ailab-bio/TACK huggingface dataset:
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc(NC9CCC(=O)NC9=O)cc8)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax: < 10 %
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)C(=O)N(C8CCC(=O)N(C)C8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: > 1000 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)C(=O)N(C8CCC(=O)N(C)C8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax:  30 %
Reported range: 10 to 50
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)C(=O)N(C8CCC(=O)NC8=O)C9)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: < 100 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)C(=O)N(C8CCC(=O)NC8=O)C9)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax: > 50 %
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)C(=O)N(C8CCC(=O)NC8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: < 100 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)C(=O)N(C8CCC(=O)NC8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax: > 50 %
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: > 1000 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax:  30 %
Reported range: 10 to 50
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C8CCC(=O)N(C)C8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: > 1000 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C8CCC(=O)N(C)C8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax:  30 %
Reported range: 10 to 50
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C8CCC(=O)NC8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: < 100 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C8CCC(=O)NC8=O)C9=O)CC7)CC6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax: > 50 %
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C8CCC(=O)NC8=O)C9=O)CC7)[C@@H](C7CC7)C6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
DC50: > 1000 nM
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb
Compound (SMILES): C#Cc1cccc2cc(O)cc(-c3ncc4c(N5CC6CCC(C5)N6)nc(OCC5(CN6CCN(CC7CCN(c8ccc9c(c8)CN(C8CCC(=O)NC8=O)C9=O)CC7)[C@@H](C7CC7)C6)CC5)nc4c3F)c12
Modality: PROteolysis-TArgeting Chimera (PROTAC)
Target protein (POI): KRAS (UniProt P01116)
POI sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM
E3 ligase: CRBN (UniProt Q96SW2)
Ligase sequence: MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Cell line: SW1990 (Homo sapiens)
Cell line description: African=0.49%; Native American=0.78%; East Asian, North=2.9%; East Asian, South=0%; South Asian=0%; European, North=60.78%; European, South=35.04%.
Mutation; HGNC; HGNC Mutation; HGNC; HGNC Mutation; HGNC; HGNC
A*26
Stable (MSS) (Sanger).
Metastatic; Spleen; 
Caucasian.
Epithelial cell of pancreas; CL=CL_0000083.
Cancer cell line
Assay: Western Blot
Dmax:  30 %
Reported range: 10 to 50
Assay description: KRAS(G 12D/C/V) Western blot protein degradation assay
Cell lines SW1990 and GP2D that express KRAS(G12D), LU65A that expresses KRAS(G12C), and NCIH727 that expresses KRAS(G12V) were seeded in 6- or 12-well tissue culture plates, and after 1 hr, test compounds were added at various concentrations and incubated at 37°C/5% CO2 for 24 hr. Cells were then washed with cold PBS, aspirated and cold RIPA buffer containing a protease/phosphatase inhibitor cocktail was added to lyse cells. After centrifugation, the total protein concentrations of cell lysates were determined using the BCA protein assay. Samples were normalized for equivalent protein concentrations, 5X SDS-PAGE loading buffer added and denatured at 100°C for 10 min. 20 pl of each sample/well was loaded on a SDS-PAGE gel and electrophoresed for 20 min at 80 V, then 120 V for 1.5 hr. Gels were then electroblotted to nitrocellulose membranes using a wet-transfer method at 250 mA for 2.5 hr. Membranes were incubated with blocking buffer for 1 hr and washed 3 times with TBST for 5 min. Membranes were then incubated with anti-KRAS and anti-P-Actin monoclonal antibodies diluted in blocking buffer at 4°C overnight per the manufacturer's recommendations. After washing 3 times, blots were incubated with appropriately labeled secondary antibodies for 1 hr at room temperature and washed again. Fluorescence imaging and quantitation was performed using a LI-COR Odyssey. Results was analyzed using GraphPad Prism 7 software. Compound concentrations that induced KRAS degradation (DC50 and Dmax) were calculated using GraphPad Prism 7 software.
Reference: METHODS AND COMPOSITIONS FOR TARGETED PROTEIN DEGRADATION (patent)
Source database: TPDdb