Inframolecular acid–base studies of the tris and tetrakis myo-inositol phosphates including the 1,2,3-trisphosphate motif

Effect of H-Bond Donor Lipids on Phosphatidylinositol-3,4,5-Trisphosphate Ionization and Clustering

The phosphoinositide, phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P₃), is a key signaling lipid in the inner leaflet of the cell plasma membrane, regulating diverse signaling pathways including cell growth and migration. In this study we investigate the impact of the hydrogen-bond donor lipids phosphatidylethanolamine (PE) and phosphatidylinositol (PI) on the charge and phase behavior of PI(3,4,5)P₃. PE and PI can interact with PI(3,4,5)P₃ through hydrogen-bond formation, leading to altered ionization behavior and charge distribution within the PI(3,4,5)P₃ headgroup. We quantify the altered PI(3,4,5)P₃ ionization behavior using a multistate ionization model to obtain micro-pK_a values for the ionization of each phosphate group. The presence of PE leads to a decrease in the pK_a values for the initial deprotonation of PI(3,4,5)P₃, which describes the removal of the first proton of the three protons remaining at the phosphomonoester groups at pH 4.0. The decrease in these micro-pK_a values thus leads to a higher charge at low pH. Additionally, the charge distribution changes lead to increased charge on the 3- and 5-phosphates. In the presence of PI, the final deprotonation of PI(3,4,5)P₃ is delayed, leading to a lower charge at high pH. This is due to a combination of hydrogen-bond formation between PI and PI(3,4,5)P₃, and increased surface charge due to the addition of the negatively charged PI. The interaction between PI and PI(3,4,5)P₃ leads to the formation of PI and PI(3,4,5)P₃-enriched domains within the membrane. These domains may have a critical impact on PI(3,4,5)P₃-signaling. We also reevaluate results for all phosphatidylinositol bisphosphates as well as for PI(4,5)P₂ in complex lipid mixtures with the multistate ionization model.

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

Determining the net charge and protonation states populated by a small molecule in an environment of interest or the cost of altering those protonation states upon transfer to another environment is a prerequisite for predicting its physicochemical and pharmaceutical properties. The environment of interest can be aqueous, an organic solvent, a protein binding site, or a lipid bilayer. Predicting the protonation state of a small molecule is essential to predicting its interactions with biological macromolecules using computational models. Incorrectly modeling the dominant protonation state, shifts in dominant protonation state, or the population of significant mixtures of protonation states can lead to large modeling errors that degrade the accuracy of physical modeling. Low accuracy hinders the use of physical modeling approaches for molecular design. For small molecules, the acid dissociation constant (pK_a) is the primary quantity needed to determine the ionic states populated by a molecule in an aqueous solution at a given pH. As a part of SAMPL6 community challenge, we organized a blind pK_a prediction component to assess the accuracy with which contemporary pK_a prediction methods can predict this quantity, with the ultimate aim of assessing the expected impact on modeling errors this would induce. While a multitude of approaches for predicting pK_a values currently exist, predicting the pK_as of drug-like molecules can be difficult due to challenging properties such as multiple titratable sites, heterocycles, and tautomerization. For this challenge, we focused on set of 24 small molecules selected to resemble selective kinase inhibitors-an important class of therapeutics replete with titratable moieties. Using a Sirius T3 instrument that performs automated acid-base titrations, we used UV absorbance-based pK_a measurements to construct a high-quality experimental reference dataset of macroscopic pK_as for the evaluation of computational pK_a prediction methodologies that was utilized in the SAMPL6 pK_a challenge. For several compounds in which the microscopic protonation states associated with macroscopic pK_as were ambiguous, we performed follow-up NMR experiments to disambiguate the microstates involved in the transition. This dataset provides a useful standard benchmark dataset for the evaluation of pK_a prediction methodologies on kinase inhibitor-like compounds.

Inframolecular acid-base and coordination properties towards Na(+) and Mg(2+) of myo-inositol 1,3,4,5,6-pentakisphosphate: a structural approach to biologically relevant species

The myo-inositol phosphates (InsPs) are specific signalling metabolites ubiquitous in eukaryotic cells. Although Ins(1,3,4,5,6)P(5) is the second most abundant member of the InsPs family, its certain biological roles are far from being elucidated, in part due to the large number of species formed by Ins(1,3,4,5,6)P(5) in the presence of metal ions. In light of this, we have strived in the past to make a complete and at the same time "biological-user-friendly" description of the Ins(1,3,4,5,6)P(5) chemistry with mono and multivalent cations. In this work we expand these studies focusing on the inframolecular aspects of its protonation equilibria and the microscopic details of its coordination behaviour towards biologically relevant metal ions. We present here a systematic study of the Ins(1,3,4,5,6)P(5) intrinsic acid-base processes, in a non-interacting medium, and over a wide pH range, analyzing the (31)P NMR curves by means of a model based on the Cluster Expansion Method. In addition, we have used a computational approach to analyse the energetic and structural features of the protonation and conformational changes of Ins(1,3,4,5,6)P(5), and how they are influenced by the presence of two physiologically relevant cations, Na(+) and Mg(2+).

