Conformational Characterization of Ipomotaosides and Their Recognition by COX-1 and 2
Abstract
:1. Introduction
2. Results and Discussion
2.1. Dynamics of Isolated Disaccharides
2.2. Ipomotaosides Dynamics
Glicosidic Linkage | |||||||
---|---|---|---|---|---|---|---|
Compound | Condition | α-l-Rha′-(1→2)-β-d-Fuc | α-l-Rha′′-(1→4)-α-l-Rha′ | α-l-Rha′′′-(1→4)-α-l-Rha′′ | |||
Φ | Ψ | Φ | Ψ | Φ | Ψ | ||
Ipomotaoside 1 | MD in pyridine | −171 ± 29 (42%) | 79 ± 40 (37%) | −75 ± 22 | −85 ± 14 | −71 ± 11 | −81 ± 10 |
−73 ± 28 (58%) | −51 ± 29 (63%) | - | - | - | - | ||
MD in water | −163 ± 15 | 86 ± 19 | −74 ± 22 | −87 ± 21 | −71 ± 15 | −82 ± 12 | |
Ipomotaoside 2 | MD in pyridine | −165 ± 14 | 82 ± 15 | −76 ± 14 | −83 ± 11 | −76 ± 14 | −83 ± 11 |
MD in water | −71 ± 26 (14%) | −51 ± 13 (14%) | −76 ± 42 | −87 ± 19 | −78 ± 40 | −88 ± 18 | |
−170 ± 31 (86%) | 81 ± 56 (86%) | - | - | - | - | ||
Ipomotaoside 3 | MD in pyridine | −183 ± 25 (47%) | 76 ± 27 (47%) | −74 ± 11 | −82 ± 10 | −75 ± 14 | −82 ± 11 |
−91 ± 29 (53%) | −35 ± 37 (53%) | - | - | - | - | ||
MD in water | −173 ± 10 | 87 ± 11 | −72 ± 26 | −82 ± 13 | −77 ± 37 | −86 ± 17 | |
Ipomotaoside 4 | MD in pyridine | −171 ± 25 (43%) | 83 ± 26 (43%) | −71 ± 39 | −85 ± 16 | −74 ± 11 | −84 ± 10 |
−85 ± 25 (57%) | −31 ± 40 (57%) | - | - | - | - | ||
MD in water | −173 ± 09 | 87 ± 09 | −97 ± 33 (34%) | −83 ± 20 (34%) | −80 ± 26 | −84 ± 15 | |
- | - | −185 ± 18 (66%) | −150 ± 18 (66%) | - | - |
Ipomotaoside | Proton 1 | Proton 2 | Average of Interproton distance from MD (Å) | Ipomotaoside | Proton 1 | Proton 2 | Average of Interproton distance from MD (Å) |
---|---|---|---|---|---|---|---|
1 | Fuc-(H1) | Fuc-(H5) | 2.4 ± 0.2 | 3 | Fuc-(H1) | Fuc-(H5) | 2.4 ± 0.2 |
Rha'-(H1) | Fuc-(H1) | 2.5 ± 0.7 | Rha'-(H1) | Fuc-(H1) | 2.5 ± 0.7 | ||
Rha'-(H1) | Fuc-(H2) | 3.2 ± 0.5 | Rha'-(H1) | Fuc-(H2) | 3.2 ± 0.4 | ||
Rha'-(H1) | Fuc-(H3) | 3.4 ± 0.8 | Rha'-(H1) | Fuc-(H3) | 3.6 ± 0.8 | ||
Rha'-(H1) | Fuc-(H4) | 5.5 ± 0.5 | Rha'-(H5) | Fuc-(H1) | 4.9 ± 0.3 | ||
Rha''-(H1) | Rha'-(H3) | 3.4 ± 0.3 | Rha''-(H1) | Rha'-(H2) | 4.7 ± 0.2 | ||
Rha''-(H1) | Rha'-(H4) | 2.5 ± 0.3 | Rha''-(H1) | Rha'-(H4) | 2.5 ± 0.2 | ||
Rha'''-(H1) | Rha''-(H4) | 2.6 ± 0.3 | Rha''-(H1) | Rha'-(H5) | 4.4 ± 0.1 | ||
2 | Fuc-(H1) | Fuc-(H5) | 2.4 ± 0.2 | Rha'''-(H1) | Rha''-(H3) | 3.3 ± 0.2 | |
Rha'-(H1) | Fuc-(H1) | 3.3 ± 0.3 | Rha'''-(H1) | Rha''-(H4) | 2.5 ± 0.3 | ||
Rha'-(H1) | Fuc-(H2) | 2.6 ± 0.3 | Rha'''-(H1) | Rha''-(H5) | 4.4 ± 0.1 | ||
Rha'-(H1) | Fuc-(H3) | 4.4 ± 0.1 | 4 | Fuc-(H1) | Fuc-(H5) | 2.4 ± 0.2 | |
Rha'-(H2) | Fuc-(H2) | 2.2 ± 0.3 | Rha'-(H1) | Fuc-(H1) | 2.5 ± 0.7 | ||
Rha'-(H2) | Fuc-(H3) | 4.7 ± 0.3 | Rha'-(H1) | Fuc-(H2) | 3.1 ± 0.5 | ||
Rha''-(H1) | Rha'-(H3) | 3.4 ± 0.2 | Rha'-(H1) | Fuc-(H3) | 3.5 ± 0.8 | ||
Rha''-(H1) | Rha'-(H4) | 2.5 ± 0.3 | Rha''-(H1) | Rha'-(H4) | 2.5 ± 0.3 | ||
Rha''-(H1) | Rha'-(H5) | 4.4 ± 0.1 | Rha''-(H1) | Rha'-(H5) | 4.3 ± 0.2 | ||
Rha''-(H2) | Rha'-(H3) | 4.1 ± 0.3 | Rha'''-(H1) | Rha''-(H4) | 2.5 ± 0.3 | ||
Rha''-(H2) | Rha'-(H4) | 4.3 ± 0.2 | Rha'''-(H1) | Rha''-(H5) | 4.4 ± 0.1 | ||
Rha'''-(H1) | Rha''-(H3) | 3.4 ± 0.2 | - | - | - | ||
Rha'''-(H2) | Rha''-(H3) | 4.1 ± 0.3 | - | - | - |
2.3. Docking on COX
3. Experimental
3.1. Nomenclature, Topologies and Software
- α1→2:Φ = O5 − C1 − O1 − C2’Ψ = C1 − O1 − C2’ − C1’
- α1→4:Φ = O5 − C1 − O1 − C4’Ψ = C1 − O1 − C4’− C3’
3.2. Topology Construction
3.3. Metadynamics
3.4. MD Simulations
3.5. ROESY Signals
3.6. Docking Procedures
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Arantes, P.R.; Sachett, L.G.; Graebin, C.S.; Verli, H. Conformational Characterization of Ipomotaosides and Their Recognition by COX-1 and 2. Molecules 2014, 19, 5421-5433. https://doi.org/10.3390/molecules19045421
Arantes PR, Sachett LG, Graebin CS, Verli H. Conformational Characterization of Ipomotaosides and Their Recognition by COX-1 and 2. Molecules. 2014; 19(4):5421-5433. https://doi.org/10.3390/molecules19045421
Chicago/Turabian StyleArantes, Pablo R., Liana G. Sachett, Cedric S. Graebin, and Hugo Verli. 2014. "Conformational Characterization of Ipomotaosides and Their Recognition by COX-1 and 2" Molecules 19, no. 4: 5421-5433. https://doi.org/10.3390/molecules19045421