X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno‐oncology.     

Free Energy Peturbation and Molecular Dynamics Simulation Studies on the Enantiomeric Discrimination of Amines by Dimethyldiketopyridino-18-Crown-6

Abstract

Discrimination of chiral amines by dimethyldiketopyridino-18-crown-6 (1) is studied by free energy peturbation (FEP) and molecular dynamics (MD) methods. 1 has two (S)-chiral centers and discriminates chiral amines through host-guest interactions. The optically active amines in this study are α-(1-naphthyl)ethylamine, methylbenzylamine, cyclohexylethylamine, and sec-butylamine. The trends in binding free energy differences obtained from FEP calculations were in excellent agreement with experimental results obtained in the gas phase. In order to explain the enantioselectivity of the host in terms of the host-guest interactions at the molecular level, we analyzed the structures generated by 10-ns MD simulations of host-guest complexes. The suggested chiral discrimination mechanism, the π-π interaction and the steric repulsion between the guest and the host, was verified by our MD simulation analysis.     

Spectroscopic and thermal degradation studies of polystyrene grafting onto poly(tetrafluoroethylene-co-hexafluoropropylene) films via electron-beam irradiation

Styrene monomers were grafted onto poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP) films by E-beam irradiation, controlling the degree of grafting by varying the radiation dose. In addition, polystyrene sulfonic acid (PSS) grafted FEP films were prepared by treating the polystyrene (PS) grafted FEP films with chlorosulfonic acid. The chemical mechanism of grafting, the substitution positions of the sulfonic acid, and the thermal degradation behaviors of the PS-grafted and PSS-grafted FEP films were investigated using FTIR-ATR spectroscopy, Raman Spectroscopy and TGA. Our results indicated that PS graft formation involved the removal of HF after C–C main chain scission, leading to the formation of an unsaturated structure. When heated, the PS-grafted FEP films underwent two-step thermal degradation, independent of the degree of grafting. The two degradation steps were assigned to the degradation of the PS grafts and the FEP matrix. Sulfonation of the PS-grafted FEP films was found to give rise to para-disubstituted sulfonic acid groups. The PSS-grafted FEP films were found to undergo a three-step thermal degradation, independent of the degree of sulfonation. The three degradation steps were assigned to removal of water molecules hydrogen bonded to the sulfonic acid groups, and the degradation of the PSS grafts and FEP matrix.     

Effect of the initial matrix material on the structure of radiation‐grafted ion‐exchange membranes: Wide‐angle and small‐angle X‐ray scattering studies

Seven different fluoropolymer films were used as matrix materials for radiation‐grafted ion‐exchange membranes. The crystallinity and preferred orientation of these membranes were studied with wide‐angle X‐ray scattering, and the lamellar structure of the membranes was examined with small‐angle X‐ray scattering. The crystallinity of poly(vinylidene fluoride) (PVDF)‐based matrix materials varied between 57 and 40%, and the crystallinity of the sulfonated samples varied between 34 and 23%. The lamellar periods of PVDF‐based matrix materials were about 115 Å, and the lamellar periods of poly(ethylene‐alt‐tetrafluoroethylene) and poly(tetrafluoroethylene‐co‐hexafluoropropylene) were 250 and 212 Å, respectively. When the samples were grafted, the lamellar periods increased. Correlation function analysis showed very clearly that the long‐range order decreased because of grafting and sulfonation processes. For those samples that showed good proton conductivity, the lamellar period also increased because of sulfonation. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1539–1555, 2002     

Thermal imidization of poly(pyromellitic dianhydride-4,4′-oxydianiline) precursors on fluoropolymers modified by surface graft-copolymerization with glycidyl methacrylate

Composite films of polyimide (PI) and poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP) or of PI and poly(tetrafluoroethylene) (PTFE) were prepared by thermal imidization of the poly(amic acid) (PAA) precursors of poly(pyromellitic dianhydride-4,4′-oxydianiline) (PMPA-ODA) on glycidyl methacrylate (GMA) graft-copolymerized FEP and PTFE films. The resulting PI/GMA-g-FEP and PI/GMA-g-PTFE composites exhibited T-peel adhesion strength of approximately 7.0 and 6.5 N/cm, respectively, compared to negligible adhesion strength for the laminates prepared from thermal imidization of the PAA on the pristine and the Ar plasma-treated FEP and PTFE films. X-ray photoelectron spectroscopy (XPS) results revealed that both the PI/GMA-g-FEP and PI/FEP-g-PTFE composite films delaminated by cohesive failure inside the FEP and PTFE films, respectively. The so-delaminated PI films with a covalently tethered FEP or PTFE surface layer were highly hydrophobic, having static water contact angles above 140°. The highly hydrophobic property depends on both the composition and roughness of the delaminated surface.     

