Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα

Covalent protein kinase inhibitors exploit currently noncatalytic cysteines in the adenosine 5′-triphosphate (ATP)-binding site via electrophiles directly appended to a reversible-inhibitor scaffold. Here, we delineate a path to target solvent-exposed cysteines at a distance >10 Å from an ATP-site-directed core module and produce potent covalent phosphoinositide 3-kinase α (PI3Kα) inhibitors. First, reactive warheads are used to reach out to Cys862 on PI3Kα, and second, enones are replaced with druglike warheads while linkers are optimized. The systematic investigation of intrinsic warhead reactivity (k_chem), rate of covalent bond formation and proximity (k_inact and reaction space volume V_r), and integration of structure data, kinetic and structural modeling, led to the guided identification of high-quality, covalent chemical probes. A novel stochastic approach provided direct access to the calculation of overall reaction rates as a function of k_chem, k_inact, K_i, and V_r, which was validated with compounds with varied linker lengths. X-ray crystallography, protein mass spectrometry (MS), and NanoBRET assays confirmed covalent bond formation of the acrylamide warhead and Cys862. In rat liver microsomes, compounds 19 and 22 outperformed the rapidly metabolized CNX-1351, the only known PI3Kα irreversible inhibitor. Washout experiments in cancer cell lines with mutated, constitutively activated PI3Kα showed a long-lasting inhibition of PI3Kα. In SKOV3 cells, compounds 19 and 22 revealed PI3Kβ-dependent signaling, which was sensitive to TGX221. Compounds 19 and 22 thus qualify as specific chemical probes to explore PI3Kα-selective signaling branches. The proposed approach is generally suited to develop covalent tools targeting distal, unexplored Cys residues in biologically active enzymes.

Replicates Number for Drug Stability Testing during Bioanalytical Method Validation-An Experimental and Retrospective Approach

Background: The stability of a drug or metabolites in biological matrices is an essential part of bioanalytical method validation, but the justification of its sample size (replicates number) is insufficient. The international guidelines differ in recommended sample size to study stability from no recommendation to at least three quality control samples. Testing of three samples may lead to results biased by a single outlier. We aimed to evaluate the optimal sample size for stability testing based on 90% confidence intervals. Methods: We conducted the experimental, retrospective (264 confidence intervals for the stability of nine drugs during regulatory bioanalytical method validation), and theoretical (mathematical) studies. We generated experimental stability data (40 confidence intervals) for two analytes—tramadol and its major metabolite (O-desmethyl-tramadol)—in two concentrations, two storage conditions, and in five sample sizes (n = 3, 4, 5, 6, or 8). Results: The 90% confidence intervals were wider for low than for high concentrations in 18 out of 20 cases. For n = 5 each stability test passed, and the width of the confidence intervals was below 20%. The results of the retrospective study and the theoretical analysis supported the experimental observations that five or six repetitions ensure that confidence intervals fall within 85–115% acceptance criteria. Conclusions: Five repetitions are optimal for the assessment of analyte stability. We hope to initiate discussion and stimulate further research on the sample size for stability testing.

Stochastic or Not? Method To Predict and Quantify the Stochastic Effects on the Association Reaction Equilibria in Nanoscopic Systems

The stochastic nature of chemical reaction and impact of the stochasticity on their evolution is soundly documented. Both theoretical predictions and emerging experimental evidence indicate the influence of stochastic effects on the equilibrium state of association reaction. In this work simple mathematical formulas are introduced to estimate these effects. First, the dependence of the ratio of observed reactants (apparent association constant, equivalent of macroscopic association constant in stochastic analysis) on the volume and the number of molecules of reagents is discussed and the limiting factors of this effect are shown. Next, the apparent association constant is approximated for nanoscale systems by closed-form formulas derived for this purpose. Finally, an estimation for the macroscopic constant value from the apparent one is provided and validated on the published experimental data. This work was inspired by chemical reactions occurring in biological compartments, but the results can be used for all systems belonging to the stochastic regime of chemical reactions.

Ternary Zn(II) Complexes of Fluorescent Zinc Probes Zinpyr-1 and Zinbo-5 with the Low Molecular Weight Component of Exchangeable Cellular Zinc Pool

