SINBA includes six integrated drug-gene interaction databases, collectively documenting a comprehensive set of drugs and pharmacologically targetable genes. The databases—DrugBank (7,509 drugs), ChEMBL (3,838), cMAP (2,556), Repurposing Hub (6,798), DGIdb (7,837), and BPdb (1,084)—cover a total of 6,164 targetable genes. This extensive resource provides a robust foundation for therapeutic prioritization, extending beyond CNS tumors.
The curated BPdb database features 1,084 brain-penetrant agents identified from B3DB29, published literature, and clinical trials, targeting 2,476 genes. Notably, 59% of BPdb drugs are FDA-approved, while the remaining 41% include compounds tested in neurotherapeutic trials or antibody-based modalities with “possible” blood-brain barrier penetration.
BPdb database
## Drug_Name ChEMBL geneSymbol Drug_type Drug_ID
## 1284 NARATRIPTAN CHEMBL1278 A12M1 Small_molecule CHEMBL1278
## 1333 SUMATRIPTAN CHEMBL128 A12M1 Small_molecule CHEMBL128
## 2668 RISPERIDONE CHEMBL85 A12M1 Small_molecule CHEMBL85
## 4093 QUETIAPINE CHEMBL716 A12M1 Small_molecule CHEMBL716
## 4193 OLANZAPINE <NA> A12M1 Small_molecule 135398745
## 4613 ASENAPINE CHEMBL3187365 A12M1 Small_molecule CHEMBL3187365
## SMILES Phase PubChem_CID BBB
## 1284 CNS(=O)(=O)CCc1ccc2[nH]cc(C3CCN(C)CC3)c2c1 4.0 4440 BBB+
## 1333 CNS(=O)(=O)Cc1ccc2[nH]cc(CCN(C)C)c2c1 4.0 5358 BBB+
## 2668 Cc1nc2n(c(=O)c1CCN1CCC(c3noc4cc(F)ccc34)CC1)CCCC2 4.0 5073 BBB+
## 4093 OCCOCCN1CCN(C2=Nc3ccccc3Sc3ccccc32)CC1 4.0 5002 BBB+
## 4193 Cc1cc2c(s1)=Nc1ccccc1NC=2N1CCN(C)CC1 0 135398745 BBB+
## 4613 CN1CC2c3ccccc3Oc3ccc(Cl)cc3C2C1 4.0 9903970 BBB+##
## 0 1.0 2.0 3.0 4.0
## Antibody 1 0 98 56 76
## Small_molecule 171 7 95 24 556##
## BBB+ possible
## 658 426You can query drug and gene information from DGIdb API
https://dgidb.org:
From drug to potential target genes
use_drugs<-c("Dasatinib")
res<-queryDgidb_V5_drug(drugs=use_drugs)
print(res[,c(1:2,6:7)])## interactionScore interactionTypes gene.name gene.conceptId
## 1 0.1914289421 NULL PDGFRA hgnc:8803
## 2 0.0196254882 NULL SYK hgnc:11491
## 3 0.0763213429 inhibitor, INHIBITORY FYN hgnc:4037
## 4 0.0140182058 NULL AXL hgnc:905
## 5 0.0789925899 inhibitor, INHIBITORY BRAF hgnc:1097
## 6 0.0007640624 NULL AR hgnc:644
## 7 0.0763213429 NULL SIK2 hgnc:21680
## 8 0.0029995288 NULL SMAD3 hgnc:6769
## 9 0.0538738891 inhibitor, INHIBITORY LCK hgnc:6524
## 10 0.0236859340 NULL PLK4 hgnc:11397
## 11 0.1144820144 NULL MAP3K10 hgnc:6849
## 12 0.0228964029 NULL SLK hgnc:11088
## 13 0.0132094632 inhibitor, INHIBITORY YES1 hgnc:12841
## 14 0.0118429670 NULL ERBB4 hgnc:3432
## 15 0.1144820144 inhibitor, INHIBITORY SRC hgnc:11283
## 16 0.1248894702 inhibitor, INHIBITORY BCR hgnc:1014
## 17 0.0312223676 NULL IRAK4 hgnc:17967
## 18 0.0202027084 NULL BRCA2 hgnc:1101
## 19 0.2747568345 NULL STAT5B hgnc:11367
## 20 0.0264189264 NULL BTK hgnc:1133
## 21 0.0429307554 NULL CRKL hgnc:2363
## 22 0.0343446043 inhibitor, INHIBITORY LYN hgnc:6735
