In vivo screen using chemical inducers of dimerization
First Claim
1. A compound having the formula:
- H1-X-B-Y-H2 wherein each of H1 and H2 may be the same or different and capable of binding to a receptor which is the same or different;
wherein each of X and Y may be present or absent and, if present, each may be the same or different spacer moiety;
wherein B is an enzyme-cleavable moiety.
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Accused Products
Abstract
The subject invention provides a compound having the formula:
H1-X-B-Y-H2
wherein each of H1 and H2 may be the same or different and capable of binding to a receptor which is the same or different;
wherein each of X and Y may be present or absent and if present, each may be the same or different spacer moiety; and wherein B is an enzyme cleavable moiety. This invention also provides a method of screening proteins for the ability to catalyze bond cleavage, comprising the steps of:
a) providing a cell that expresses a pair of fusion proteins which upon dimerization change a cellular readout;
b) providing the compound of the invention which dimerizes the pair of fusion proteins, said compound comprising two portions coupled by a bond that is cleavable by the protein to be screened; and
c) screening for the cellular readout, wherein a change the cellular readout indicates catalysis of bond cleavage by the protein to be screened. Finally, the invention also provides a method of screening proteins for the ability to catalyze bond formation, comprising the steps of:
a) providing a cell that expresses a pair of fusion proteins which upon dimerization activate a cellular readout:
b) providing a first compound and a second compound, each being capable of binding to one of the pair of fusion proteins, said first and second compound comprising a portion through which the first and second compounds are coupled to form the inventive compound by the action of the bond forming protein to be screened; and
c) screening for the cellular readout, wherein a change in the cellular readout indicates catalysis of bond formation by the protein to be screened.
14 Citations
157 Claims
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1. A compound having the formula:
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H1-X-B-Y-H2 wherein each of H1 and H2 may be the same or different and capable of binding to a receptor which is the same or different;
wherein each of X and Y may be present or absent and, if present, each may be the same or different spacer moiety;
wherein B is an enzyme-cleavable moiety. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50, 58, 59, 60, 67, 73)
H1-X-B′ with a second compound having the formula;
H2-Y-B′ wherein B′ and
B″
are moieties that react to form B in the presence of an enzyme.
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28. The compound of claim 27, wherein the enzyme is selected from the group of enzymes consisting of transferases, lyases, isomerases, and ligases.
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29. The compound of claim 28, wherein the transferase is selected from the group consisting of, a carbon transferase, an aldehyde or ketone transferase, an acyl transferase, a glycosyl transferase, an alkyl or aryl trasferase, a N-containing group transferase, a P-containing group transferase, an S-containing group transferase, an O-containing group transferase, and a Se-containing group transferase.
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30. The compound of claim 28, wherein the lyase is selected from the group consisting of a C—
- C lyase, a C—
O lyase, a C—
N lyase, a C—
S lyase, and a P—
O lyase.
- C lyase, a C—
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31. The compound of claim 28, wherein the isomerase is selected from the group consisting of racemases, epimerases, cis-trans isomerases, intra-oxidoreductases, intra-transferases (mutases), and intramolecular lyases.
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32. The compound of claim 28, wherein the ligase is selected from the group consisting of a C—
- O ligase, a C—
S ligase, a C—
N ligase, a C—
C ligase, and a P—
O ligase.
- O ligase, a C—
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44. A complex comprising the compound of claim 1 complexed to an enzyme.
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45. The complex of claim 44, wherein the compound is capable of binding to the enzyme with an IC50 of less than 100 mM.
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46. The complex of claim 44, wherein the compound is capable of binding to the enzyme with an IC50 of less than 10 mM.
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47. The complex of claim 44, wherein the compound is capable of binding to the enzyme with an IC50 of less than 1 mM.
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48. The complex of claim 44, wherein the compound is capable of binding to the enzyme with an IC50 of less than 100 mM.
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49. The complex of claim 44, wherein the compound is capable of binding to the enzyme with an IC50 of less than 10 mM.
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50. The complex of claim 44, wherein the compound is capable of binding to the enzyme with an IC50 of less than 1 mM.
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58. A composition comprising the compound of claim 1, and the compound of claim 33.
