Project description:Recognition and binding of anions in water is difficult due to the ability of water molecules to form strong hydrogen bonds and to solvate the anions. The complexation of two different carboxylates with 1-(4-carbomethoxypyrrolidone)-terminated PAMAM dendrimers was studied in aqueous solution using NMR and ITC binding models. Sodium 2-naphthoate and sodium 3-hydroxy-2-naphthoate were chosen as carboxylate model compounds, since they carry structural similarities to many non-steroidal anti-inflammatory drugs and they possess only a limited number of functional groups, making them ideal to study the carboxylate-dendrimer interaction selectively. The binding stoichiometry for 3-hydroxy-2-naphthoate was found to be two strongly bound guest molecules per dendrimer and an additional 40 molecules with weak binding affinity. The NOESY NMR showed a clear binding correlation of sodium 3-hydroxy-2-naphthoate with the lyophilic dendrimer core, possibly with the two high affinity guest molecules. In comparison, sodium 2-naphthoate showed a weaker binding strength and had a stoichiometry of two guests per dendrimer with no additional weakly bound guests. This stronger dendrimer interaction with sodium 3-hydroxy-2-naphthoate is possibly a result of the additional interactions of the dendrimer with the extra hydroxyl group and an internal stabilization of the negative charge due to the hydroxyl group. These findings illustrate the potential of the G4 1-(4-carbomethoxy) pyrrolidone dendrimer to complex carboxylate guests in water and act as a possible carrier of such molecules.
Project description:Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.
Project description:Designing ligands that bind their target biomolecules with high affinity and specificity is a key step in small-molecule drug discovery, but accurately predicting protein-ligand binding free energies remains challenging. Key sources of errors in the calculations include inadequate sampling of conformational space, ambiguous protonation states, and errors in force fields. Noncovalent complexes between a host molecule with a binding cavity and a druglike guest molecule have emerged as powerful model systems. As model systems, host-guest complexes reduce many of the errors in more complex protein-ligand binding systems, as their small size greatly facilitates conformational sampling, and one can choose systems that avoid ambiguities in protonation states. These features, combined with their ease of experimental characterization, make host-guest systems ideal model systems to test and ultimately optimize force fields in the context of binding thermodynamics calculations. The Open Force Field Initiative aims to create a modern, open software infrastructure for automatically generating and assessing force fields using data sets. The first force field to arise out of this effort, named SMIRNOFF99Frosst, has approximately one tenth the number of parameters, in version 1.0.5, compared to typical general small molecule force fields, such as GAFF. Here, we evaluate the accuracy of this initial force field, using free energy calculations of 43 α and β-cyclodextrin host-guest pairs for which experimental thermodynamic data are available, and compare with matched calculations using two versions of GAFF. For all three force fields, we used TIP3P water and AM1-BCC charges. The calculations are performed using the attach-pull-release (APR) method as implemented in the open source package, pAPRika. For binding free energies, the root-mean-square error of the SMIRNOFF99Frosst calculations relative to experiment is 0.9 [0.7, 1.1] kcal/mol, while the corresponding results for GAFF 1.7 and GAFF 2.1 are 0.9 [0.7, 1.1] kcal/mol and 1.7 [1.5, 1.9] kcal/mol, respectively, with 95% confidence ranges in brackets. These results suggest that SMIRNOFF99Frosst performs competitively with existing small molecule force fields and is a parsimonious starting point for optimization.
Project description:Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.
Project description:When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in conventional free energy methods where the use of fixed protonation states is the norm. In the present paper, we apply a simple two-step approach to calculate the pH-dependent binding free energy of a model cucubit[7]uril host/guest system. By use of λ-dynamics with an enhanced sampling protocol, adaptive landscape flattening, pKa shifts and reference binding free energies upon complexation were determined. This information enables the construction of pH-dependent binding profiles that accurately capture the pKa shifts and reproduce binding free energies at the different pH conditions that were observed experimentally. Our calculations illustrate a general framework for computing pH-dependent binding free energies but also point to some issues in modeling the molecular charge distributions within this series of molecules with CGenFF. However, by introducing some minor charge modifications to the CGenFF force field, we saw significant improvement in accuracy of the calculated pKa shifts.
Project description:We show that H-bonded host-guest systems associate in ionic liquids (ILs), pure salts with melting point below room temperature, in which dipole-dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (Ka) obtained from titrations of four H-bonded host-guest systems in two organic solvents and two ionic liquids yield smaller yet comparable Ka values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy, which confirms that the binding is not solely due to (de)solvation processes. Our results indicate that classic H-bonded host-guest supramolecular chemistry takes place in ILs. This implies that strong H-bonds are only moderately affected by surroundings composed entirely of charges, which can be interpreted as an indication that the balance of Coulombic to covalent forces in strong H-bonds is not tipped towards the former.
