Control of the stability of a protein-RNA complex by the position of fluorine in a base analogue

Single-atom substitution enables supramolecular diversity from dipeptide building blocks

Dipeptides are popular building blocks for supramolecular gels that do not persist in the environment and may find various applications. In this work, we show that a simple substitution on the aromatic side-chain of phenylalanine with either fluorine or iodine enables supramolecular diversity upon self-assembly at neutral pH, leading to hydrogels or crystals. Each building block is characterized by ¹H- and ¹³C-NMR spectroscopy, LC-MS, circular dichroism, and molecular models. The supramolecular behaviour is monitored with a variety of techniques, including circular dichroism, oscillatory rheology, transmission electron microscopy, attenuated total reflectance Fourier-transformed infrared spectroscopy, visible Raman spectroscopy, synchrotron-radiation single-crystal X-ray diffraction and UV Resonance Raman spectroscopy, allowing key differences to be pinpointed amongst the halogenated analogues.

Inhibitory Effect of 8-Halogenated 7-Deaza-2'-deoxyguanosine Triphosphates on Human 8-Oxo-2'-deoxyguanosine Triphosphatase, hMTH1, Activities

hMTH1 (8-oxo-2'-deoxyguanine triphosphatase) hydrolyzes oxidized nucleoside triphosphates; its presence is non-essential for survival of normal cells but is required for survival of cancer cells. In this study, 8-halogenated-7-deaza-2'-deoxyguanosine triphosphate (8-halogenated-7-deazadGTP) derivatives were synthesized. Interestingly, these triphosphates were poor substrates for hMTH1, but exhibited strong competitive inhibition against hMTH1 at nanomolar levels. This inhibitory effect is attributed to slower rate of hydrolysis, possibly arising from enzyme structural changes, specifically different stacking interactions with 8-halogenated-7-deazadGTP. This is the first example of using nucleotide derivatives to inhibit hMTH1, thus demonstrating their potential as antitumor agents.

Fluorine bonding enhances the energetics of protein-lipid binding in the gas phase

This paper reports on the first experimental study of the energies of noncovalent fluorine bonding in a protein-ligand complex in the absence of solvent. Arrhenius parameters were measured for the dissociation of gaseous deprotonated ions of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and four fluorinated analogs of stearic acid (SA), which contained (X =) 13, 15, 17, or 21 fluorine atoms. In all cases, the activation energies (E(a)) measured for the loss of neutral XF-SA from the (Lg + XF-SA)⁷⁻ ions are larger than for SA. From the kinetic data, the average contribution of each > CF₂ group to E(a) was found to be ~1.1 kcal mol⁻¹, which is larger than the ~0.8 kcal mol⁻¹ value reported for > CH₂ groups. Based on these results, it is proposed that fluorocarbon–protein interactions are inherently stronger (enthalpically) than the corresponding hydrocarbon interactions.

Understanding substituent effects in noncovalent interactions involving aromatic rings

Noncovalent interactions involving aromatic rings such as π-stacking, cation/π, and anion/π interactions are central to many areas of modern chemistry. Decades of experimental studies have provided key insights into the impact of substituents on these interactions, leading to the development of simple intuitive models. However, gas-phase computational studies have raised some doubts about the physical underpinnings of these widespread models. In this Account we review our recent efforts to unravel the origin of substituent effects in π-stacking and ion/π interactions through computational studies of model noncovalent dimers. First, however, we dispel the notion that so-called aromatic interactions depend on the aromaticity of the interacting rings by studying model π-stacked dimers in which the aromaticity of one of the monomers can be "switched off". Somewhat surprisingly, the results show that not only is aromaticity unnecessary for π-stacking interactions, but it actually hinders these interactions to some extent. Consequently, when thinking about π-stacking interactions, researchers should consider broader classes of planar molecules, not just aromatic systems. Conventional models maintain that substituent effects in π-stacking interactions result from changes in the aryl π-system. This view suggests that π-stacking interactions are maximized when one ring is substituted with electron-withdrawing groups and the other with electron donors. In contrast to these prevailing models, we have shown that substituent effects in π-stacking interactions can be described in terms of direct, local interactions between the substituents and the nearby vertex of the other arene. As a result, in polysubstituted π-stacked dimers the substituents operate independently unless they are in each other's local environment. This means that in π-stacked dimers in which one arene is substituted with electron donors and the other with electron acceptors the interactions will be enhanced only to the extent provided by each substituent on its own, unless the substituents on opposing rings are in close proximity. Overall, this local, direct interaction model predicts that substituent effects in π-stacking interactions will be additive and transferable and will also depend on the relative position of substituents on opposing rings. For cation/π and anion/π interactions, similar π-resonance-based models pervade the literature. Again, computational results indicate that substituent effects in model ion/π complexes can be described primarily in terms of direct interactions between the ion and the substituent. Changes in the aryl π-system do not significantly affect these interactions. We also present a simple electrostatic model that further demonstrates this effect and suggests that the dominant interaction for simple substituents is the interaction of the charged ion with the local dipole associated with the substituents. Finally, we discuss substituent effects in electrostatic potentials (ESPs), which are widely used in discussions of noncovalent interactions. In the past, widespread misconceptions have confused the relationship between changes in ESPs and local changes in the electron density. We have shown that computed ESP plots of diverse substituted arenes can be reproduced without altering the aryl π-density. This is because substituent-induced changes in the ESP above the center of aryl rings result primarily from through-space effects of substituents rather than through changes in the distribution of the π-electron density.

Local nature of substituent effects in stacking interactions

Popular explanations of substituent effects in π-stacking interactions hinge upon substituent-induced changes in the aryl π-system. This entrenched view has been used to explain substituent effects in countless stacking interactions over the past 2 decades. However, for a broad range of stacked dimers, it is shown that substituent effects are better described as arising from local, direct interactions of the substituent with the proximal vertex of the other ring. Consequently, substituent effects in stacking interactions are additive, regardless of whether the substituents are on the same or opposite rings. Substituent effects are also insensitive to the introduction of heteroatoms on distant parts of either stacked ring. This local, direct interaction viewpoint provides clear, unambiguous explanations of substituent effects for myriad stacking interactions that are in accord with robust computational data, including DFT-D and new benchmark CCSD(T) results. Many of these computational results cannot be readily explained using traditional π-polarization-based models. Analyses of stacking interactions based solely on the sign of the electrostatic potential above the face of an aromatic ring or the molecular quadrupole moment face a similar fate. The local, direct interaction model provides a simple means of analyzing substituent effects in complex aromatic systems and also offers simple explanations of the crystal packing of fluorinated benzenes and the recently published dependence of the stability of protein-RNA complexes on the regiochemistry of fluorinated base analogues [J. Am. Chem. Soc.2011, 133, 3687-3689].