Compounds and methods for treatment of thrombosis

A compound of formula II:

• or a pharmaceutically acceptable salt or prodrug thereof, wherein
• R19 is H, C1-6 alkyl, or when taken together with R20 forms a fused 5- or 6-membered ring;
• R20 is H, OH, SH, NH2, NO2, optionally substituted C1-6 alkyl, halogen, C1-3 perfluoroalkyl, or when together with Z′ forms a fused 5- or 6-membered ring;
• e is N, NO, or CR21a, wherein R21a is H, halogen, or C1-3 perfluoroalkyl;
• g is N, NO, or CR21b wherein R21b is H, halogen, C1-6 alkyl, C1-3 perfluoroalkyl, C1-3 alkenyl, C7-16 aralkyl, C2-15 heteroaralkyl, C1-6 alkoxy, C7-16 aralkoxy, C2-15 heteroaralkoxy, C2-7 alkoxycarbonyl, C8-17 aralkoxycarbonyl, C3-16 heteroaralkoxycarbonyl, C2-7 alkylaminocarbonyl, C8-17 aralkylaminocarbonyl, C3-16 heteroaralkylaminocarbonyl, C1-6 alkylthio, C7-16 aralkylthio, C2-15 heteroaralkylthio, C2-7 alkylthiocarbonyl, C8-17 aralkylthiocarbonyl, C3-16 heteroaralkylthiocarbonyl;
• Z′ is NR22, (H, H), wherein R22 is H, C1-6 alkyl, OH, NH2, NO2, CO2R22a, wherein R22a is C1-6 alkyl;
• T is a bond, O, S, or NR23, where R23 is H, OH, or optionally substituted C1-6alkyl, C1-6 alkenyl, C7-11 aralkyl, C8-16 aralkenyl, C2-15 heteroaralkyl, or C3-15 heteroaralkenyl, wherein
• when T is O, S, or NR23, B is a natural or unnatural alpha-amino acid residue of D- or L-configuration, or an optionally substituted C1-6 alkyl, C3-8 cycloalkyl, C1-6 alkenyl, C7-16 aralkyl, C8-17 aralkylcarbonyl, C8-16 aralkenyl, C6 or C10 aryl, C2-15 heteroaralkyl, C3-16 heteroaralkylcarbonyl, C3-15 heteroaralkenyl, C2-7 acyl, C4-9 cycloalkylcarbonyl, C7-11 aroyl, C2-10 heterocyclyloyl, C4-9 cycloalkoxycarbonyl, C7 or C11 aryloxycarbonyl, C3-10 heterocyclyloxycarbonyl, C3-16 heteroaralkyloxycarbonyl, aminocarbonyl, C2-7 alkylaminocarbonyl, C3-13 dialkylaminocarbonyl, C4-9 cycloalkylaminocarbonyl, C8-17 aralkylaminocarbonyl, C7 or C11 arylaminocarbonyl, C3-10 heterocyclylaminocarbonyl, C3-16 heteroaralkylaminocarbonyl, C2-7 alkylthiocarbonyl, C4-9 cycloalkylthiocarbonyl, C7-11 arylthiocarbonyl, C8-17 aralkylthiocarbonyl, C2-10 heterocyclylthiocarbonyl, C3-16 heteroaralkylthiocarbonyl, aminothiocarbonyl, C2-7 alkylaminothiocarbonyl, C3-13 dialkylaminothiocarbonyl, C4-9 cycloalkylaminothiocarbonyl, C8-17 aralkylaminothiocarbonyl, C7 or C11 arylaminothiocarbonyl, C3-10 heterocyclylaminothiocarbonyl, C3-16 heteroaralkylaminothiocarbonyl, C1-6 alkylsulfonyl, C3-8 cycloalkylsulfonyl, C7-16 aralkylsulfonyl, C6 or C10 arylsulfonyl, C2-9 heterocyclylsulfonyl, or C2-15 heteroaralkylsulfonyl,
