Limits...
Structure-Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin.

Hartman AM, Mondal M, Radeva N, Klebe G, Hirsch AK - Int J Mol Sci (2015)

Bottom Line: Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide-π interaction.Biochemical results are in agreement with SBDD.These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition.

View Article: PubMed Central - PubMed

Affiliation: Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands. a.m.hartman@student.rug.nl.

ABSTRACT
Aspartic proteases are a class of enzymes that play a causative role in numerous diseases such as malaria (plasmepsins), Alzheimer's disease (β-secretase), fungal infections (secreted aspartic proteases), and hypertension (renin). We have chosen endothiapepsin as a model enzyme of this class of enzymes, for the design, preparation and biochemical evaluation of a new series of inhibitors of endothiapepsin. Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide-π interaction. Biochemical results are in agreement with SBDD. These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition.

No MeSH data available.


Related in: MedlinePlus

Comparison of the binding mode of crystal structure of 1 and modeled structure of 2 in the active site of endothiapepsin. Color code: inhibitor skeleton: C: green, purple, N: blue, O: red, F: light cyan; enzyme skeleton: C: gray. H bonds below 3.2 Å are shown as black dashed lines (PDB code: 4KUP) [7].
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4581293&req=5

ijms-16-19184-f004: Comparison of the binding mode of crystal structure of 1 and modeled structure of 2 in the active site of endothiapepsin. Color code: inhibitor skeleton: C: green, purple, N: blue, O: red, F: light cyan; enzyme skeleton: C: gray. H bonds below 3.2 Å are shown as black dashed lines (PDB code: 4KUP) [7].

Mentions: When the para-methyl group of the mesityl substituent of 1 is removed, the IC50 value increases to 30.0 μM (8), which suggests that the para-methyl group was involved in lipophilic interactions with I300. Removal of a second methyl group (7) leads to another two-fold increase in IC50 to 59.0 µM. When the last methyl group (ortho) is removed, i.e., the unsubstituted phenyl derivative 9, the IC50 value (49.0 µM) is in the same range as for the aromatic ring with one methyl group (7), which indicates that one of the ortho methyl groups was not involved in any lipophilic interactions. Upon introduction of a trifluoromethyl group in the para position of the phenyl ring (2), the IC50 value, decreases two-fold to 7.0 µM with respect to the initial hit 1, which could be due to the better liphophilic interactions and stronger amide–π interactions. However, the IC50 value increases to 244.0 µM in case of the meta-trifluoromethyl-substituted derivative 3. This observation suggests that the para trifluoromethyl group is involved in more lipophilic interaction than the meta trifluoromethyl group. In case of ortho-fluorophenyl (4) and -bromophenyl (6) substituents, the IC50 values are in the same range as the unsubstituted phenyl derivative (9), which indicates that fluoro and bromo substituents in the ortho position do not have a strong influence on the binding event. Introduction of a hydroxyl group in the ortho position along with a methyl group in the meta position (5) leads to an IC50 value of 36.0 µM, which suggests that the hydroxyl group in the ortho position might be involved in H bonding. Therefore, the highest potency observed for 2 might be ascribed to the strongly electron-withdrawing properties of the trifluoromethyl substituent in para position, which makes the aromatic ring electron-deficient, which, in turn, should strengthen the amide–π interaction. The alignment of dipole moments of the amide bond and the aromatic ring is not ideal (i.e., antiparallel) as observed from dipole-moment calculations using molecular modeling using the software Moloc (Figure 3) [12]. Lipophilic interactions between the fluorine atoms and nearby lipophilic residue I300 certainly also contribute to the potency. A superimposition of hit 1 and the modeled binding pose of the most potent inhibitor 2 is shown in Figure 4. Moreover, because of the higher stability towards oxidative metabolism, trifluoromethylphenyl should reduce the risk for toxicity compared to mesityl. At the same time, the presence of fluorine atoms can enhance the lipophilicity and consequently the in vivo uptake and transport of biologically active compounds.


