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Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.

Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA - BMC Struct. Biol. (2011)

Bottom Line: We employed several scoring methods in order to find the best protein conformations.Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: MTi, Inserm U973 - University Paris Diderot, 35 rue Helene Brion, Bat, Lamarck, 75013 Paris, France.

ABSTRACT

Background: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.

Results: In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.

Conclusions: NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

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Related in: MedlinePlus

Side chains of the protein residues moving after the refinement with AMMOS (in pink sticks). The top AMMOS scored poses of terphenyl are shown in yellow sticks. (A) CaM, the 2K0F model 31; (B) HsCen2, the 2A4J model 5.
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Figure 7: Side chains of the protein residues moving after the refinement with AMMOS (in pink sticks). The top AMMOS scored poses of terphenyl are shown in yellow sticks. (A) CaM, the 2K0F model 31; (B) HsCen2, the 2A4J model 5.

Mentions: As previously shown [50,51], post-docking optimization may help to further improve both docking poses and scores. We performed additional energetic analysis (see Tables 1 and 2) of docking poses on the selected best MRC to optimize the predicted binding modes and to re-calculate the interaction energies taking into account desolvation effects due to ligand binding. Firstly, we carried out an energy minimization of the docking poses on the selected NMR conformations and X-ray structures of both proteins using the program AMMOS [52]. The included flexible side chains of the protein receptor around the bound terphenyl enabled to relax the complex structures in the binding pocket. The energy gain due to the AMMOS relaxation for the best scored poses is shown in Tables 1 and 2. The important energy decrease during this step is due to reducing clashes between the docked ligand and some residues of the protein binding pocket, as well as internal ligand energy optimization. Figure 7 represents the side-chain orientations after the energy minimization for the different docking poses. The residues slightly moving due to the optimization are F88, L101, M105, E110, M120, E123, and M140 for CaM (Figure 7A) and F113, L126, E132, M145, E148 and E161 for HsCen2 (Figure 7B). Interestingly, it can be seen that Met residues M105, M120 and M140 are among the moving residues, as discussed above. As seen in Figure 7, the changes due to the optimization are not very large, still small variations of the docked complex structure can affect the interaction energy prediction (see Tables 1 and 2, the AMMOS energy, before and after AMMOS refinement). It has been previously discussed that even small receptor movements can lead to important modifications into the molecular recognition pattern and/or binding energy prediction errors [53]. To this end, the AMMOS refinement step could be useful to "rescue" some docking poses with bad energy score after docking on a rigid receptor (e.g. the docking pose 19 on the 2K0F model 160, Table 1).


Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.

Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA - BMC Struct. Biol. (2011)

Side chains of the protein residues moving after the refinement with AMMOS (in pink sticks). The top AMMOS scored poses of terphenyl are shown in yellow sticks. (A) CaM, the 2K0F model 31; (B) HsCen2, the 2A4J model 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116463&req=5

Figure 7: Side chains of the protein residues moving after the refinement with AMMOS (in pink sticks). The top AMMOS scored poses of terphenyl are shown in yellow sticks. (A) CaM, the 2K0F model 31; (B) HsCen2, the 2A4J model 5.
Mentions: As previously shown [50,51], post-docking optimization may help to further improve both docking poses and scores. We performed additional energetic analysis (see Tables 1 and 2) of docking poses on the selected best MRC to optimize the predicted binding modes and to re-calculate the interaction energies taking into account desolvation effects due to ligand binding. Firstly, we carried out an energy minimization of the docking poses on the selected NMR conformations and X-ray structures of both proteins using the program AMMOS [52]. The included flexible side chains of the protein receptor around the bound terphenyl enabled to relax the complex structures in the binding pocket. The energy gain due to the AMMOS relaxation for the best scored poses is shown in Tables 1 and 2. The important energy decrease during this step is due to reducing clashes between the docked ligand and some residues of the protein binding pocket, as well as internal ligand energy optimization. Figure 7 represents the side-chain orientations after the energy minimization for the different docking poses. The residues slightly moving due to the optimization are F88, L101, M105, E110, M120, E123, and M140 for CaM (Figure 7A) and F113, L126, E132, M145, E148 and E161 for HsCen2 (Figure 7B). Interestingly, it can be seen that Met residues M105, M120 and M140 are among the moving residues, as discussed above. As seen in Figure 7, the changes due to the optimization are not very large, still small variations of the docked complex structure can affect the interaction energy prediction (see Tables 1 and 2, the AMMOS energy, before and after AMMOS refinement). It has been previously discussed that even small receptor movements can lead to important modifications into the molecular recognition pattern and/or binding energy prediction errors [53]. To this end, the AMMOS refinement step could be useful to "rescue" some docking poses with bad energy score after docking on a rigid receptor (e.g. the docking pose 19 on the 2K0F model 160, Table 1).

Bottom Line: We employed several scoring methods in order to find the best protein conformations.Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: MTi, Inserm U973 - University Paris Diderot, 35 rue Helene Brion, Bat, Lamarck, 75013 Paris, France.

ABSTRACT

Background: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.

Results: In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.

Conclusions: NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

Show MeSH
Related in: MedlinePlus