## 23 0.0063601119 NULL FGFR1 hgnc:3688
## 24 0.0074662183 NULL MAPK14 hgnc:6876
## 25 0.0051646022 NULL PPARD hgnc:9235
## 26 0.0163545735 inhibitor, INHIBITORY BLK hgnc:1057
## 27 0.9616489208 inhibitor, INHIBITORY DDR2 hgnc:2731
## 28 0.0245318602 NULL ABL2 hgnc:77
## 29 0.1717230216 NULL ABI1 hgnc:11320
## 30 0.1717230216 inhibitor, INHIBITORY SRMS hgnc:11298
## 31 0.1144820144 NULL TET2 hgnc:25941
## 32 0.0981274409 NULL TEC hgnc:11719
## 33 0.0221578092 inhibitor, INHIBITORY MS4A2 hgnc:7316
## 34 0.0070091029 NULL JAK2 hgnc:6192
## 35 0.0082758083 NULL MAP2K1 hgnc:6840
## 36 0.0286205036 NULL MAP3K20 hgnc:17797
## 37 0.1144820144 inhibitor, INHIBITORY FBLN2 hgnc:3601
## 38 0.0312223676 NULL LIMK1 hgnc:6613
## 39 0.0029229450 NULL ABCB1 hgnc:40
## 40 0.0858615108 NULL PTK6 hgnc:9617
## 41 0.0298648733 NULL NF1 hgnc:7765
## 42 0.0044894908 NULL ERBB2 hgnc:3430
## 43 0.0221578092 NULL TAOK1 hgnc:29259
## 44 0.0624447351 NULL CDC42BPA hgnc:1737
## 45 0.0624447351 NULL DYRK3 hgnc:3094
## 46 0.0245318602 inhibitor, INHIBITORY FRK hgnc:3955
## 47 0.0095845407 NULL PIK3CA hgnc:8975
## 48 0.0159742346 NULL MAP2K2 hgnc:6842
## 49 0.0286205036 NULL IDH2 hgnc:5383
## 50 0.1017617906 NULL CSF3R hgnc:2439
## 51 0.0327091470 NULL PKN2 hgnc:9406
## 52 0.0165516165 NULL HRAS hgnc:5173
## 53 0.0048034412 NULL KDR hgnc:6307
## 54 0.0066688552 NULL IDH1 hgnc:5382
## 55 0.0381606715 NULL TNK2 hgnc:19297
## 56 0.0014310252 NULL GMNN hgnc:17493
## 57 0.1717230216 NULL FES hgnc:3657
## 58 0.0327091470 inhibitor, INHIBITORY FGR hgnc:3697
## 59 0.2909190013 inhibitor, INHIBITORY KIT hgnc:6342
## 60 0.1030338129 NULL CBL hgnc:1541
## 61 0.0654182939 inhibitor, INHIBITORY HCK hgnc:4840
## 62 0.0214653777 NULL ABCG2 hgnc:74
## 63 0.0298648733 NULL ACVR1 hgnc:171
## 64 0.0981274409 NULL ARID1A hgnc:11110
## 65 0.0624447351 inhibitor, INHIBITORY FAU hgnc:3597
## 66 0.1144820144 inhibitor, INHIBITORY FAUNA@ ncbigene:2198
## 67 0.4197673861 inhibitor, INHIBITORY EPHA2 hgnc:3386
## 68 0.0214653777 NULL FGFR3 hgnc:3690
## 69 0.0312223676 NULL APC hgnc:583
## 70 0.0071551259 NULL KRAS hgnc:6407
## 71 0.0214653777 NULL MAP4K5 hgnc:6867
## 72 0.0254404476 NULL MINK1 hgnc:17565
## 73 0.1777273230 inhibitor, INHIBITORY ABL1 hgnc:76
## 74 0.0127202238 inhibitor, INHIBITORY CSF1R hgnc:2433
## 75 0.0521690192 inhibitor, INHIBITORY PDGFRB hgnc:8804
## 76 0.0104074559 NULL AURKB hgnc:11390From gene to potential drugs
use_genes<-c("CD4","PARP1")
res<-queryDgidb_V5_gene(genes=use_genes)
print(res[,c(1:2,6:8)])## interactionScore interactionTypes