• or when T is a bond, B is OH, SH, NH2, NO2, SO3H, CO2H or an optionally substituted C1-6 alkyl, C1-16 alkenyl, C7-16 aralkyl, C8-16 aralkenyl, C2-15 heteroaralkyl, C3-15 heteroaralkenyl, C2-7 acyl, C7-11 aroyl, C3-10 heteroaroyl, C2-7 alkoxycarbonyl, C4-9-cycloalkoxycarbonyl, C8-7 aralkoxycarbonyl, C7 or C11 aryloxycarbonyl, C3-16 heteroaralkyloxycarbonyl, C2-10 heterocyclyloxycarbonyl, aminocarbonyl, C2-7 alkylaminocarbonyl, C3-13 dialkylaminocarbonyl, C4-9 cycloalkylaminocarbonyl, C8-17 aralkylaminocarbonyl, C7 or C11 arylaminocarbonyl, C3-10 heterocyclylaminocarbonyl, C3-16 heteroaralkylaminocarbonyl, C2-7 alkylthiocarbonyl, C4-9 cycloalkylthiocarbonyl, C7-11 arylthiocarbonyl, C8-17 aralkylthiocarbonyl, C2-10 heterocyclylthiocarbonyl, C3-16 heteroaralkylthiocarbonyl, C1-6 alkylsulfonyl, C3-8 cycloalkylsulfonyl, C7-16 aralkylsulfonyl, C6 or C10 arylsulfonyl, C2-9 heterocyclylsulfonyl, or C2-15 heteroaralkylsulfonyl;
• f is a bond, O, S, or NR24, wherein R24 is H, OH, or C1-6 alkyl, wherein
• when f is O, S, or NR24, V is H or an optionally substituted C1-6 alkyl, C7-16 aralkyl, C2-15 heteroaralkyl, C2-7 acyl, C7-11 aroyl, C3-10 heteroaroyl, C2-7 alkoxycarbonyl, C4-9 cycloalkoxycarbonyl, C8-17 aralkoxycarbonyl, C7 or C11 aryloxycarbonyl, C3-16 heteroaralkyloxycarbonyl, C2-10 heterocyclyloxycarbonyl, aminocarbonyl, C2-7 alkylaminocarbonyl, C3-13 dialkylaminocarbonyl, C4-9 cycloalkylaminocarbonyl, C8-17 aralkylaminocarbonyl, C7 or C11 arylaminocarbonyl, C3-10 heterocyclylaminocarbonyl, C3-16 heteroaralkylaminocarbonyl, C2-7 alkylthiocarbonyl, C4-9 cycloalkylthiocarbonyl, C7-11 arylthiocarbonyl, C8-17 aralkylthiocarbonyl, C2-10 heterocyclylthiocarbonyl, C3-16 heteroaralkylthiocarbonyl, C1-6 alkylsulfonyl, C3-8 cycloalkylsulfonyl, C7-16 aralkylsulfonyl, C6 or C10 arylsulfonyl, C2-9 heterocyclylsulfonyl, or C2-15 heteroaralkylsulfonyl, or when f is a bond, V is H, OH, SH, NH2, SO3H, CO2H, or an optionally substituted C1-6 alkyl, hydroxy-C1-6 alkyl, C3-8 cycloalkyl, C1-6 alkenyl, C7-16 aralkyl, C8-16 aralkenyl, C2-15 heteroaralkyl, C3-15 heteroaralkyl, C6 or C10 aryl, C1-9 heterocyclyl, C2-7 alkylaminocarbonyl, C3-13 dialkylaminocarbonyl, C4-9 cycloalkylaminocarbonyl, C8-17 aralkylaminocarbonyl, C7 or C11 arylaminocarbonyl, C2-10 heterocyclylaminocarbonyl, C2-7 alkoxycarbonyl, C4-9 cycloalkoxycarbonyl, C8-17 aralkoxycarbonyl, C7 or C11 aryloxycarbonyl, C3-10 heterocyclyloxycarbonyl, C3-16 heteroaralkyloxycarbonyl, C2-7 alkylthiocarbonyl, C4-9 cycloalkylthiocarbonyl, C7-11 arylthiocarbonyl, C8-17 aralkylthiocarbonyl, C2-10 heterocyclylthiocarbonyl, C3-16 heteroaralkylthiocarbonyl, C2-7 acyl, C7-11 aroyl, C3-10 heteroaroyl, C1-6 alkylsulfonyl, C3-8 cycloalkylsulfonyl, C7-16 aralkylsulfonyl, C6 or C10 arylsulfonyl, C2-9 heterocyclylsulfonyl, C2-15 heteroaralkylsulfonyl, C1-6 alkylaminosulfonyl, C3-8 cycloalkylaminosulfonyl, C2-12 dialkylaminosulfonyl, C7-17 aralkylaminosulfonyl, C6 or C10 arylaminosulfonyl, C1-9 heterocyclylaminosulfonyl, C2-15 heteraralkylaminosulfonyl, C1-6 alkylsulfinyl, C3-8 cycloalkylsulfinyl, C7-16 aralkylsulfinyl, C6 or C10 arylsulfinyl, C2-9 heterocyclylsulfinyl, or C2-15 heteroaralkylsulfinyl.

