Binding Enthalpy Research Articles

Density functional theoretical analysis of micro-adsorption of isotopes of hydrogen molecule and atom by uranium

Tritium, the heaviest among hydrogen isotopes can be safely stored as metal hydride (tritide). The (depleted) uranium metal is being considered in international thermonuclear experimental reactor (ITER) because of its compatible physicochemical properties. The fundamental understanding of U–H isotopes interaction will help in the efficient storage of H isotopes in depleted uranium metal. Hence, density functional theoretical (DFT) analysis has been performed to investigate the micro-adsorption of hydrogen and its isotopic molecules on uranium atom. The geometrical configurations of UXn, U (X2)n and UX4-(X2)n (X = H, D, T; n = 1–9) cluster were analyzed using different DFT functional (PBE, PBEO, M06 and M06-2X). In the case of U-(H2)4 and U-(H2)5, one H2 molecule was seen to be dissociated to give UH2(H2)3 and UH2(H2)4 cluster as observed earlier in the experiment. The formation of U (X2)n and UX4-(X2)n microclusters was explained by calculating binding enthalpy, natural population analysis and electron density at the bond critical points (BCP). Further, more insights were derived by computing the type of interactions between U and H2 isotopic molecules. The Kubas interaction of a U atom with a H2 molecule was identified by an elongation of the H–H bond without breakage and a reduction in its stretching frequency due to binding. The interaction of U and H2 isotopic molecules was confirmed to be Kubas type of interaction whose strength lies in between the covalent bond of metal hydrides and the van der Waals bond of materials. Further, σ-donation from H2 to d and f orbitals of U atom and π-back-donation from U to the anti-bonding orbital of H2, and atoms-in-molecules analysis indicates that the electron density at the bond critical points of the bound H2 is similar to that of Kubas systems. The Kubas type of interaction suggests that the reversible adsorption of hydrogen molecules might be favored with U metal. From structural and binding enthalpy (BE) analysis, UH4-(H2)8 polyhydride was predicted to be the largest super polyhydride and found to be stable by 8.2 kcal/mol over UH4-(H2)6 polyhydride and thus confirmed its plausibility. To the best of our knowledge UH4-(H2)8 is the largest metal polyhydride ever been reported with twenty hydrogen atoms displaying high gravimetric density of 7.80, 14.47 and 20.21 wt% for H2, D2 and T2 respectively. The present DFT results thus draw further attention for more computational and experimental studies in this important uranium-hydrogen system for efficient reuse of depleted uranium metal as tritium storage material.

Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor’s keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.

Novel Inhibitors of 2′-O-Methyltransferase of the SARS-CoV-2 Coronavirus

The COVID-19 pandemic is still affecting many people worldwide and causing a heavy burden to global health. To eliminate the disease, SARS-CoV-2, the virus responsible for the pandemic, can be targeted in several ways. One of them is to inhibit the 2′-O-methyltransferase (nsp16) enzyme that is crucial for effective translation of viral RNA and virus replication. For methylation of substrates, nsp16 utilizes S-adenosyl methionine (SAM). Binding of a small molecule in the protein site where SAM binds can disrupt the synthesis of viral proteins and, as a result, the replication of the virus. Here, we performed high-throughput docking into the SAM-binding site of nsp16 for almost 40 thousand structures, prepared for compounds from three libraries: Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library. For the top scoring ligands, semi-empirical quantum-chemical calculations were performed, to better estimate protein–ligand binding enthalpy. Relying upon the calculated binding energies and predicted docking poses, we selected 21 compounds for experimental testing.

Computational design of stapled peptide inhibitor against SARS-CoV-2 receptor binding domain.

Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic‐based treatment for COVID‐19. The gateway of the virus to the host cell is mediated by the binding of the receptor binding domain (RBD) of the virus spike protein to the angiotensin‐converting enzyme 2 (ACE2) of the human cell. Therefore, the RBD of SARS‐CoV‐2 can be used as a target to design therapeutics. The α1 helix of ACE2, which forms direct contact with the RBD surface, has been used as a template in the current study to design stapled peptide therapeutics. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD‐ACE2 binding. Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD‐ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result higher binding affinity. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS‐CoV‐2.

An assessment of density functionals for predicting CO2 adsorption in diamine-functionalized metal-organic frameworks.