## 1 0.2966125 NULL
## 2 3.2627374 negative modulator, INHIBITORY
## 3 9.7882122 other/unknown, NA
## 4 3.2627374 inhibitor, INHIBITORY
## 5 3.2627374 NULL
## 6 3.2627374 NULL
## 7 3.2627374 agonist, ACTIVATING
## 8 3.2627374 negative modulator, INHIBITORY
## 9 3.2627374 inhibitor, INHIBITORY
## 10 3.2627374 inhibitor, INHIBITORY
## 11 0.1977417 NULL
## 12 3.2627374 binder, NA
## 13 3.2627374 NULL
## 14 3.2627374 inhibitor, INHIBITORY
## 15 3.2627374 inhibitor, INHIBITORY
## 16 0.7250528 NULL
## 17 1.5058788 NULL
## 18 2.0078384 NULL
## 19 0.6692795 NULL
## 20 1.0039192 inhibitor, INHIBITORY
## 21 0.3928379 inhibitor, other/unknown, INHIBITORY, NA
## 22 2.0078384 inhibitor, INHIBITORY
## 23 1.2777153 inhibitor, other/unknown, INHIBITORY, NA
## 24 1.0039192 NULL
## 25 0.5736681 inhibitor, INHIBITORY
## 26 0.7086488 other/unknown, inhibitor, NA, INHIBITORY
## 27 2.0078384 inhibitor, INHIBITORY
## 28 0.6692795 inhibitor, INHIBITORY
## 29 0.4015677 NULL
## 30 1.0039192 inhibitor, INHIBITORY
## 31 1.0039192 NULL
## 32 2.0078384 NULL
## 33 0.6692795 inhibitor, INHIBITORY
## 34 1.0039192 inhibitor, INHIBITORY
## 35 0.2151255 inhibitor, INHIBITORY
## 36 2.0078384 NULL
## 37 2.0078384 NULL
## 38 2.0078384 NULL
## 39 0.3346397 inhibitor, other/unknown, INHIBITORY, NA
## 40 4.0156768 inhibitor, other/unknown, INHIBITORY, NA
## 41 2.0078384 NULL
## 42 1.0039192 inhibitor, INHIBITORY
## drug.name
## 1 ANTI-THYMOCYTE GLOBULIN
## 2 KELIXIMAB
## 3 ZANOLIMUMAB
## 4 IBALIZUMAB
## 5 HERBIMYCIN
## 6 TREGALIZUMAB
## 7 TREGALIZUMAB
## 8 PRILIXIMAB
## 9 CEDELIZUMAB
## 10 CLENOLIXIMAB
## 11 ANTISENSE OLIGONUCLEOTIDES
## 12 VRC-01LS
## 13 TRX1
## 14 TRX-1
## 15 SEMZUVOLIMAB
## 16 ANTIVIRAL AGENT
## 17 4-[3-(1,4-DIAZEPAN-1-YLCARBONYL)-4-FLUOROBENZYL]PHTHALAZIN-1(2H)-ONE
## 18 CEP-9722
## 19 NIACINAMIDE
## 20 NIRAPARIB TOSYLATE MONOHYDRATE
## 21 OLAPARIB
## 22 AMELPARIB DIHYDROCHLORIDE DIHYDRATE
## 23 VELIPARIB
## 24 BGP-15
## 25 PAMIPARIB
## 26 NIRAPARIB
## 27 RUCAPARIB PHOSPHATE
## 28 RUCAPARIB CAMSYLATE
## 29 TRABECTEDIN
## 30 SENAPARIB
## 31 ORAL AZACITIDINE
## 32 NIRAPARIB TOSYLATE
## 33 E-7016
## 34 TALAZOPARIB TOSYLATE
## 35 TALAZOPARIB
## 36 NICARAVEN
## 37 PARP-1/2 INHIBITOR ABT-767
## 38 PARP INHIBITOR E7016
## 39 RUCAPARIB
## 40 INIPARIB
## 41 INO-1001
## 42 2X-121
## drug.conceptId queryGene
## 1 ncit:C278 CD4
## 2 ncit:C188517 CD4
## 3 ncit:C91701 CD4
## 4 rxcui:2043283 CD4
## 5 ncit:C1124 CD4
## 6 iuphar.ligand:9864 CD4
## 7 ncit:C152722 CD4
## 8 ncit:C188634 CD4
## 9 chembl:CHEMBL2108266 CD4
## 10 ncit:C188527 CD4
## 11 ncit:C1291 CD4
## 12 chembl:CHEMBL4298127 CD4
## 13 drugbank:DB05863 CD4
## 14 chembl:CHEMBL2109474 CD4
## 15 ncit:C188511 CD4
## 16 ncit:C281 CD4
## 17 drugbank:DB08058 PARP1
## 18 drugbank:DB14882 PARP1
## 19 rxcui:7405 PARP1
## 20 rxcui:2640208 PARP1
## 21 rxcui:1597582 PARP1
## 22 chembl:CHEMBL5314421 PARP1
## 23 ncit:C60768 PARP1
## 24 chembl:CHEMBL4747845 PARP1
## 25 ncit:C120553 PARP1
## 26 rxcui:1918231 PARP1
## 27 ncit:C78186 PARP1
## 28 rxcui:1862578 PARP1
## 29 rxcui:1716278 PARP1
## 30 ncit:C168601 PARP1
## 31 ncit:C118288 PARP1
## 32 rxcui:2637447 PARP1
## 33 chembl:CHEMBL3527000 PARP1
## 34 rxcui:2099703 PARP1
## 35 rxcui:2099704 PARP1
## 36 ncit:C76580 PARP1
## 37 ncit:C96795 PARP1
## 38 ncit:C91387 PARP1
## 39 rxcui:1862579 PARP1
## 40 ncit:C62526 PARP1
## 41 ncit:C61315 PARP1
## 42 drugbank:DB16063 PARP1