| 1. |
|
|
| 2. |
|
|
| 3. |
- Ahlström, Marie M, et al.
(författare)
-
Virtual screening and scaffold hopping based on GRID molecular interaction fields.
- 2005
-
Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 45:5, s. 1313-23
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, a set of strategies for structure-based design using GRID molecular interaction fields (MIFs) to derive a pharmacophoric representation of a protein is reported. Thrombin, one of the key enzymes involved in the blood coagulation cascade, was chosen as the model system since abundant published experimental data are available related to both crystal structures and structurally diverse sets of inhibitors. First, a virtual screening methodology was developed either using a pharmacophore representation of the protein based on GRID MIFs or using GRID MIFs from the 3D structure of a set of chosen thrombin inhibitors. The search was done in a 3D multiconformation version of the Available Chemical Directory (ACD) database, which had been spiked with 262 known thrombin inhibitors (multiple conformers available per compound). The model managed to find 80% of the known thrombin inhibitors among the 74,291 conformers in the ACD by only searching 5% of the database; hence, a 15-fold enrichment of the library was achieved. Second, a scaffold hopping methodology was developed using GRID MIFs, giving the scaffold interaction pattern and the shape of the scaffold, together with the distance between the anchor points. The scaffolds reported by Dolle in the Journal of Combinatorial Chemistry summaries (2000 and 2001) and scaffolds built or derived from ligands cocomplexed with the thrombin enzyme were parameterized using a new set of descriptors and saved into a searchable database. The scaffold representation from the database was then compared to a template scaffold (from a thrombin crystal structure), and the thrombin-derived scaffolds included in the database were found among the top solutions. To validate the usefulness of the methodology to replace the template scaffold, the entire molecule was built (scaffold and side chains) and the resulting compounds were docked into the active site of thrombin. The docking solutions showed the same binding pattern as the cocomplexed compound, hence, showing that this method can be a valuable tool for medicinal chemists to select interchangeable core structures (scaffolds) in an easy manner and retaining the binding properties from the original ligand.
|
|
| 4. |
- Bergmann, Rikke, et al.
(författare)
-
SHOP: Scaffold HOPping by GRID-Based Similarity Searches
- 2007
-
Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 50:11, s. 2708-2717
-
Tidskriftsartikel (refereegranskat)abstract
- A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.
|
|
| 5. |
|
|
| 6. |
|
|
| 7. |
|
|
| 8. |
- Neuhoff, Sibylle, et al.
(författare)
-
pH-Dependent passive and active transport of acidic drugs across Caco-2 cell monolayers
- 2005
-
Ingår i: European Journal of Pharmaceutical Sciences. - : Elsevier BV. - 0928-0987 .- 1879-0720. ; 25:2-3, s. 211-220
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to investigate pH-dependent passive and active transport of acidic drugs across Caco-2 cells. Therefore, the bidirectional pH-dependent transport of two acidic drugs, indomethacin and salicylic acid, across Caco-2 cells was studied in the physiological pH range of the gastrointestinal tract. The transport of both drugs decreased with increased pH, as expected from the pH-partition hypothesis. Net absorption occurred when the basolateral pH exceeded the apical pH. Concentration dependence and transporter inhibition studies indicated passive transport for indomethacin and a mixture of pH-dependent passive and active influx for salicylic acid. Unexpectedly, active and passive drug transport results were indistinguishable in temperature dependency studies. The transport of salicylic acid (apical pH 5.0; basolateral pH 7.4) was partly blocked by inhibitors of the proton-dependent transporters MCT1 (SLC16A1) and OATP-B (SLC21A9, SLCO2B1). This study shows that the asymmetry in bidirectional transport of acidic drugs is affected by both passive and active components in the presence of pH gradients across Caco-2 cells. Thus, combined studies of concentration-dependency and transport-inhibition are preferred when acidic drug transport is studied in a pH gradient. The findings of this in vitro study can be extrapolated to in vivo situations involving an acidic microclimate.
|
|
| 9. |
|
|
| 10. |
|
|
