Fundamentals of Ligand-Protein Interactions

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The conformational changes of both partners of a ligand-protein complex, the small-molecule ligand in its the protein binding site (in many cases the catalytically active site of an enzyme) are a central aspect many drug actions, as well as a crucial challenge in computational approaches to drug design. In one of the earliest publications in the this field, we showed for a small set of ligands occurring both in the Protein Data Bank (PDB) and the Cambridge Structural Database (CSD) that flexible compounds are not usually bound to a protein in their global vacuum energy conformation, and oftentimes not even in any local vacuum energy conformation. While this study used the largest set of data and best methodology available at that time, both the number of structures in either experimental database and the software and hardware resource available have since grown exponentially. We are thus revisiting this important topic with an analysis of orders of magnitudes more structures, and computations performed at a high level of computational quantum-chemical theory. Among other milestones achieved so far in this project, we have extracted all occurrences of small-molecule ligands recently made available in PDB's LigandExpo. As of May 2008, this was a set of over 350,000 distinct sets of 3D coordinates (current set size: 1.9 million). We have added extensive annotation coming from several different sources. Using these annotations in a chain of filters, we have generated "high-quality" subsets of ligand structures of high quality and reliability numbering from just about one thousand to about 5,000 occurrences depending on the stringency applied. We have conducted high-level quantum-chemical calculations of conformational energies for these high-quality ligand sets. In the first round, vacuum energy calculations were run partly on our own Linux cluster, partly on the Biowulf cluster of the CIT, NIH. Up to a thousand CPUs were used simultaneously in this computationally massive project, with individual jobs taking from a few hours to several weeks of CPU-time. We obtained results from about 360 runs that completed successfully. These results clearly showed that the possibility for high conformational energies are fully confirmed by these quantum-chemical calculations. To explore the possible influence of aqueous environment on ligand conformational energies - after all, vacuum is not really where drug molecules typically operate - a second round of quantum chemical calculations was conducted, employing the SCI-PCM solvent model in Gaussian 03. These runs were even more demanding in terms of computer resources than the vacuum calculations. To analyze the energetic uncertainty as a function of the positional uncertainty, which in turn is a function of the crystallographic resolution, we conducted sampling of conformations with a resolution-dependent torsion distribution centered around the crystal structure conformation at the molecular mechanics force field level. The advent of ever more-powerful experimental instrumentation such as free electron lasers opens up new possibilities in answering these questions. Related to this topic is a study recently begun on tautomerism of small organic molecules, which is an important question both in chemoinformatics and databases (Project 3), efficient drug design (Projects 2 and 3), and the present project of better understanding protein-ligand interactions and the crystal structures aiding in this quest. This work has been performed by Dr. Laura Guasch-Pamies. The tautomerism work is continuing with interesting results of combined experimental, quantum-chemical and chemoinformatics analysis, which have been described in papers either accepted or under review, and/or studied for further analyses. The work in this field has laid the groundwork for exciting new research involving crystal structures of aldose reductase and other cancer- and HPV-related proteins. A number of papers reviewing the current status and the future possibilities of the field have been published in this project, including most recently the role of ultra-high resolution crystallography. This topic has gained new importance with the increased emphasis of docking in the CADD Group's work.