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59. The composition of claim 58, further comprising an enzyme.
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60. A composition comprising the complex of claim 44.
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67. The method of claim 62, wherein the compound which dimerizes the pair of fusion proteins is the compound of claim 1.
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73. The method of claim 69, wherein either the first or the second compound is the compound of claim 23.
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33. A compound having the formula:
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H1-X-B′ wherein H1 is capable of binding to a receptor;
wherein X is a spacer moiety which may be present or absent; and
wherein B′
is a moiety capable of binding to an enzyme.- View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 51, 52, 53, 54, 55, 56, 57, 61, 68)
H2-Y-B″ wherein H2 is capable of binding to a receptor;
wherein Y is a spacer moiety which may be present or absent; and
wherein B″
is a moiety that reacts with B′
in the presence of the enzyme.
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51. A complex comprising the compound of claim 33 complexed to an enzyme.
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52. The complex of claim 51, wherein the compound is capable of binding to the enzyme with an IC50 of less than 100 mM.
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53. The complex of claim 51, wherein the compound is capable of binding to the enzyme with an IC50 of less than 10 mM.
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54. The complex of claim 51, wherein the compound is capable of binding to the enzyme with an IC50 of less than 1 mM.
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55. The complex of claim 51, wherein the compound is capable of binding to the enzyme with an IC50 of less than 100 mM.
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56. The complex of claim 51, wherein the compound is capable of binding to the enzyme with an IC50 of less than 10 mM.
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57. The complex of claim 51, wherein the compound is capable of binding to the enzyme with an IC50 of less than 1 mM.
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61. A composition comprising the complex of claim 51.
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68. The method of claim 62, wherein the compound which dimerizes the pair of fusion proteins is the compound of claim 43.
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62. A method of screening proteins for the ability to catalyze bond cleavage, comprising the steps of:
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a) providing a cell that expresses a pair of fusion proteins which upon dimerization change a cellular readout;
b) providing a compound which dimerizes the pair of fusion proteins, said compound comprising two portions coupled by a bond that is cleavable by the protein to be screened; and
c) screening for the cellular readout, wherein a change in the cellular readout indicates catalysis of bond cleavage by the protein to be screened. - View Dependent Claims (63, 64, 65, 66, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90)
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69. A method of screening proteins for the ability to catalyze bond formation, comprising the steps of:
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a) providing a cell that expresses a pair of fusion proteins which upon dimerization activate a cellular readout;
b) providing a first compound and a second compound, each being capable of binding to one of the pair of fusion proteins, said first and second compound comprising a portion through which the first and second compounds are coupled by the action of the bond forming protein to be screened; and
c) screening for the cellular readout, wherein a change in the cellular readout indicates catalysis of bond formation by the protein to be screened. - View Dependent Claims (70, 71, 72)
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91. A compound having the formula:
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H1-Y-H2 wherein H1 is methorexate or an analog thereof;
wherein H2 is capable of binding to a receptor, and wherein Y is a moiety providing a covalent linkage between H1 and H2, which may be present or absent, and when absent, H1 is covalently linked to H2. - View Dependent Claims (92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132)
Mtx-Y-H2.
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95. The compound of claim 91, having the formula:
Dex-Y-Mtx.
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96. The compound of claim 95, having the formula:
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97. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 100 mM.
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98. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 10 mM.
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99. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 1 mM.
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100. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 100 μ
- M.
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101. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 10 μ
- M.
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102. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 1 μ
- M.
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103. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 100 nM.
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104. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 10 nM.
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105. The compound of claim 91, wherein H2 is capable of binding to a receptor with a IC50 of less than 1 nM.
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106. The compound of claim 95 having the formula:
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107. The compound of claim 95 having the formula:
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108. The compound of claim 95 having the formula:
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109. The compound of claim 95 having the formula:
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110. The compound of claim 95, having the formula:
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111. A complex between the compound of claim 91 and a fusion protein which comprises a binding domain capable of binding to methotrexate, wherein H1 of the compound binds to the binding domain of the fusion protein.
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112. The complex of claim 111, wherein the binding domain is that of the dihydrofolate reductase (DHFR).
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113. The complex of claim 111, wherein H1 is capable of binding to the binding domain of the fusion protein with an IC50 of less than 100 nM.
