Nuclear receptor ligands and ligand binding domains

Details Nuclear receptor ligands and ligand binding domains Nuclear receptor ligands and ligand binding domains

1997-11-26

2001-07-24

Kemmerer, Elizabeth (Department: 1646)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Chemical analysis

C702S019000, C702S020000, C530S350000

Reexamination Certificate

active

06266622

ABSTRACT:

INTRODUCTION
1. Technical Field
This invention relates to computational methods for designing ligands that bind to nuclear receptors, crystals of nuclear receptors, synthetic ligands of nuclear receptors and methods of using synthetic ligands.
2. Background
Nuclear receptors represent a superfamily of proteins that specifically bind a physiologically relevant small molecule, such as hormone or vitamin. As a result of a molecule binding to a nuclear receptor, the nuclear receptor changes the ability of a cell to transcribe DNA, i.e. nuclear receptors modulate the transcription of DNA, although they may have transcription independent actions. Unlike integral membrane receptors and membrane associated receptors, the nuclear receptors reside in either the cytoplasm or nucleus of eukaryotic cells. Thus, nuclear receptors comprise a class of intracellular, soluble ligand-regulated transcription factors.
Nuclear receptors include receptors for glucocorticoids (GRs), androgens (ARs), mineralocorticoids (MRs), progestins (PRs), estrogens (ERs), thyroid hormones (TRs), vitamin D (VDRs), retinoids (RARs and RXRs), peroxisomes (XPARs and PPARs) and icosanoids (IRs). The so called “orphan receptors” are also part of the nuclear receptor superfamily, as they are structurally homologous to the classic nuclear receptors, such as steroid and thyroid receptors. To date, ligands have not been identified with orphan receptors but it is likely that small molecule ligands will be discovered in the near future for this class of transcription factors. Generally, nuclear receptors specifically bind physiologically relevant small molecules with high affinity and apparent Kd's are commonly in the 0.01-20 nM range, depending on the nuclear receptor/ligand pair.
Development of synthetic ligands that specifically bind to nuclear receptors has been largely guided by the trial and error method of drug design despite the importance of nuclear receptors in a myriad of physiological processes and medical conditions such as hypertension, inflammation, hormone dependent cancers (e.g. breast and prostate cancer), modulation of reproductive organ function, hyperthyroidism, hypercholesterolemia and obesity. Previously, new ligands specific for nuclear receptors were discovered in the absence of information on the three dimensional structure of a nuclear receptor with a bound ligand. Before the present invention, researchers were essentially discovering nuclear receptor ligands by probing in the dark and without the ability to visualize how the amino acids of a nuclear receptor held a ligand in its grasp.
Consequently, it would be advantageous to devise methods and compositions for reducing the time required to discover ligands to nuclear receptors, synthesize such compounds and administer such compounds to organisms to modulate physiological processes regulated by nuclear receptors.
SUMMARY OF THE INVENTION
The present invention provides for crystals of nuclear receptor ligand binding domains with a ligand bound to the ligand binding domain (LBD). The crystals of the present invention provide excellent atomic resolution of the amino acids that interact with nuclear receptor ligand, especially thyroid receptor ligands. The three dimensional model of a nuclear receptor LBD with a ligand bound reveals a previously unknown structure for nuclear receptors and shows that the ligand is bound in a water inaccessible binding cavity of the ligand binding domain of the nuclear receptor.
The present invention also provides for computational methods using three dimensional models of nuclear receptors that are based on crystals of nuclear receptor LBDs. Generally, the computational method of designing a nuclear receptor ligand determines which amino acid or amino acids of a nuclear receptor LBD interact with a chemical moiety (at least one) of the ligand using a three dimensional model of a crystallized protein comprising a nuclear receptor LBD with a bound ligand, and selecting a chemical modification (at least one) of the chemical moiety to produce a second chemical moiety with a structure that either decreases or increases an interaction between the interacting amino acid and the second chemical moiety compared to the interaction between the interacting amino acid and the corresponding chemical moiety on the natural hormone.
Also provided is a method of modulating the activity of a nuclear receptor. The method can be in vitro or in vivo. The method comprises administering in vitro or in vivo a sufficient amount of a compound of the following formula:
where the compound fits specially and preferentially into a nuclear hormone receptor LBD of interest. The method is exemplified by modulating the activity of a thyroid receptor (TR). For modulating TR activity, a compound of Formula I is employed that fits spacially and preferentially into a TR ligand binding domain (TR LBD), including compounds specific for a TR LBD isoform of interest. Of particular interest are the TR LBD isoforms &agr; (TR-&agr;) and &bgr; (TR-&bgr;). Additional compounds of interest include derivatives of Formula I, such as those compounds having the biphenyl (&phgr;-X-&phgr;) or single phenyl (&phgr;-X or X-&phgr;) nucleus of Formula I and its corresponding substituent groups described herein. Compounds that are interactively designed using structural information gleaned from these compounds and which modulate nuclear hormone receptor activity also are of interest.
The present invention also includes a method for identifying a compound capable of selectively modulating the activity of a nuclear receptor. This aspect of the invention is exemplified by a method for identifying a compound capable of selectively modulating the activity of a TR isoform. The method comprises modeling test compounds that fit spacially and preferentially into a TR LBD isoform of interest using an atomic structural model of a TR LBD isoform bound to a test compound, screening the test compounds in a biological assay for TR isoform activity characterized by binding of a test compound to a TR LBD isoform, and identifying a test compound that selectively modulates the activity of a TR isoform. The compounds may be those of Formula I or derivatives thereof, including compounds having a biphenyl or single phenyl nucleus of Formula I.
Further included is a method for identifying agonist or antagonist ligands of a nuclear receptor using the atomic coordinates of a LBD in conjunction with a computerized modeling system. This aspect of the invention is exemplified by identifying a TR agonist or antagonist ligand by providing the atomic coordinates of a TR LBD to a computerized modeling system, modeling ligands which fit spacially into the TR LBD, and identifying in a biological assay for TR activity a ligand which increases or decreases TR activity. The compounds can be those of Formula I or derivatives thereof, including compounds having a biphenyl or single phenyl nucleus of Formula I.
Also provided is a method of identifying a compound that selectively modulates the activity of one type of nuclear receptor compared to other nuclear hormone receptors. The method is exemplified by modeling test compounds which fit spacially into a TR LBD using an atomic structural model of a TR LBD, selecting a compound comprising conformationally constrained structural features that interact with conformationally constrained residues of a TR LBD, and identifying in a biological assay for TR activity a compound that selectively binds to a TR LBD compared to other nuclear receptors. The conformationally constrained features involved in receptor-selective ligand binding can be identified by comparing atomic models of receptor isoforms bound to the same and/or different ligands. The methods facilitate design and selection of compounds that have increased selectivity for a particular nuclear receptor. The compounds may be those of Formula I or derivatives thereof, including compounds having the biphenyl or single phenyl nucleus of Formula I.
Another aspect of the invention is a method for increasing the r

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