Development of radiation-grafted FEP-g-polystyrene membranes: Some property–structure correlations

Property–structure correlation in proton exchange membranes, prepared by simultaneous radiation grafting of styrene into FEP films and their subsequent sulfonation, was evaluated. The distribution of ionic sites across the membrane matrix was determined by microprobe measurements. The properties of these membranes, such as ion exchange capacity, swelling and ionic resistivity as a function of the degree of grafting, were studied. The thermal stability of membranes was studied using thermogravimetric analysis and ion exchange capacity measurements. Membranes undergo considerable structural changes in terms of the increase in the ionic content, enhanced hydrophilicity and decrease in crystallinity with the increasing degree of grafting. A correlation between some physical properties and stuctural changes occurring during the membrane preparation was established.     

Radiation‐grafted solid polymer electrolyte membrane: studies of fluorinated ethylene propylene (FEP) copolymer‐g‐acrylic acid grafted membranes and their sulfonated derivatives

Acrylic acid was grafted onto FEP by simultaneous radiation technique and the resulting membranes were sulfonated. Results of dynamic mechanical properties of the membranes showed that storage modulus and temperature at tan δ_(max) increases on grafting. X‐ray diffraction (XRD) analysis of the grafted and sulfonated membranes showed decreasing trend in crystallinity with increase in degree of grafting. From scanning electron microscopy (SEM) studies it was confirmed that grafting takes place by the front mechanism. Copyright © 2004 John Wiley & Sons, Ltd.     

Fluoride ions at the Cu–fluoropolymer interface

Nanometer thick films of sputtered and evaporated Cu were deposited on the surfaces of the fluoropolymers poly(tetrafluoroethylene) (PTFE), poly(tetrafluoroethylene‐co‐hexafluoropropylene) (FEP) and poly(tetrafluoroethylene‐co‐perfluoropropyl vinyl ether) (PFA) and studied by both angle‐resolved XPS at takeoff angles of 10°, 45° and 80° and in situ argon ion etching. Higher yields of the fluoride ion to fluoropolymer ratio were detected for sputtered than evaporated Cu. PFA and FEP show enhanced interaction with sputtered Cu to produce fluoride ions relative to the more polycrystalline PTFE. At intermediate depths (takeoff angle of 45°), PFA and FEP exhibit the strongest fluoride F 1s signals compared with the fluoropolymer peaks. The amount of fluoride ion detected reaches a maximum after brief Ar ion etching and then decreases with prolonged etching. Compared with untreated fluoropolymers, improved adhesion of evaporated Cu was observed on the fluoropolymer surfaces that were argon ion etched to expose fluoride ions. Copyright © 2013 John Wiley & Sons, Ltd.     

Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?

In the context of computational drug design, we examine the effectiveness of the enhanced sampling techniques in state-of-the-art free energy calculations based on alchemical molecular dynamics simulations. In a paradigmatic molecule with competition between conformationally restrained E and Z isomers whose probability ratio is strongly affected by the coupling with the environment, we compare the so-called λ-hopping technique to the Hamiltonian replica exchange methods assessing their convergence behavior as a function of the enhanced sampling protocols (number of replicas, scaling factors, simulation times). We found that the pure λ-hopping, commonly used in solvation and binding free energy calculations via alchemical free energy perturbation techniques, is ineffective in enhancing the sampling of the isomeric states, exhibiting a pathological dependence on the initial conditions. Correct sampling can be restored in λ-hopping simulation by the addition of a “hot-zone” scaling factor to the λ-stratification (FEP⁺ approach), provided that the additive hot-zone scaling factors are tuned and optimized using preliminary ordinary replica-exchange simulation of the end-states.