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114. The complex of claim 111, wherein H1 is capable of binding to the binding domain of the fusion protein with an IC50 of less than 10 nM.
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115. The complex of claim 111, wherein H1 is capable of binding to the binding domain of the fusion protein with an IC50 of less than 1 nM.
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116. The complex of claim 111, wherein H1 is capable of binding to the binding domain of the fusion protein with an IC50 of less than 100 pM.
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117. The complex of claim 111, wherein H1 is capable of binding to the binding domain of the fusion protein with an IC50 of less than 10 pM.
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118. The complex of claim 111, wherein H1 is capable of binding to the binding domain of the fusion protein with an IC50 of less than 1 pM.
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119. The complex of claim 111, wherein the fusion protein is DHFR-(DNA-binding domain).
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120. The complex of claim 111, wherein the fusion protein is DHFR-LexA.
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121. The complex of claim 111, wherein the fusion protein is DHFR-(transcription activation domain).
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122. The complex of claim 111, wherein the fusion protein is DHFR-B42.
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123. A complex between the compound of any one of claims of claims 106-110, and the fusion protein DHFR-LexA.
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124. The complex between the compound of any one of claims of claims 106-110, and the fusion protein DHFR-B42.
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125. A cell comprising the complex of claim 111.
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126. The cell of claim 125, where the cell is selected from the group consisting of yeast, bacteria or mammalian.
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127. The cell of claim 125, where the cell is selected from the group consisting of S. cerevisiae, and E. coli.
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128. A method of dimerizing two fusion proteins inside a cell using the compound of claim 91, comprising the steps of
a) providing a cell that expresses a first fusion protein which comprises a binding domain that binds to H1 and second fusion protein which comprises a binding domain that binds to H2, and b) contacting the compound of claim 91 with the cell so as to dimerize the two fusion proteins. -
129. The method of claim 128, wherein the first fusion protein or the second fusion protein is DHFR-(DNA-binding domain).
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130. The method of claim 128, wherein the first fusion protein or the second fusion protein is DHFR-LexA.
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131. The method of claim 128, wherein the first fusion protein or the second fusion protein is DHFR-(transcription activation domain).
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132. The method of claim 128, wherein the first fusion protein or the second fusion protein is DHFR-B42.
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133. A method for identifying a molecule that binds a known target in a cell from a pool of candidate molecules, comprising:
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(a) covalently bonding each molecule in the pool of candidate molecules to a methotrexate moiety or an analog of methotrexate to form a screening molecule;
(b) introducing the screening molecule into a cell which expresses a first fusion protein comprising a binding domain capable of binding methotrexate, a second fusion protein comprising the known target, and a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the screening molecule to bind to the first fusion protein and to the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the small molecule that binds the known target. - View Dependent Claims (134, 135, 136, 137, 141, 142, 143, 144, 145, 146)
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138. A method for identifying a protein target to which a molecule is capable of binding, comprising:
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(a) providing a screening molecule comprising a methotrexate moiety or an analog of methotrexate covalently bonded to a ligand which has a specificity for an unknown protein target;
(b) introducing the screening molecule into a cell which expresses a first fusion protein comprising a binding domain capable of binding methotrexate, a second fusion protein comprising the unknown protein target, and a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the screening molecule to bind to the first fusion protein and to the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the unknown protein target. - View Dependent Claims (139, 140)
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147. A method for identifying a molecule that binds a known target in a cell from a pool of candidate molecules, comprising:
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(a) covalently bonding each molecule in the pool of candidate molecules to a methotrexate moiety to form a screening molecule;
(b) introducing the screening molecule into a cell which expresses a first fusion-protein comprising a binding domain capable of binding methotrexate, a second fusion protein comprising the known target, and a reporter gene wherein expression of the reporter gene is conditioned on the proximity of the first fusion protein to the second fusion protein;
(c) permitting the screening molecule to bind to the first fusion protein and to the second fusion protein so as to activate the expression of the reporter gene;
(d) selecting which cell expresses the reporter gene; and
(e) identifying the small molecule that binds the known target. - View Dependent Claims (148, 149, 150, 151, 152, 153, 154, 155, 156, 157)
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Specification