Diamine-functionalized M2(dobpdc) (M = Mg, Mn, Fe, Co, Zn) metal-organic frameworks (MOFs) are among a growing class of crystalline solids currently being intensively investigated for carbon capture as they exhibit a novel cooperative and selective CO2 adsorption mechanism and a step-shaped isotherm. To understand their CO2 adsorption behavior, ab initio calculations with near-chemical accuracy (∼6 kJ/mol, an average experimental error) are required. Here, we present density functional theory (DFT) calculations of CO2 adsorption in m-2-m-Zn2(dobpdc) (m-2-m = N,N'-dimethylethyle-nediamine and dobpdc4- = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate) with different exchange-correlation functionals, including semilocal functionals [Perdew-Burke-Ernzerhof (PBE) and two revised PBE functionals], semiempirical pairwise corrections (D3 and Tkatchenko-Scheffler), nonlocal van der Waals (vdW) correlation functionals-vdW-optB88 (or vdW-DF-optB88), vdW-DF1, vdW-DF2, vdW-DF2-B86R (or rev-vdW-DF2), vdW-DF-cx (and vdW-DF-cx0), and revised VV10-and the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (GGA). Overall, we find that revPBE+D3 and RPBE+D3 show the best balance of performance for both the lattice parameters and the CO2 binding enthalpy of m-2-m-Zn2(dobpdc). revPBE+D3 and RPBE+D3 predict the m-2-m-Zn2(dobpdc) lattice parameters to within 1.4% of experiment and predict CO2 binding enthalpies of -68 kJ/mol, which compare reasonably well with the experiment (-57 kJ/mol). Although PBE (-57.7 kJ/mol), vdW-DF1 (-49.6 kJ/mol), and vdW-DF2 (-44.3 kJ/mol) are also found to predict the CO2 binding enthalpy with good accuracy, they overestimate lattice parameters and bond lengths. The other functionals considered predict the lattice parameters with the same accuracy as revPBE+D3 and RPBE+D3, but they overbind CO2 by around 26-50 kJ/mol. We find that the superior performance of revPBE+D3 and RPBE+D3 is sustained for the formation enthalpy and the lattice parameters of ammonium carbamate, a primary product of the cooperative CO2 insertion in diamine-functionalized M2(dobpdc) MOFs. Moreover, we find that their performance is derived from their larger repulsive exchange contributions to the CO2 binding enthalpy than the other functionals at the relevant range of the reduced density gradient value for the energetics of CO2 adsorption in the m-2-m-Zn2(dobpdc) MOF. A broader examination of the performance of RPBE+D3 for the structural parameters and CO2 binding enthalpies of 13 diamine-functionalized Mg2(dobpdc) MOFs further demonstrates that RPBE+D3 successfully reproduces experimental CO2 binding enthalpies and reveals a logarithmic relationship between the step pressure and the CO2 binding enthalpy of the diamine-functionalized Mg2(dobpdc) MOFs, consistent with experiments where available. The results of our benchmarking study can help guide the further development of versatile vdW-corrected DFT methods with predictive accuracy.

Supercomputer Search for the New Inhibitors of the Coagulation Factor XIIa

A virtual structure-oriented screening of candidates for inhibitors of blood coagulation factor XIIa was carried out. This coagulation factor is one of the most promising therapeutic targets for the development of anticoagulants without disturbing normal hemostasis. The screening was carried out in the database of organic compounds of the Voronezh State University, consisting of more than 19 thousand molecules. At the first stage of virtual screening, ligands were positioned in the active center of factor XIIa using the SOL docking program. At the second stage, for the best ligands, the protein-ligand binding enthalpy was calculated using the MOPAC program and the PM7 quantum-chemical method, taking into account the solvent in the COSMO continuum model. All calculations were carried out using the supercomputing resources at Lomonosov Moscow State University. In total, more than 30 thousand ligand conformers are docked, and for more than 400 of the best of them, the protein-ligand binding enthalpy was calculated. 16 compounds are selected as the most promising candidates for subsequent in vitro testing of their ability to inhibit factor XIIa.

Gutmann's Donor and Acceptor Numbers for Ionic Liquids and Deep Eutectic Solvents.