"Chelatable iron pool": inositol 1,2,3-trisphosphate fulfils the conditions required to be a safe cellular iron ligand

Mammalian cells contain a pool of iron that is not strongly bound to proteins, which can be detected with fluorescent chelating probes. The cellular ligands of this biologically important "chelatable", "labile" or "transit" iron are not known. Proposed ligands are problematic, because they are saturated by magnesium under cellular conditions and/or because they are not "safe", i.e. they allow iron to catalyse hydroxyl radical formation. Among small cellular molecules, certain inositol phosphates (InsPs) excel at complexing Fe(3+) in such a "safe" manner in vitro. However, we previously calculated that the most abundant InsP, inositol hexakisphosphate, cannot interact with Fe(3+) in the presence of cellular concentrations of Mg(2+). In this work, we study the metal complexation behaviour of inositol 1,2,3-trisphosphate [Ins(1,2,3)P(3)], a cellular constituent of unknown function and the simplest InsP to display high-affinity, "safe", iron complexation. We report thermodynamic constants for the interaction of Ins(1,2,3)P(3) with Na(+), K(+), Mg(2+), Ca(2+), Cu(2+), Fe(2+) and Fe(3+). Our calculations indicate that Ins(1,2,3)P(3) can be expected to complex all available Fe(3+) in a quantitative, 1:1 reaction, both in cytosol/nucleus and in acidic compartments, in which an important labile iron subpool is thought to exist. In addition, we calculate that the fluorescent iron probe calcein would strip Fe(3+) from Ins(1,2,3)P(3) under cellular conditions, and hence labile iron detected using this probe may include iron bound to Ins(1,2,3)P(3). Therefore Ins(1,2,3)P(3) is the first viable proposal for a transit iron ligand.

Synergy of Intramolecular Hydrogen-Bonding Network in myo-Inositol 2-Monophosphate: Theoretical Investigations into the Electronic Structure, Proton Transfer, and pKa

This work demonstrates the pivotal role that an intramolecular hydrogen-bonding network (intra-HBN) plays in the determination of the conformation of myo-inositol 2-monophosphate (Ins(2)P1), a member of the inositol phosphate family of compounds, which are important participants in the role that phosphates play in biological and environmental chemistry. For biologically significant compounds that contain phosphate and hydroxyl groups, Ins(2)P1 is a model system for studying both the primary forces that determine their conformations and their chemical properties from the effect of phosphate group addition. We performed ab initio calculations to determine the intra-HBN within important thermally accessible conformations for neutral Ins(2)P1 and its anions, Ins(2)P1(1-) and Ins(2)P1(2-). The results show that the global minima prefer 1a/5e structures where the phosphate group is in the axial position with all -OH groups in the equatorial positions. The calculations of transition state structures for ring inversion at each ionization state predict an activation energy of 18.16 kcal/mol for the neutral species in water, while the activation energy is lower for the charged compounds, 15.62 kcal/mol for Ins(2)P1(1-) and 12.48 kcal/mol for Ins(2)P1(2-). The pK(a) values of Ins(2)P1 were calculated by modeling the solvent as a polarizable continuum medium (PCM) and as explicit solvent molecules. These values are in good agreement with experimental data. A novel four-center pattern of hydrogen bonding was found to stabilize the system. The intramolecular proton transfer across a low barrier hydrogen bond between the charged phosphate and hydroxyl groups was found to occur under standard conditions with an activation energy that is less than 0.5 kcal/mol.

Conformational and inframolecular studies of the protonation of adenophostin analogues lacking the adenine moiety

Four adenophostin analogues lacking the adenine moiety were subjected to 31P- and 1H-NMR titrations in order to determine the acid-base behaviour of the individual ionisable groups of the molecules and the complex interplay of intramolecular interactions resulting from the protonation process. For the two trisphosphorylated compounds, the curve pattern of the phosphorus nuclei corresponds to the superimposition of the titration curves of a monophosphorylated polyol and a polyol carrying two vicinal phosphates, suggesting that the two phosphate moieties behave independently. Also, the general shape of 1H-NMR titration curves of the studied compounds is very close to that of adenophostin A, indicating that the adenine moiety does not specifically interact with the phosphorylated sugar moieties. The curves show, however, that both trisphosphorylated compounds adopt slightly different preferential conformations which could contribute to explain the difference in their affinity for Ins(1,4,5)P3 receptor. Their macroscopic as well as the microscopic protonation constants are higher than those of adenophostin A, indicating that the adenine moiety plays a base-weakening effect on the phosphate groups. Further analysis of the microscopic protonation constants confirms that the compound whose conformation is the closest to that of adenophostin A also shows the highest biological activity. The two bisphosphorylated analogues studied behave very similarly, suggesting that the deletion of the hydroxymethyl group on the pentafuranosyl ring only weakly influences the protonation process of the phosphate groups that bear the glucopyranose moiety.