun. 358:686, 2007.

Outeiro, T.F., Kontopoulos, E., Altmann, S.M., Kufareva, I., Strathearn, K.E., Amore, A.M., Volk, C.B., Maxwell, M.M., Rochet, J.C., McLean, P.J., Young, A.B., Abagyan, R., Feany, M.B., Hyman, B.T., Kazantsev, A.G. Sirtuin 2 inhibitors rescue α -synuclein-mediated toxicity in models of Parkinson's disease. Science 317:516, 2007.

Raduner, S., Bisson, W., Abagyan, R., Altmann, K.H., Gertsch, J. Self-assembling cannabinomimetics: supramolecular structures of N-alkyl amides. J. Nat. Prod. 70:1010, 2007.

Szewczuk, L.M., Saldanha, S.A., Ganguly, S., Bowers, E.M., Javoroncov, M., Karanam, B., Culhane, J.C., Holbert, M.A., Klein, D.C., Abagyan, R., Cole, P.A. De novo discovery of serotonin N-acetyltransferase inhibitors. J. Med. Chem. 50:5330, 2007.

Totrov, M., Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 18:178, 2008.