A computer comprising a processor in electrical communication with a memory;

• said memory having stored therein
• (i) atomic coordinates, or surrogates thereof, in one or more of the files listed in FIG. 16 for all of the non-hydrogen atoms of residues serine 195, histidine 57, and aspartic acid 102 of Factor XI catalytic domain or atomic coordinates that have a root mean square deviation from the backbone atoms of said residues of less than 0.4 Å;
• and
• (ii) a program for displaying a three-dimensional model of said Factor XI catalytic domain.

A computer comprising a processor in electrical communication with a memory;

• said memory having stored therein
• (i) x-ray diffraction data for all of the non-hydrogen atoms of residues serine 195, histidine 57, and aspartic acid 102 of Factor XI catalytic domain or x-ray diffraction data for amino acids that have a root mean square deviation from the backbone atoms of said residues of less than 0.4 Å;
• and
• (ii) a program for displaying a three-dimensional model of said Factor XI catalytic domain.

A computer comprising a processor in electrical communication with a memory;

• said memory having stored therein a pharmacophore model of Factor XI ligands and a program for displaying said model, said model comprising at least three of the following:
• (i) an electrophilic carbon atom that binds to the side chain oxygen atom (OG) of Ser195 such that the electrophilic carbon atom is 1.4 to 4.0 Å from said oxygen atom;
• (ii) at least one hydrogen bond donor group to interact with Asp 189 such that the non-hydrogen atoms of the hydrogen bond donor groups are 2.0 to 4.2 Å away from the side chain oxygens of Asp 189;
• (iii) a hydrophobic group that makes one or more van der Waals contacts with residues of the active site and is less than 5.0 Å away from the CB atom of Ala97;
• (iv) a hydrogen bond donor group which makes a hydrogen bond with the main chain carbonyl of Ser214 such that the distance between the hydrogen-bonded atoms is less than 4.0 Å;
• (v) a hydrogen bond donor group that makes a hydrogen bond with the main chain carbonyl of Gly216 such that the distance between the hydrogen-bonded atoms is less than 4.0 Å;
• (vi) a hydrogen bond acceptor group that makes a hydrogen bond with the main chain nitrogen of Gly216 such that the distance between the hydrogen-bonded atoms is less than 4.0 Å;
• (vii) a hydrogen bond acceptor group that makes a hydrogen bond with a side chain nitrogen of His57 such that the distance between the hydrogen-bonded atoms is less than 4.0 Å;
• (viii) a group that makes one or more van der Waals contacts with the side chains of residues of Lys192 and/or Leu146;
• (ix) a group that makes one or more van der Waals contacts with the side chains of residues of Cys191 and/or Cys219;
• and
• (x) a group or groups that make participate in one or more polar interactions with the side chain of residue of His174, Glu98, and/or Glu217.

A method for manufacturing a Factor XIa ligand, said method comprising the steps of:

• (a) obtaining the atomic coordinates of at least a portion of Factor XI catalytic domain with a ligand;
• (b) selecting one or more moieties in said ligand to be modified;
• wherein said modified ligand maintains the ability to bind said Factor XI;
• and
• (c) modifying said ligand based on said determination.

A method of determining the three-dimensional structure of a Factor XI of interest, said method comprising the steps of:

• (a) crystallizing said Factor XI catalytic domain of interest;
• (b) generating an X-ray diffraction pattern from said crystallized Factor XI catalytic domain of interest;
• and
• (c) applying at least a portion of the atomic coordinates in one or more of the files listed in FIG. 16 to said diffraction pattern to generate a three-dimensional electron density map of at least a portion of said Factor XI catalytic domain of interest.

A purified Factor XI protein or fragment thereof comprising a mutation, wherein said mutation is

• (a) a mutation that enhances the ability of Factor XI catalytic domain to crystallize,
• (b) a mutation of a residue that is otherwise post-translationally modified in an organism used for recombinant expression,
• (c) a mutation that alters the charge of Factor XI,
• (d) a mutation that eliminates a free, reactive sulfhydryl group of a cysteine,
• (e) a combination of mutations that together alter the distribution of charge density without altering the overall charge of Factor XI,
• (f) a mutation of the NH2— or COOH-terminal residue of Factor XI, or
• (g) a mutation that alters the folding of Factor XI.