An experimental and computational methodology for the analysis of the Lewis acid/base responses of ionic liquids (ILs) and deep eutectic solvents (DES) is proposed. It is based on the donor and acceptor of the electronic charge ability of Lewis acid and bases concepts (donicity and acceptor numbers, DN and AN, respectively) proposed by Viktor Gutmann. The binding enthalpy between the IL/DES with the probe antimony pentachloride (SbCl5) in dichloroethane displays good correlations with experimental data. This approach could serve as a first approximation to predict the responses to H-bonding abilities of new IL or DES. Although useful, the problems encountered to model the electron AN of these solvents limit the usefulness of the approach to completely describe their polarity properties. The experimental data were recorded using UV–Vis spectroscopy for a wide range of ILs and a couple of DES. Two reactions were used as benchmarks to test the reliability of the DN model to discuss the reactivity of real systems in these neoteric solvents.

Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants

SARS-CoV-2 virus is the cause of COVID-19 pandemic and belongs to RNA viruses, showing great tendency to mutate. Several dozens of mutations have been observed on the SARS-CoV-2 virus, during the last two years. Some of the mutated strains show a greater infectivity and are capable of suppressing the earlier strains, through interference. In this work, kinetic and thermodynamic properties were calculated for strains characterized by various numbers and locations of mutations. It was shown that mutations lead to changes in chemical composition, thermodynamic properties and infectivity. Through competition, the phenomenon of interference of various SARS-CoV-2 strains was explained, which results in suppression of the wild type by mutant strains. Standard Gibbs energy of binding and binding constant for the Omicron (B.1.1.529) strain were found to be ΔBG⁰ = −45.96 kJ/mol and KB = 1.13 ∙ 10+8 M−1, respectively.

Investigation of the Molecular Details of the Interactions of Selenoglycosides and Human Galectin-3.

Human galectin-3 (hGal-3) is involved in a variety of biological processes and is implicated in wide range of diseases. As a result, targeting hGal-3 for clinical applications has become an intense area of research. As a step towards the development of novel hGal-3 inhibitors, we describe a study of the binding of two Se-containing hGal-3 inhibitors, specifically that of di(β-D-galactopyranosyl)selenide (SeDG), in which two galactose rings are linked by one Se atom and a di(β-D-galactopyranosyl)diselenide (DSeDG) analogue with a diseleno bond between the two sugar units. The binding affinities of these derivatives to hGal-3 were determined by 15N-1H HSQC NMR spectroscopy and fluorescence anisotropy titrations in solution, indicating a slight decrease in the strength of interaction for SeDG compared to thiodigalactoside (TDG), a well-known inhibitor of hGal-3, while DSeDG displayed a much weaker interaction strength. NMR and FA measurements showed that both seleno derivatives bind to the canonical S face site of hGal-3 and stack against the conserved W181 residue also confirmed by X-ray crystallography, revealing canonical properties of the interaction. The interaction with DSeDG revealed two distinct binding modes in the crystal structure which are in fast exchange on the NMR time scale in solution, explaining a weaker interaction with hGal-3 than SeDG. Using molecular dynamics simulations, we have found that energetic contributions to the binding enthalpies mainly differ in the electrostatic interactions and in polar solvation terms and are responsible for weaker binding of DSeDG compared to SeDG. Selenium-containing carbohydrate inhibitors of hGal-3 showing canonical binding modes offer the potential of becoming novel hydrolytically stable scaffolds for a new class of hGal-3 inhibitors.

Temperature effects on calcium binding to caseins

The kinetics of binding of calcium ions in molar excess to individual caseins and casein ingredients was studied in pH 6.4 aqueous solutions using stopped-flow absorption spectroscopy. An initial second-order reaction, faster for β-casein than for αs-casein due to lower energy of activation (ΔEa1,β = 8.2 kJ∙mol−1; ΔEa1,α = 18.1 kJ∙mol−1, respectively), is followed by a slower first-order reaction with similar energies of activation (ΔEa2,β = 25.3 kJ∙mol−1 and ΔEa2,α = 20.7 kJ∙mol−1) as determined from temperature dependence of rate between 25 °C and 50 °C. Sodium caseinate reacts faster with calcium than both αs-casein and β-casein in the first reaction of the two consecutive reactions, while the rate of the second falls between αs-casein and β-casein. Global spectral analysis showed the UV–visible spectra of the reaction intermediates of the caseins to be more similar to the final products than to the initial casein reactants. Dynamic and static light scattering indicated decreasing particle sizes and increasing particle surface upon calcium-binding most significantly at low temperatures. The calcium binding to casein was found endothermic by isothermal titration calorimetry. Calcium binding seems to be controlled by enthalpy/entropy compensation corresponding to an isoequilibrium temperature of 38 °C in agreement with binding of calcium to o-phosphoserine rather than to aspartate or glutamate side chains of the caseins. Binding capacity and affinity for calcium to αs-casein and sodium caseinate both increased with increasing temperature in agreement with the endothermic nature of the binding. Decreasing enthalpy of binding for each calcium indicating a decrease in heat capacity of the caseins upon calcium-binding. The small difference between binding enthalpy and energy of activation for association of calcium to αs-casein lead to the conclusion that calcium dissociation goes through an early transition state. The rate of calcium dissociation hardly depends on temperature also explaining why calcium binding to caseins is important for calcium bioaccessibility.