The intracellular exchangeable Zn(II) is usually measured with synthetic fluorescent zinc sensors. 4',5'-Bis[bis(2-pyridylmethyl)aminomethyl]-2',7'-dichlorofluorescein (Zinpyr-1) is a sensor containing the fluorescein platform and a duplicated chelating unit. Its advantages include brightness and a relatively high affinity for Zn(II), K_d = 0.7 nM. 2-(4,5-Dimethoxy-2-hydroxyphenyl)-4-(2-pyridylmethyl)aminomethylbenzoxazole (Zinbo-5) is a member of a growing family of ratiometric synthetic Zn(II) probes, offering a possibility to determine Zn(II) concentration independently of the sensor concentration. Cells, however, contain high, millimolar or nearly millimolar concentrations of low molecular weight ligands (LMWLs) capable of binding Zn(II) ions. Previously, we demonstrated that such LMWLs can perturb the performance of some fluorescent zinc sensors by competition and formation of ternary Zn(sensor) (LMWL) complexes. Here we tested Zinpyr-1 and Zinbo-5 in this respect. Despite structural differences, both sensors formed such ternary complexes. We determined their stability constants ^CK_tern and performed numerical simulations of Zn(II) distributions at physiological concentrations of selected LMWLs. Glutamic acid was found to provide the strongest ternary complexes with either of the studied sensors. Zn(Zinpyr-1)(Glu) was an absolutely dominant Zn(II)/Zinpyr-1 species (more than 96% of the exchangeable Zn(II)), and Zn(Zinbo-5)(Glu) was the most abundant one (more than 40%) in these simulations. Our results indicate that under cellular conditions these sensors are able to report Zn(II) complexed to LMWLs rather than free Zn²⁺ ions. On the other hand, the specific affinity of Zn(Zinpyr-1) and Zn(Zinbo-5) for Glu creates interesting opportunities for determining glutamic acid in biological samples.

Ternary Zn(II) Complexes of FluoZin-3 and the Low Molecular Weight Component of the Exchangeable Cellular Zinc Pool

Knowledge of the nature of exchangeable (labile) intracellular Zn(II) is increasingly important for biomedical research. The detection and quantitative determination of Zn(II) ions is usually performed by using Zn(II)-specific fluorescent sensors, among which 2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) has been used most widely. Selectivity of this sensor for Zn(II) over other divalent cations was demonstrated, but possible interference in its performance by other compounds has not been investigated. Many potential low molecular weight ligands for Zn(II) ions (LMWLs) are abundant in the cell. In this study we demonstrate that FluoZin-3 is susceptible to competition for Zn(II) from LMWLs and also forms strong ternary complexes with some of them. We determined the set of conditional stability constants ^C K_tern for ternary Zn(FluoZin-3)(LMWL) complexes using fluorescence titrations and applied it to model the response of exchangeable zinc to FluoZin-3. We found that competition and formation of ternary complexes with LMWLs together strongly affect (net reduce) the Zn(FluoZin-3) fluorescence. This effect may cause a significant underestimation of exchangeable Zn(II). We also demonstrated a strong pH dependence of this effect. Reduced glutathione (GSH) emerged as the most important Zn(II) partner among the LMWLs, characterized with K_tern = 2.8 ± 0.2 × 10⁶ M^-1. Our experiments and calculations suggest that Zn(LMWL) complexes contribute to the exchangeable cellular zinc pool.

Numerical Simulations Reveal Randomness of Cu(II) Induced Aβ Peptide Dimerization under Conditions Present in Glutamatergic Synapses

The interactions between the Aβ1-40 molecules species and the copper ions (Cu(II)) were intensively investigated due to their potential role in the development of the Alzheimer Disease (AD). The rate and the mechanism of the Cu(II)-Aβ complexes formation determines the aggregation pathway of the Aβ species, starting from smaller but more cytotoxic oligomers and ending up in large Aβ plaques, being the main hallmark of the AD. In our study we exploit the existing knowledge on the Cu(II)-Aβ interactions and create the theoretical model of the initial phase of the copper- driven Aβ aggregation mechanism. The model is based on the direct solution of the Chemical Master Equations, which capture the inherent stochastics of the considered system. In our work we argue that due to a strong Cu(II) affinity to Aβ and temporal accessibility of the Cu(II) ions during normal synaptic activity the aggregation driven by Cu(II) dominates the pure Aβ aggregation. We also demonstrate the dependence of the formation of different Cu(II)-Aβ complexes on the concentrations of reagents and the synaptic activity. Our findings correspond to recent experimental results and give a sound hypothesis on the AD development mechanisms.

Revised stability constant, spectroscopic properties and binding mode of Zn(II) to FluoZin-3, the most common zinc probe in life sciences

2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) is used very broadly in life sciences as intra- and extracellular Zn(II) sensor selective for Zn(II) over Co(II), Ca(II) and Mg(II) ions at their physiological concentrations. It has been used for determination of relative and absolute levels of exchangeable Zn(II) in cells and extracellular fluids. Despite its popularity, the knowledge of its acid/base and Zn(II) coordination abilities and of its spectroscopic properties remained very limited. Also the published conditional dissociation constant ((C)Kd) values at pH7.4 are slightly discrepant, (15nM or 8.9nM). In this work we determined the (C)Kd for Zn(II) complexation by FluoZin-3 at pH7.4 with nitrilotriacetic acid (NTA) as competitor using two independent methods: fluorimetry and UV-Vis spectroscopy. For the first time, we investigated FluoZin-3 alone and complexed with Zn(II) in the wide range of pH, determining the total of eight pKa values from fluorescence spectra and from various regions of UV-Vis spectra. The validated values of (C)Kd (9.1±0.4nM; -log (C)Kd=8.04) and of the absolute (pH-independent) stability constant log βZnL (8.16±0.05) were provided by fluorescence spectroscopy experiments performed at 1μM concentrations. Our experiments demonstrated that both of aminocarboxylate moieties of FluoZin-3 bind the Zn(II) ion synergistically.

