Process for the identification of a compound which inhibits the binding of the second bromodomain of each of human BRD-2, BRD-3, and BRD-4

摘要

A process for the identification of compounds with a molecular weight in the range 100 to 750 which inhibit the binding of the first and/or second bromodomains of human BRD-2 to 4 to acetylated lysine residues of their physiological partner proteins which comprises selecting those compounds which are able to:
a) form a hydrogen bonding interaction in which the compound accepts a hydrogen bond from the sidechain NH2 group of the asparagine residue found at:;BRD-2BRD-2BRD-3BRD-4BRD-4BD1BD2BD1BRD-3 BD2BD1BD2ASN156ASN429ASN116ASN391ASN140ASN433
or
b) accept a water-mediated hydrogen bond in which the compound accepts a hydrogen bond from a water that is itself hydrogen-bonded to the sidechain hydroxyl of the tyrosine residue found at;BRD-2BRD-3BRD-4BD1BRD-2 BD2BD1BRD-3 BD2BD1BRD-4 BD2TYR113TYR386TYR73TYR348TYR97TYR390
and
c) which are also able to form a Van der Waals interaction with a lipophilic binding region of a binding pocket such that one or more heavy atoms of the said compounds lie within a 5 Å range of any of the heavy atoms of the following bromodomain residues which define the binding pocket:;BRD-2BRD-2BRD-3BRD-4BRD-4BD1BD2BD1BRD-3 BD2BD1BD2TRP97TRP370TRP57TRP332TRP81TRP374PRO98PRO371PRO58PRO333PRO82PRO375ASP161ASP434ASP121GLU396ASP145GLU438ILE162VAL435ILE122VAL397ILE146VAL439MET165MET438MET125MET400MET149MET442
pharmaceutical compositions containing such compounds, and their use in therapy.

主权项

1. A process for the identification of a compound which inhibits the binding of the second bromodomain of each of human BRD-2, BRD-3, and BRD-4 to acetylated lysine residues of their physiological partner proteins which process comprises the steps of:
1) selecting compounds with a molecular weight in the range 100 to 750 Da; and 2) determining which of those selected compounds is an interacting compound, wherein an interacting compound will:
a) form a hydrogen bonding interaction in which the compound accepts a hydrogen bond from the sidechain NH2 group of the asparagine residue found at: ASN429 of BRD-2 BD2, or ASN391 of BRD-3 BD2, or ASN433 of BRD-4 BD2 and
b) form a Van der Waals interaction with a lipophilic binding region of a binding pocket such that one or more heavy atoms of the said compounds lie within a 7.5 Å range of at least one heavy atom of each of the 3 residues of the second bromodomain wherein said bromodomain residues are selected from the group consisting of:PRO371, ASP434, and VAL435 of BRD-2 BD2;PRO333, GLU396, and VAL397 of BRD-3 BD2; andPRO375, GLU438, and VAL439 of BRD-4 BD2and 3) testing the ability of the interacting compound to inhibit the binding of the second bromodomain to a fluorescent ligand in a fluorescent anisotropy binding assay; wherein the fluorescent ligand is a compound having the structure  conjugated with a fluorescent label at the terminal amino group (—NH2) of the compound; and wherein the interacting compound which is able to inhibit the binding of the second bromodomain to the fluorescent ligand in the fluorescent anisotropy binding assay is identified as the compound which inhibits the binding of the second bromodomain of each of human BRD-2, BRD-3 and BRD-4 to the acetylated lysine residues of their physiological partner proteins.