Structure-Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin.

Hartman AM, Mondal M, Radeva N, Klebe G, Hirsch AK - Int J Mol Sci (2015)

Comparison of the binding mode of crystal structure of 1 and modeled structure of 2 in the active site of endothiapepsin. Color code: inhibitor skeleton: C: green, purple, N: blue, O: red, F: light cyan; enzyme skeleton: C: gray. H bonds below 3.2 Å are shown as black dashed lines (PDB code: 4KUP) [7].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581293&req=5

ijms-16-19184-f004: Comparison of the binding mode of crystal structure of 1 and modeled structure of 2 in the active site of endothiapepsin. Color code: inhibitor skeleton: C: green, purple, N: blue, O: red, F: light cyan; enzyme skeleton: C: gray. H bonds below 3.2 Å are shown as black dashed lines (PDB code: 4KUP) [7].
Mentions: When the para-methyl group of the mesityl substituent of 1 is removed, the IC50 value increases to 30.0 μM (8), which suggests that the para-methyl group was involved in lipophilic interactions with I300. Removal of a second methyl group (7) leads to another two-fold increase in IC50 to 59.0 µM. When the last methyl group (ortho) is removed, i.e., the unsubstituted phenyl derivative 9, the IC50 value (49.0 µM) is in the same range as for the aromatic ring with one methyl group (7), which indicates that one of the ortho methyl groups was not involved in any lipophilic interactions. Upon introduction of a trifluoromethyl group in the para position of the phenyl ring (2), the IC50 value, decreases two-fold to 7.0 µM with respect to the initial hit 1, which could be due to the better liphophilic interactions and stronger amide–π interactions. However, the IC50 value increases to 244.0 µM in case of the meta-trifluoromethyl-substituted derivative 3. This observation suggests that the para trifluoromethyl group is involved in more lipophilic interaction than the meta trifluoromethyl group. In case of ortho-fluorophenyl (4) and -bromophenyl (6) substituents, the IC50 values are in the same range as the unsubstituted phenyl derivative (9), which indicates that fluoro and bromo substituents in the ortho position do not have a strong influence on the binding event. Introduction of a hydroxyl group in the ortho position along with a methyl group in the meta position (5) leads to an IC50 value of 36.0 µM, which suggests that the hydroxyl group in the ortho position might be involved in H bonding. Therefore, the highest potency observed for 2 might be ascribed to the strongly electron-withdrawing properties of the trifluoromethyl substituent in para position, which makes the aromatic ring electron-deficient, which, in turn, should strengthen the amide–π interaction. The alignment of dipole moments of the amide bond and the aromatic ring is not ideal (i.e., antiparallel) as observed from dipole-moment calculations using molecular modeling using the software Moloc (Figure 3) [12]. Lipophilic interactions between the fluorine atoms and nearby lipophilic residue I300 certainly also contribute to the potency. A superimposition of hit 1 and the modeled binding pose of the most potent inhibitor 2 is shown in Figure 4. Moreover, because of the higher stability towards oxidative metabolism, trifluoromethylphenyl should reduce the risk for toxicity compared to mesityl. At the same time, the presence of fluorine atoms can enhance the lipophilicity and consequently the in vivo uptake and transport of biologically active compounds.

Bottom Line: Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide-π interaction.Biochemical results are in agreement with SBDD.These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition.

View Article: PubMed Central - PubMed

Affiliation: Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands. a.m.hartman@student.rug.nl.

ABSTRACT
Aspartic proteases are a class of enzymes that play a causative role in numerous diseases such as malaria (plasmepsins), Alzheimer's disease (β-secretase), fungal infections (secreted aspartic proteases), and hypertension (renin). We have chosen endothiapepsin as a model enzyme of this class of enzymes, for the design, preparation and biochemical evaluation of a new series of inhibitors of endothiapepsin. Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide-π interaction. Biochemical results are in agreement with SBDD. These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition.

No MeSH data available.


Related in: MedlinePlus