Project description:A series of new self-buffering ionic liquids (ILs) based on Good's buffers (GBs) anions and the tetrabutylphosphonium cation ([P4444]+) was here synthesized and characterized. The self-buffering behaviour of the GB-ILs was confirmed by measuring their protonation constants by potentiometry. Further, their ability to form aqueous biphasic systems with the biodegradable potassium citrate salt was evaluated, and further investigated for the extraction of proteins, using bovine serum albumin (BSA) as a model protein. If these ionic structures display self-buffering characteristics as well as a low toxicity towards the luminescent bacteria Vibrio fischeri, they were additionally found to be highly effective in the formation of ABS and in the extraction of BSA - extraction efficiencies of 100% to the IL-rich phase obtained in a single-step. The BSA secondary structure in the aqueous IL-rich solutions was evaluated through infrared spectroscopic studies revealing the protein-friendly nature of the synthesized ILs. Dynamic light scattering (DLS), "COnductor-like Screening MOdel for Real Solvents" (COSMO-RS), and molecular docking studies were finally carried out to better understand the main driving forces of the extraction process. The results suggest that van der Waals and hydrogen-bonding interactions are important driving forces of the protein migration towards the GB-IL-rich phase, while the molecular docking investigations demonstrated a stabilizing effect of the studied ILs over the protein.
Project description:We systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.
Project description:Within the framework of designing new self-assembled metallosupramolecular architectures for drug delivery, seven [Pd2L4]4+ metallacages (L = 2,6-bis(pyridine-3-ylethynyl)pyridine) featuring different groups in exo-position, selected to enhance the cage solubility in aqueous environment, were synthesized. Thus, carboxylic acids, sugars, and PEG groups were tethered to the bispyridyl ligands directly or via disulfide bond formation, as well as via click chemistry. The ligands and respective cages were characterized by different methods, including NMR spectroscopy and high-resolution electrospray mass spectrometry (HR-ESI-MS). While the two ligands featuring carboxylic acid-functionalized groups showed improved solubility in water, the other ligands were soluble only in organic solvents. Unfortunately, all the respective self-assembled cages were also insoluble in water. Afterwards, the encapsulation properties of the anticancer drug cisplatin in selected [Pd2L4]X4 cages (X = NO3- , BF4- ) were studied by 1H, 1H DOSY, and 195Pt NMR spectroscopy. The effect of the counter ions as well as of the polarity of the solvent in the drug encapsulation process were also investigated, and provided useful information on the host-guest properties of these experimental drug delivery systems. Our results provide further experimental support for previous studies that suggest the desolvation of guests from surrounding solvent molecules and the resulting solvent rearrangement may actually be the primary driving force for determining guest binding affinities in metallacages, in the absence of specific functional group interactions.
Project description:The thermally activated delayed fluorescence (TADF) donor-acceptor (D-A) molecule, DMAC-TRZ, is used as a TADF emitter "probe" to distinguish the environmental effects of a range of solid-state host materials in guest-host systems. Using the guest's photophysical behavior in solution as a benchmark, a comprehensive study using a variety of typical TADF organic light-emitting diode hosts with different characteristics provides a clearer understanding of guest-host interactions and what affects emitter performance in solid state. We investigate which are the key host characteristics that directly affect charge-transfer (CT) state energy and singlet triplet energy gaps. Using time-resolved photoluminescence measurements, we use the CT state energy distribution obtained from the full width at half-maximum (fwhm) of the emission band and correlate this with other photophysical properties such as the apparent dynamic red shift of CT emission on-set to estimate the disorder-induced heterogeneity of D-A dihedral angles and singlet triplet gaps. Further, the delayed emission stabilization energy value and time-dependent CT band fwhm are shown to be related to a combination of host's rigidity, emitter molecule packing, and the energy difference between guest and host lowest energy triplet states. Concentration dependence studies show that emitter dimerization/aggregation can improve as well as reduce emission efficiency depending on the characteristics of the host. Two similar host materials, mCPCN and mCBPCN, with optimum host characteristics show completely different behaviors, and their hosting potential is extensively explored. We demonstrate that type I and type III TADF emitters behave differently in the same host and that the materials with intrinsic small ΔE ST have the smallest disorder-induced CT energy and reverse intersystem crossing rate dispersion. We also present an optimized method to define the actual triplet energy of a guest-host system, a crucial parameter in understanding the overall mechanism of the TADF efficiency of the system.