A Library of Protein-Ligand Interaction Sites forde novo Ligand Design

Kiminobu Satoxsat@kuicr.kyoto-u.ac.jp

Minoru Kanehisa

kanehisa@kuicr.kyoto-u.ac.jp

Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan

1 Introduction
Under the Human Genome Project, all 100,000 genes of the human genome will be sequenced alongwith bacterial and other genomes. This vast amount of information will become essential to discover
new enzyme-substrate interactions or to design new ligands that can be used as drugs and in otherapplications. The elucidation of protein structures lags behind the determination of protein sequences.
The homology modeling and other ecient techniques can rapidly produce approximate 3-D structuresof target proteins, but they cannot readily be used for drug design since obtained protein 3-D structure
models are imprecise. Combinatorial libraries of chemical compounds are useful as practical screening
methods, but it is necessary to develop novel computational methods for understanding principles
of molecular varieties. For small molecules that interact with proteins, such as GTP and NAD,
their binding sites are usually well characterized and de ned. Thus, collection and organization oflocal structural knowledge, including the information of ligand binding sites of proteins and atomiclocations of ligands, must be precious resources that could be used computationally for drug design orin other applications. We report here a new library of ligand binding sites, which contains informationof interacting atomic pairs between proteins and ligands, and other information such as indirectinteraction caused by water molecules or metal ions.

2 Data and Method
2.1

Data collection

Currently, we are focusing on interactions between proteins and several ligands with hydrophobic
ring groups such as AMP, ADP, ATP, GMP, GDP, GTP, NAD (NADH, NADPH) and FAD. For
constructing a library of ligand binding sites, we extracted 521 entries from PDB release 84.0, each ofwhich contains structural information of proteins that bind to these ligands. If multiple ligands bindto a protein in a PDB entry, each of the ligand binding sites was represented as a distinct entry in ourlibrary. To construct the library, we focus on a set of interactions between atoms of proteins (host)and atoms of ligands. The set of atoms in proteins that interact with ligands is de ned as follows.
Given a ligand that constitutes of n atoms, let hi be a set of atoms of a host protein whose distances
to the atom i of the ligand are less than or equal to 5
A. By de nition, union of hi , which is denoted as
H , represents a whole set of host atoms that interact with atoms of the ligand. For interacting pairsof atoms, we extracted information about atomic distances, type of interactions (bonds), intercalated
atoms (e.g. water molecules and metal ions such as M n2+ , M g 2+ , etc.), and type of atoms.
2.2

Representation of atom pairs information

To characterize the interactions between a ligand atom i and a host atom j , we de ne bond index= P bondi 1 P bondj . If atom i from the interacting pair is a constituent of an n-phosphate group,
P bondi = 0. If i does not make any type of bond, P bondi = 1. If i can be a donor or an acceptor ofP bond298

a hydrogen bond, P bondi = 2. If i can form a salt link, P bondi = 3. For atom j constituting the hostprotein, P bondj = 0 if j is a main chain atom. If j is an atom of a hydrophobic amino acid residue,P bondj = 1. If j can be a donor or an acceptor of hydrogen bond, or can form a salt link, P bondj = 2.
If j is a charged or polar atom, P bondj = 3. Furthermore, the ligand atom i is discriminated by anindex gp whether it is a constituent of a ring group or not. If i is a ring group atom, gpi = 1, otherwise
gpi = 0. According to these de nitions, we de ne the scoring function of interacting atomic pairs by
the following equation:
Pbond
1 Ppena
Pscore =Pdistance

where Pdistance is the distance between two atoms. If the ligand atom i is charged and the host atom
j is hydrophobic, non-polar or uncharged, or if i is uncharged and a ring group constituent (gpi = 1),
1
Ppena =:
Pdistance

If both i and j have the same charge,
Ppena=0Pbond
Pdistance:

If i and j have opposite charges, or if i is uncharged and gpi = 0,Ppena=PbondPdistance:

In addition to the scoring for atomic pairs, intercalated water molecules or metal ions are dealt
separately to discriminate them from host-ligand atomic pairs.

3 Result and Discussion
For all possible interacting host-ligand atomic pairs in the PDB entries, Pscore was calculated by thescoring function de ned above. Since the calculated Pscore would re ect some degree of possibility ofbond formation, it is stored in our library of ligand binding sites with additional bond information
extracted from description in PDB. The information of bond formation ability could be used todiscover novel ligands and ligand-host interactions. The LIGAND database contains information ofenzymatic reactions, metabolic ligands and chemical reactions that appear in the KEGG PATHWAY
database [1]. The constructed library for ligand binding sites contains more information concernedwith atomic pairs and circumstances of the binding pockets. Thus the information may be regarded
as supplementary information of LIGAND. Currently, the library is a at text-based le providing
matrices, which store Pscore in their elements. The matrix based representation of ligand binding
information would be e ective for various applications, such as de novo ligand design, since it is easy
to calculate for various purposes. On the other hand, we also devised an approach to visualize it forecient and intuitive understanding of ligand-protein interactions.

Acknowledgments
We especially acknowledge Dr. Hiroyuki Ogata for precious advice. This work was supported in partby the Grant-in-Aid for Scienti c Research on the Priority Area `Genome Science' from the Ministryof Education, Science, Sports and Culture in Japan. The computation time was provided by theSupercomputer Laboratory, Institute for Chemical Research, Kyoto University.

References[1] Goto, S., Nishioka, T., and Kanehisa, M., LIGAND: Chemical Database for Enzyme Reactions,Bioinformatics, 14(7):591{599, 1998.
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