Binding studies of dopamine HCl drug with the mixed {sodium bis(2-ethylhexyl) sulfosuccinate + sodium dodecylsulfate} micelles: Physicochemical, spectroscopic, calorimetric and computational approach

Taking into consideration the importance of dopamine HCl as neurotransmitter in controlling central nervous system activities, the studies of binding interactions of dopamine HCl drug with micellar system (imitator of biomembranes) have been conducted by utilizing experimental as well as computational techniques. The systematic knowledge of physicochemical, spectroscopic and calorimetric properties is helpful to understand the physiological actions of biologically active additives in the living organisms. Therefore, mixed aggregation behavior of sodium bis(2-ethylhexyl) sulfosuccinate, AOT and sodium dodecylsulfate, SDS has been explored at diverse mole fractions of AOT, αAOT = 0.25, 0.39 and 0.50 in (1, 2 and 3) × 10−3 mol kg−1 dopamine HCl(aq) solutions by employing different techniques. From conductivity studies, the thermodynamic parameters (∆G°m, ∆H°m and ∆S°m), the molecular interaction parameter (βint) and the excess Gibbs free energy of micellization (∆Gmex) were ascertained at T = (298.15, 308.15, and 318.15) K. Isentropic compressibility (κs), partial specific volume (φv) and partial specific isentropic compressibility (φκ) parameters were computed from the density and sound velocity studies. Binding constant (Kb) and standard Gibbs free energy of binding (∆Gbο) have been evaluated from UV–visible absorption studies for dopamine HCl(aq) solutions at all the studied mole fractions of surfactant mixtures. Through dynamic light scattering (DLS) measurements, the hydrodynamic diameters (Dh) of mixed micellar aggregates have been acquired. Isothermal titration calorimetric (ITC) studies were executed to obtain the values of partitioning constant / binding constant (K), standard molar enthalpy of binding (ΔrHᴼ), standard molar entropy of binding (ΔrSᴼ), and stoichiometry of partitioning / binding (n) of drug with micellar system. Through density functional theory (DFT) calculations, the band gap between HOMO and LUMO for the dopamine-HCl bound mixed micelle system, and interactive features have been obtained. Aforementioned studies favor the supremacy of hydrophilic-hydrophilic / ionic and electrostatic interactions causing the binding among the hydrophilic / ionic groups of dopamine HCl (−OH, H+, Cl−), AOT (–SO3−, –OCO, Na+), and SDS (–OSO3−, Na+).

Supramolecular co-encapsulation of a photosensitizer and chemotherapeutic drug in cucurbit[8]uril for potential chemophototherapy.

Supramolecular strategies as well as combinatorial approaches have been proposed to improve cancer therapeutics. In this work, we investigated the encapsulation of the photosensitizer acridine orange (AO) and the chemotherapeutic drug oxaliplatin (OxPt) in cucurbit[8]uril (CB[8]), and tested their effect both separate and combined on tumoral cells cultivated in vitro. Binding constants and enthalpies of reaction for the AO@CB[8], (AO)2@CB[8] and OxPt@CB[8] complexes were determined by isothermal titration calorimetry. In the case of AO, a negative cooperativity for the binding of the second AO molecule was found, in agreement with previous fluorescence titration data. We show herein that the AO@CB[8] complex was effectively incorporated within the cells and showed important phototoxicity, while the OxPt@CB[8] complex was cytotoxic only at long incubation times (24h). Pre-treatment of the cells with the OxPt@CB[8] complex for 24h inhibited any photodynamic action by the later treatment with the AO@CB[8] complex. However, when both complexes were co-incubated for 90min, the combined cytotoxicity/phototoxicity was superior to any of the treatments individually. A cooperative effect was identified that added up to an extra 30% cytotoxicity/phototoxicity. The results point to an interesting system where a photosensitizer and chemotherapeutic drug are co-encapsulated in a macrocycle to develop chemophototherapy applications.

Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method.

For gaining insights into interactions in periodic systems, an analysis is developed based on the fragment molecular orbital method combined with periodic boundary conditions. The adsorption energy is decomposed into guest and surface polarization and deformation energy, guest-surface and guest-guest interactions, and the vibrational free energy. The analysis is applied to the adsorption of guest molecules to Ih (001) ice surface. The cooperativity effects result in a non-linear change in the adsorption energy with coverage due to many-body effects. The role of dispersion is found to be dominant for guests with long hydrophobic tails. A rule is proposed relating the length of the alkyl tail with the formation of the guest layer. The computed binding enthalpies are in good agreement with experimental values. For high coverage, adsorbed molecules can form an ordered layer known as self-assembled monolayer.

Calmodulin binding to the dehydrogenase domain of NADPH oxidase 5 alters its oligomeric state

Superoxide generated by NADPH Oxidase 5 (Nox5) is regulated by Ca2+ through the interaction of its self-contained Ca2+ binding domain and dehydrogenase domain (DH). Recently, calmodulin (CaM) has been reported to enhance the Ca2+ sensitivity of Nox5 by binding to the CaM-binding domain sequence (CMBD), in which the interaction between CaM and Nox5 is largely unclear. Here, we used the CMBD peptide and truncated DH constructs, and separately studied their interaction with CaM by fluorescence, calorimetry, and dynamic light scattering. Our results revealed that each half-domain of CaM binds one CMBD peptide with a binding constant near 106 M-1 and a binding enthalpy change of −3.81 kcal/mol, consistent with an extended 1:2 CaM:CMBD structure. However, the recombinant truncated DH proteins exist as oligomers, possibly trimer and tetramer. The oligomeric states are concentration and salt dependent. CaM binding appears to stabilize the DH dimer complexed with CaM. The thermodynamics of CaM binding to the DH is comparable to the peptide-based study except that the near unity binding stoichiometry and a large conformational change were observed. Our result suggests that the oligomeric states of Nox5, mediated by its DH domain and CaM, may be important for its superoxide-generating activity.

Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations.

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Site-selective covalently immobilized alpha 1A adrenergic receptor for thermodynamic and extra-thermodynamic study of four ligands binding to the receptor by chromatographic methods

Immobilized G protein-coupled receptor is a versatile tool to study ligand-receptor interactions. In this work, we synthesized the immobilized alpha 1A adrenergic receptor (α1A-AR), a GPCR subtype mediating smooth muscle contraction, through a site-selective covalent method that relies on the reaction between haloalkane dehalogenase tagged α1A-AR and macroporous silica gel coated with 6-chlorohexanoic acid. To investigate thermodynamic and extra-thermodynamic parameters for ligand binding, we utilized the covalently immobilized receptor as stationary phase to perform frontal analysis and injection-amount dependent analysis as well as compared with the random immobilization method. Terazosin gave the association constant of 1.48 × 105 M−1 to α1A-AR, indicating that the oriented immobilization of α1A-AR enhances the ligand-binding activity by one order of magnitude in comparison with the random immobilization method (7.9 × 104 M−1). The binding of phentolamine and tamsulosin to the receptor was accompanied by a large absolute heat capacity (ΔCp) of 1.28 ± 0.23 kJ mol−1, demonstrating that the binding enthalpy and entropy appear to compensate for one another. These results indicated that the covalent immobilization of the receptor onto solid support has a profound impact on the ligand-binding activity of the receptor and the determination of ligand-receptor binding parameters. The receptor immobilized through the site-selective method will act as a benchmark for chromatographic determination of binding parameters in ligand-receptor interactions and can be used as an effective approach for rapid analysis of drug-protein interactions with high accuracy.

Mechanism of Mucin Recognition by Lectins: A Thermodynamic Study.

