## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Inhibitory Action of PDHK1 Activity In Vitro: In the case of human PDHK1 (hPDHK1, NCBI Reference Database Accession number NM_2610.3), a 1.3 kbp fragment encoding this protein was isolated from human liver cDNA by polymerase chain reaction (PCR). Modified hPDHK1 cDNA wherein FLAG-Tag sequence was added to the N terminus was prepared by PCR and ligated to the NdeI/EcoRI site of pET-17b vector (Merck MGaA, model number 69663-3). The recombinant construct was transformed into Escherichia coli DH5a (TOYOBO, model number DNA-903). The recombinant clones were identified, and plasmid DNA was isolated and subjected to the DNA sequence analysis. One clone which had the expected nucleic acid sequence was selected for expression work.For expression of hPDHK1 activity, Escherichia coli strain BL21(DE3) cells (Merck KGaA, model number 69450-4) were transformed with the pET17b vector containing modified hPDHK1 cDNA. The Escherichia coli were grown to an optical density 0.6 (600 nmol/L) at 30° C. Protein expression was induced by the addition of 500 μmol/L isopropyl-β-thiogalactopyranoside. The Escherichia coli were cultured at 20° C. for 17-18 hr and harvested by centrifugation.The harvested Escherichia coli was resuspended in a suspension buffer (20 mmol/L N-(2-hydroxyethyl)piperazine-N′-2-ethanesulfonic acid-sodium hydroxide (HEPES-NaOH), 500 mmol/L sodium chloride, 1% ethylene glycol, and 0.1% polyoxyethylene-polyoxypropylene block copolymer (Pluronic F-68), complete, EDTA-free (pH 8)) and disrupted by a microfluidizer M-110H (MIZUHO INDUSTRIAL CO., LTD.) or ultrasonication. The precipitate was removed by centrifugation and the supernatant was added to DDDDK-tagged Protein PURIFICATION GEL (MBL, model number 3329). DDDDK-tagged Protein PURIFICATION GEL was washed with a washing buffer (20 mmol/L HEPES-NaOH, 500 mmol/L sodium chloride, 1% ethylene glycol, 0.1% pluronic F-68 (pH 8)) and the bound protein was eluted with elution buffer 1 (20 mmol/L HEPES-NaOH, 100 μg/mL peptide (amino acid sequence DYKDDDDK) (SEQ ID NO: 1), 500 mmol/L sodium chloride, 1% ethylene glycol, 0.1% pluronic F-68 (pH 8)).The eluted fractions containing FLAG-Tagged protein were pooled, concentrated by an ultrafiltration method, added to a gel filtration column (HiLoad 26/60 Superdex 200 (GE Healthcare, model number 17-1070-01)), and eluted with elution buffer 2 (20 mmol/L HEPES-NaOH, 150 mmol/L sodium chloride, 0.5 mmol/L ethylenediaminetetraacetic acid (EDTA), 1% ethylene glycol, 0.1% pluronic F-68 (pH 8)). The eluted fractions were pooled and preserved at −80° C.0.03 U/mL PDH (porcine heart PDH complex, Sigma P7032) and 0.5 μg/mL hPDHK1 were mixed in an assay buffer (50 mmol/L 3-morpholinopropanesulfonic acid (pH 7), 20 mmol/L dipotassium hydrogen phosphate, 60 mmol/L potassium chloride, 2 mmol/L magnesium chloride, 0.4 mmol/L EDTA, 0.2% poloxamer, 2 mmol/L dithiothreitol), and the mixture was incubated at 4° C. overnight to obtain a PDH/hPDHK1 complex solution. In the assay buffer, 0.03 U/mL PDH was mixed and incubated at 4° C. overnight to prepare a PDH solution.The test compounds were diluted with dimethyl sulfoxide (DMSO). To measure an inhibitory action of the test compound on the PDHK activity in the PDH/hPDHK1 complex solution, PDH/hPDHK1 complex solution (20 μL), test compound (1.5 μL) and 0.35 μmol/L ATP (diluted with assay buffer) (8.5 μL) were added to a 384 well microplate (Greiner Bio-One 781801) and PDHK reaction was performed at room temperature for 45 min (test compound well). DMSO (1.5 μL) was added to control wells instead of test compound. In addition, DMSO (1.5 μL) was added to blank wells instead of the test compound, and PDH solution was added instead of the PDH/hPDHK1 complex solution.
- Target name: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: C[C@H]1CN(C(=O)c2ccc(F)c(-c3ccnn3C)c2)Cc2cnc([C@@](C)(O)C(F)(F)F)n21
- Properties:
- ChEMBL ID: CHEMBL6025353
- Molecular weight: 451.42
- Heavy atoms: 32
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 4
- TPSA: 76.18
- LogP: 3.41
- Rotatable bonds: 3
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.38
- QED: 0.62

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 8.3
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 5; units nM; pChEMBL 8.3; comment 965871

## Query Molecule B
- Canonical SMILES: C[C@H]1CN(C(=O)c2ccc(C#N)c(-c3ccc(F)cn3)c2)Cc2cnc([C@@](C)(O)C(F)(F)F)n21
- Properties:
- ChEMBL ID: CHEMBL5953311
- Molecular weight: 473.43
- Heavy atoms: 34
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 5
- TPSA: 95.04
- LogP: 3.94
- Rotatable bonds: 3
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.3
- QED: 0.58

## Molecule Similarity
- Weighted Tanimoto: 0.62

Answer: 8.22