| Literature DB >> 32864079 |
Paolo Suating1, Thong T Nguyen1, Nicholas E Ernst1, Yang Wang2, Jacobs H Jordan1, Corinne L D Gibb1, Henry S Ashbaugh2, Bruce C Gibb1.
Abstract
Science still does not have the ability to accurately predict the affinity that ligands have for proteins. In an attempt to address this, the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind predictive challenges is a community-wide exercise aimed at advancing computational techniques as standard predictive tools in rational drug design. In each cycle, a range of biologically relevant systems of different levels of complexity are selected to test the latest modeling methods. As part of this on-going exercise, and as a step towards understanding the important factors in context dependent guest binding, we challenged the computational community to determine the affinity of a series of negatively and positively charged guests to two constitutionally isomeric cavitand hosts: octa-acid 1, and exo-octa acid 2. Our affinity determinations, combined with molecular dynamics simulations, reveal asymmetries in affinities between host-guest pairs that cannot alone be explained by simple coulombic interactions, but also point to the importance of host-water interactions. Our work reveals the key facets of molecular recognition in water, emphasizes where improvements need to be made in modelling, and shed light on the complex problem of ligand-protein binding in the aqueous realm. This journal is © The Royal Society of Chemistry 2020.Entities:
Year: 2020 PMID: 32864079 PMCID: PMC7424593 DOI: 10.1039/c9sc06268h
Source DB: PubMed Journal: Chem Sci ISSN: 2041-6520 Impact factor: 9.825
Fig. 1Structures and space-filling models of the two hosts in this study: octa-acid (1) and exo-octa-acid (2).23
Scheme 1Synthesis of exo-octa-acid 2.
Fig. 2Guests used in this study. Guests G1–G4 were used as the sodium salts, and guests G5–G8 were used as their chloride salts.
Thermodynamic data from ITC for the binding of guests G1–G8 with hosts OA 1 and exo-OA 2 in 10 mM phosphate buffer at pH = 11.5
| Guest | Octa acid |
| ||||
| Δ | Δ | – | Δ | Δ | – | |
|
| –20.8 ± 0.1 | –23.2 ± 0.1 | 2.4 ± 0.3 | — | — | — |
|
| –28.9 ± 0.1 | –40.2 ± 1.1 | 11.0 ± 1.0 | –5.5 ± 1.1 | — | — |
|
| –33.9 ± 0.1 | –50.2 ± 0.0 | 16.3 ± 0.1 | –14.1 ± 0.3 | –25.2 ± 0.6 | 11.1 ± 0.3 |
|
| –28.3 ± 0.2 | –28.0 ± 0.7 | –0.3 ± 0.5 | –15.1 ± 0.1 | –30.5 ± 2.9 | 15.4 ± 2.8 |
|
| –19.8 ± 0.0 | –31.3 ± 0.2 | 11.5 ± 0.2 | –23.3 ± 0.1 | –25.8 ± 0.0 | 2.5 ± 0.1 |
|
| –20.8 ± 0.1 | –30.5 ± 1.4 | 9.6 ± 1.4 | –24.4 ± 0.0 | –13.6 ± 0.1 | –10.8 ± 0.1 |
|
| –25.4 ± 0.2 | –24.0 ± 0.7 | –1.4 ± 0.5 | –29.2 ± 0.4 | –20.8 ± 0.3 | –8.4 ± 0.2 |
|
| –34.5 ± 0.1 | –32.7 ± 0.8 | –1.7 ± 0.6 | –32.1 ± 0.0 | –21.1 ± 0.2 | –11.0 ± 0.1 |
Data and errors in this table were determined as follows. The ΔH and ΔG values were obtained by carrying out at least three separate experiments, averaging each set of data, and calculating the respective standard deviation. These average ΔH and ΔG values were then used to calculate an average –TΔS value, and the corresponding standard deviation calculated using the standard equation for the propagation of uncertainties (for subtraction).
Data for this host–guest combination was determined as part of SAMPL4 in 50 mM borate.27
No binding observed.
Determined by 1H NMR spectroscopy.
Data for this host–guest combination was determined as part of SAMPL5 in 50 mM phosphate.28
Fig. 3Differences in the average free energy change (Differences in the average free energy change (〈ΔΔG〉) of binding negative () of binding negative (, G1–G4) and positive (, G5–G8) guests to hosts 1 and 2. Both the position on the vertical and the circle diameters correspond to the magnitude of the average free energy of complexation (see main text).
Fig. 4(a) Chemical structure and space-filling model of theoretical host tri-exo-mono-endo-OA 3. The unique endo-carboxylate is indicated in red in the former and by an arrow in the latter. (b) Free energies for observing n waters within the non-polar pockets of 1, 2 and 3. The probabilities, p(n), of observing n waters within the pocket are reported in the inset. The free energy is determined from the probability as G(n) = –RT ln p(n), which corresponds to the free energy required to constrain the pocket to contain only n waters. In the case of guest binding the empty pocket (n = 0) is the most important state to consider. The error bars in the simulation data are comparable to or smaller than the figure symbols. The maximum error estimate across all hosts for the free energy of emptying a cavitand, G(0), is ±0.4 kJ mol–1.
Fig. 5Total number of hydrogen bonds between water and the four rim carboxylates of OA 1 and exo-OA 2 as a function of the position (z) of the guests adamantane, G8, and adamantane carboxylate (Ada-CO2–) along the cavitand C4-axis of symmetry. The position (z) was defined by the zero-plane perpendicular to the C4-axis of symmetry – itself defined by the eight ether-oxygens atoms at the rim of the pocket – and the center of mass of the adamantane guest as it was moved along the C4 host axis. Error bars have been neglected for clarity, however, the error in the number of hydrogen bonds at a given separation z is 0.25.