Isothermal titration microcalorimetry (ITC) can directly determine the thermodynamic binding parameters of biological molecules including affinity constant, binding stoichiometry, heat of binding (enthalpy) and indirectly the entropy, and free energy of binding. ITC has been extensively used to study the binding of lectins to mono- and oligosaccharides, but limitedly in applications to lectin-glycoprotein interactions. Inherent experimental challenges to ITC include sample precipitation during the experiment and relative high amount of sample required, but careful design of experiments can minimize these problems and allow valuable information to be obtained. For example, the thermodynamics of binding of lectins to multivalent globular and linear glycoproteins (mucins) have been described. The results are consistent with a dynamic binding mechanism in which lectins bind and jump from carbohydrate to carbohydrate epitope in these molecules leading to increased affinity. Importantly, the mechanism of binding of lectins to mucins appears similar to that for a variety of protein ligands binding to DNA. Recent results also show that high-affinity lectin-mucin cross-linking interactions are driven by favorable entropy of binding that is associated with the bind and jump mechanism. The results suggest that the binding of ligands to biopolymers, in general, may involve a common mechanism that involves enhanced entropic effects that facilitate binding interactions.

A (partial) resolution of binding enthalpy discrepancies in ITC studies of Ba2+ crown ether complexation: The importance of calibration

By conducting binding experiments at a range of temperatures T using isothermal titration calorimetry (ITC), one can obtain two estimates of the binding enthalpy — calorimetric (ΔH°cal) from the experiments at each T, and van't Hoff (ΔH°vH) from the T dependence of the binding constant K°. From thermodynamics it is clear that these two must be identical, but early efforts to demonstrate this for ITC data indicated significant inconsistency. In an extensive 2004 study of the Ba2+ + 18-crown-6 ether complexation used in prior comparisons, Mizoue and Tellinghuisen found modest (10–20%) but statistically significant differences, which were tentatively attributed to problems converting the calorimetric estimates to their standard state values, as implied by the superscript ° in the notation. In the present work the 2004 results are reanalyzed using results obtained since then from temperature, heat, and volume calibration of the instrument and a better determination of the data variance function required for the weighted least-squares fitting of the data. The new results show consistency for temperatures 5–30 °C but persistent statistically significant differences from 35 to 46 °C. Several possible explanations for the remaining discrepancies are examined, with methods that include fitting the K and ΔHcal data together.

The complexation of levofloxacin hemihydrate with divalent metal ions in aqueous medium at variable temperatures: Combined UV–Visible spectroscopic and DFT studies

Herein, we have studied the binding of levofloxacin hemihydrate (LFH) drug with different metal ions e.g., alkali earth metal ions and transition metal ions through spectrophotometry and Density Function Theory (DFT) studies. The binding constant (Kf) of LFH with alkali earth metal ions was observed to be increased with the boost of temperature while the opposite trend was observed in the case of transition metal ions. The Kf values were experienced to be reduced with the increase of size of the alkali earth metal ions. The Kf values in case of transition metal follow the order Cu2+ > Ni2+ > Co2+ > Zn2+. The Gibbs free energy (ΔG0) of binding values reveal that binding phenomena are spontaneous in nature. The values of enthalpy (ΔH0) and entropy (ΔS0) of binding suggest that hydrophobic interactions are the key forces for the binding of LFH and alkali earth metal ions while electrostatic, dipole-dipole, ion-dipole, and hydrogen bonding are the key forces in case of transition metal ions. The enthalpy-entropy compensation parameters were also estimated and explained in detail. From the DFT study, the bond lengths, bond angles, HOMO and LUMO orbitals energy, band gap, hardness, and the highest wavelengths of the drug/ drug-metal complexes have been calculated and explained with appropriate reasoning.

Thermodynamic study of pH and sodium chloride impact on gemcitabine binding to cucurbit[7]uril in aqueous solutions

In solutions of pH < 5, cucurbit[7]uril (Q[7]) spontaneously includes a molecule of the anticancer drug gemcitabine within its cavity, forming a supramolecular complex. The results of ITC calorimetric studies of the gemcitabine cation (Gem) complexation with the Q[7] macrocycle in 20 mM aqueous HCOOH–HCOONa buffer mixtures with pH ranging from 5 to 2, indicate that the acidification of the solution facilitates binding of the drug by cucurbit[7]uril. In mixtures with a fixed pH = 4 and an increasing concentration of sodium chloride (10–4000 mM), the binding constant of Gem by Q[7] decreases rapidly, as is the absolute value of the binding enthalpy. This phenomenon illustrates the hindering effect of the association of sodium cations with Q[7] portals on gemcitabine binding, which is confirmed by ESI MS measurements. However, gemcitabine is still efficiently bound by cucurbit[7]uril (logK≥3) in aqueous 10 – 250 mM sodium chloride solutions. The Q[7] macrocycle may therefore be used as a stabilizing agent for this drug in pharmaceutical formulations.