Kotoko Nakata

Ab initio quantum mechanical study of the binding energies of human estrogen receptor α with its ligands: An application of fragment molecular orbital method

We have theoretically examined the relative binding affinities (RBA) of typical ligands, 17β‐estradiol (EST), 17α‐estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4‐hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4‐hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the α‐subtype of the human estrogen receptor ligand‐binding domain (hERα LBD), by calculating their binding energies. The ab initio fragment molecular orbital (FMO) method, which we have recently proposed for the calculations of macromolecules such as proteins, was applied at the HF/STO‐3G level. The receptor protein was primarily modeled by 50 amino acid residues surrounding the ligand. The number of atoms in these model complexes is about 850, including hydrogen atoms. For the complexes with EST, RAL, OHT, and DES, the binding energies were calculated again with the entire ERαLBD consisting of 241 residues or about 4000 atoms. No significant difference was found in the calculated binding energies between the model and the real protein complexes. This indicates that the binding between the protein and its ligands is well characterized by the model protein with the 50 residues. The calculated binding energies relative to EST were very well correlated with the experimental RBA (the correlation coefficient r = 0.837) for the ligands studied in this work. We also found that the charge transfer between ER and ligands is significant on ER–ligand binding. To our knowledge, this is the first achievement of ab initio quantum mechanical calculations of large molecules such as the entire ERαLBD protein.

VISCANA : Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening

We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.

Development of the receptor database (RDB): application to the endocrine disruptor problem.

MOTIVATION To represent various aspects of receptors effectively, we developed the receptor database (RDB), using an object-oriented database management system ACEDB and the Internet/WWW technology. RESULTS RDB was constructed so that the system collects data items such as attributes of proteins from distributed data sources of the Internet, and so that it provides various viewing tools effectively, depending on different types of receptor data. Such sources include standard international biological databases such as the up-to-date database of PIR, Swiss Prot, PDB, GenBank and GDB. Application to the endocrine disruptor problem is presented. AVAILABILITY RDB is available through the Internet at http://impact.nihs.go.jp/RDB.html.

Modeling of signaling pathways for endocrine disruptors

The so called endocrine disruptors have become an important working hypothesis for a wide range of toxicology researchers. This hypothesis has also attracted those who have worked on designer estrogens or selective estrogen receptor modulators. Already numbers of substances have been identified as such chemicals, but there remain a large number of chemicals waiting to be tested for their endocrine modulating capabilities. Because of the time and costs required for wet lab tests, it is unrealistic to apply these kinds of tests to all such suspicious or probable chemicals. Thus some theoretical methods must be developed for this purpose. However the conventional QSAR (quantitative structure activity relationships) approach is of limited relevance to this problem, because these methods do not take detailed mechanisms of molecular interactions in biological systems into account. Thus we have developed a database complex system that enables one to trace molecular interactions triggered by interaction of receptors with xenobiotic chemicals. The main components of this database complex are a potential endocrine disruptor database, a receptor database, a cell signaling networks database, a transcription factor database, and an affinity binding database based on modes of actions.

AN INTEGRATED RECEPTOR DATABASE (IRDB)

Various receptor data were collected, edited and integrated into an Integrated Receptor Database (IRDB). The data stored includes structural data (amino acid sequences, their secondary-structure and three-dimensional structure), functional data, binding affinity, cell signaling data etc. The purpose of this database is to allow structural biologists, drug designers and toxicologists to analyse and elucidate receptor-ligand dockings and the resultant post-binding signal transduction pathways. IRDB is available on line (http://impact.nihs.go.jp/RDB.html)

Global information network on chemicals (GINC) and its Asian component

The Global Information Network on Chemicals (GINC) is an effort to build a global information network that links international, national, and other organizations working for the safe management of chemicals in order to exchange information and improve communications. The project was originally proposed in 1993 by one of the authors then at the National Institute of Health Sciences (NIHS) of Japan to the International Program on Chemical Safety (IPCS), which is a joint project of World Health Organization (WHO), International Labor Organization (ILO), and United Nations Environment Program (UNEP). The base support system was first implemented at NIHS using the Internet/World Wide Web (WWW) technology in 1995. The project was then endorsed by the Intergovernmental Forum on Chemical Safety (IFCS) and was adopted by the Inter-Organization Program for the Sound Management of Chemicals (IOMC). However, the base system (http://www.nihs.go.jp/GINC/index.html) has been developed and maintained solely by the NIHS group under the support of the Ministry of Health and Welfare (MHW), Japan. Asia, particularly East Asia and the Pacific region, was chosen as the feasibility study region for this project. During the period from December 1994 to July 2002, NIHS hosted eight meetings on this project held in Tokyo.

Integrated Receptor Database

A database for receptors on cell membrane has been developed. The system can collect data items such as attributes of proteins from distributed data sources on the Internet. Such sources include internationally standard biological databases such as the updated genetic database of PIR, Swiss Prot, PDB, GenBank, EMBL and GDB. The system provides various viewing tools that e ectively displays di erent types of receptor data; DNA sequences, amino acids sequences, DNA binding sites, ligand binding sites, gene and disease information, and the protein structural information. It can also display three dimensional images using a freeware program RASMOL. DNA binding sites, ligand binding sites and active sites are classi ed by coloring the sequences. PDB matching sites are classi ed by italicization. CSNDB (Cell Signaling Networks Database), which is a database for cellular signal transduction of human is also linked in the system. The database may be useful for quick reference for ligand membrane receptors and signal transduction in the drug design.

Building A Receptor Database

We have developed a database of receptors, which gather data from information sources on the Internet. The source of this database is a variety of genomic and biological information on the internet; PIR, Swiss Prot, PDB, GenBank, EMBL, GDB, etc... The system provides the detail structure and functional information on receptors, such as ligand binding site and DNA binding site, which were picked up from the references, and the three dimensional structures. The system was implemented on the unix workstation (IRIS, INDIGO 2), using an object oriented database management system ACEDB (A Caenorhabditis elegans Data Base). ACEDB is an object oriented database management system, which has been developed as part of the Caenorhabditis elegans genome research. This database is a generalized genome database, and can be used to create new database without the need for any reprogramming or in fact any sophisticated computer skills. The system provides various viewing tools that e ectively display di erent types of receptor data; DNA sequences, amino acids sequences, DNA binding sites, ligand binding sites, gene and disease information, and the protein structural information. It can also display three dimensional structure of molecules using a freeware molecular graphics RASMOL. The detail information for ligand and signal transduction, which are picked up from references, are also included. The system has also a browser interface so that database can be accessed via World Wide Web. The information regarding the sites of action on the receptor are highly interesting in biologically, medically and pharmacologically. The database may be useful for quick reference for ligand-membrane receptors and signal transduction in the drug design. We may use the database for the functional and structural analyses of receptors.