On the ability of CuAβ1-x peptides to form ternary complexes: Neurotransmitter glutamate is a competitor while not a ternary partner

In the light of conflicting reports on the ability of copper(II) complexes of amyloid beta (Aβ) peptides to form ternary complexes with small molecules co-present in the biological milieu, we performed a study of coordination equilibria in the system containing Cu(II) ions, the Aβ1-16 peptide, glutamic acid and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid, HEPES) buffer. Using potentiometry, isothermal titration calorimetry (ITC), UV-visible spectroscopy and EPR, we concluded that glutamic acid was not able to form such a ternary complex, but can efficiently compete for the Cu(II) ion with the Aβ peptide at Glu concentrations relevant for the synaptic cleft. We also found that the literature constants for Cu(II) complexes with Glu were overestimated, but this effect was partially compensated by the formation of a ternary Cu(Glu)(HEPES) complex. Our results indicate that small molecules co-present with Cu(II) ions and Aβ peptides in the synaptic cleft are not very likely to enhance Cu(II)/Aβ interactions, but instead should be considered as a Cu(II) buffering system that may help prevent these interactions and participate in Cu(II) clearance from the synaptic cleft.

Unbound position II in MXCXXC metallochaperone model peptides impacts metal binding mode and reactivity: Distinct similarities to whole proteins

The effect of position II in the binding sequence of copper metallochaperones, which varies between Thr and His, was investigated through structural analysis and affinity and oxidation kinetic studies of model peptides. A first Cys-Cu(I)-Cys model obtained for the His peptide at acidic and neutral pH, correlated with higher affinity and more rapid oxidation of its complex; in contrast, the Thr peptide with the Cys-Cu(I)-Met coordination under neutral conditions demonstrated weaker and pH dependent binding. Studies with human antioxidant protein 1 (Atox1) and three of its mutants where S residues were replaced with Ala suggested that (a) the binding affinity is influenced more by the binding sequence than by the protein fold (b) pH may play a role in binding reactivity, and (c) mutating the Met impacted the affinity and oxidation rate more drastically than did mutating one of the Cys, supporting its important role in protein function. Position II thus plays a dominant role in metal binding and transport.

Selenocysteine containing analogues of Atx1-based peptides protect cells from copper ion toxicity

Seleno-substituted model peptides of copper metallochaperone proteins display particularly high Cu(i) affinity andin vitroanti-oxidative reactivity.

Human annexins A1, A2, and A8 as potential molecular targets for Ni(II) ions

Nickel is harmful for humans, but molecular mechanisms of its toxicity are far from being fully elucidated. One of such mechanisms may be associated with the Ni(II)-dependent peptide bond hydrolysis, which occurs before Ser/Thr in Ser/Thr-Xaa-His sequences. Human annexins A1, A2, and A8, proteins modulating the immune system, contain several such sequences. To test if these proteins are potential molecular targets for nickel toxicity we characterized the binding of Ni(II) ions and hydrolysis of peptides Ac-KALTGHLEE-am (A1-1), Ac-TKYSKHDMN-am (A1-2), and Ac-GVGTRHKAL-am (A1-3), from annexin A1, Ac-KMSTVHEIL-am (A2-1) and Ac-SALSGHLET-am (A2-2), from annexin A2, and Ac-VKSSSHFNP-am (A8-1), from annexin A8, using UV-vis and circular dichroism (CD) spectroscopies, potentiometry, isothermal titration calorimetry, high-performance liquid chromatography (HPLC), and electrospray ionization mass spectrometry (ESI-MS). We found that at physiological conditions (pH 7.4 and 37 °C) peptides A1-2, A1-3, A8-1, and to some extent A2-2 bind Ni(II) ions sufficiently strongly in 4N complexes and are hydrolyzed at sufficiently high rates to justify the notion that these annexins can undergo nickel hydrolysis in vivo. These results are discussed in the context of specific biochemical interactions of respective proteins. Our results also expand the knowledge about Ni(II) binding to histidine peptides by determination of thermodynamic parameters of this process and spectroscopic characterization of 3N complexes. Altogether, our results indicate that human annexins A1, A2, and A8 are potential molecular targets for nickel toxicity and help design appropriate cellular studies.

cis-Urocanic acid as a potential nickel(ii) binding molecule in the human skin

cis-Urocanic acid, a component of human skin, is an efficient ligand for allergenic Ni²⁺ ions, forming high spin complexes.