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On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein.

ABSTRACT: The stereoselective affinity of small-molecule binding to proteins is typically broadly explained in terms of the thermodynamics of the final bound complex. Using Brownian dynamics simulations, we show that the preferential binding of the MDM2 protein to the geometrical isomers of Nutlin-3, an effective anticancer lead that works by inhibiting the interaction between the proteins p53 and MDM2, can be explained by kinetic arguments related to the formation of the MDM2:Nutlin-3 encounter complex. This is a diffusively bound state that forms prior to the final bound complex. We find that the MDM2 protein stereoselectivity for the Nutlin-3a enantiomer stems largely from the destabilization of the encounter complex of its mirror image enantiomer Nutlin-3b, by the K70 residue that is located away from the binding site. On the other hand, the trans-Nutlin-3a diastereoisomer exhibits a shorter residence time in the vicinity of MDM2 compared with Nutlin-3a due to destabilization of its encounter complex by the collective interaction of pairs of charged residues on either side of the binding site: Glu25 and Lys51 on one side, and Lys94 and Arg97 on the other side. This destabilization is largely due to the electrostatic potential of the trans-Nutlin-3a isomer being largely positive over extended continuous regions around its structure, which are otherwise well-identified into positive and negative regions in the case of the Nutlin-3a isomer. Such rich insight into the binding processes underlying biological selectivity complements the static view derived from the traditional thermodynamic analysis of the final bound complex. This approach, based on an explicit consideration of the dynamics of molecular association, suggests new avenues for kinetics-based anticancer drug development and discovery.

SUBMITTER: ElSawy KM

PROVIDER: S-EPMC3905064 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein.

ElSawy Karim M KM Verma Chandra S CS Lane David P DP Caves Leo S D LS

Cell cycle (Georgetown, Tex.) 20131121 24

The stereoselective affinity of small-molecule binding to proteins is typically broadly explained in terms of the thermodynamics of the final bound complex. Using Brownian dynamics simulations, we show that the preferential binding of the MDM2 protein to the geometrical isomers of Nutlin-3, an effective anticancer lead that works by inhibiting the interaction between the proteins p53 and MDM2, can be explained by kinetic arguments related to the formation of the MDM2:Nutlin-3 encounter complex. ...[more]

PMID: 24270847

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Project description:Highlights • 10 different astaxanthin (AST) geometrical isomers were analyzed by Raman spectroscopy.• Raman spectroscopy can distinguish all the geometrical isomers of AST molecules.• Structures and vibrational modes of all the AST isomers are obtained due to DFT calculations. Astaxanthin is a carotenoid widely used in food additives, nutritional product and medicines, which shows many physiological functions such as antioxidant, anti-inflammatory, anti-hypertensive and anti-diabetic activities. It has been recognized that astaxanthin has all-trans and nine cis isomers, and these geometrical isomers have very different biological activities. The process of selective enrichment, metabolism and isomerization of astaxanthin in animals remains to be studied. Therefore, identifying isomers and obtaining their structural parameters are important for understanding the active mechanism of different molecular isomers. Although the traditional methods such as high-performance liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) spectroscopy can be used to distinguish these isomers, these methods generally require considerable testing time, cost, sample volume, and hardly be applied in vivo. In this work, Raman spectroscopy combined with density functional theory (DFT) calculation was introduced to study different geometrical isomers of astaxanthin. The theoretical and experimental Raman spectra are in agreement, and we have demonstrated that all the known ten geometrical isomers of astaxanthin can be readily distinguished using this spectroscopic approach. The astaxanthin molecular vibrational modes, geometric structures, energies of ten geometric isomers are systematically scrutinized. Moreover, a lot of structural and Raman problems unsolved previously have been solved by the DFT-based spectral analysis. Therefore, this work provides an effective way for identification of different astaxanthin geometrical isomers, and may have important significance for promoting the research of astaxanthin isomers on biological property mechanisms and related applications in food molecular science.

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On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein.

Publications

On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein.

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