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.     

Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions

The adenosine A_2A receptor (A_2AAR) is a class A G-protein-coupled receptor (GPCR). It is an immune checkpoint in the tumor micro-environment and has become an emerging target for cancer treatment. In this study, we aimed to explore the effects of cancer-patient-derived A_2AAR mutations on ligand binding and receptor functions. The wild-type A_2AAR and 15 mutants identified by Genomic Data Commons (GDC) in human cancers were expressed in HEK293T cells. Firstly, we found that the binding affinity for agonist NECA was decreased in six mutants but increased for the V275A mutant. Mutations A165V and A265V decreased the binding affinity for antagonist ZM241385. Secondly, we found that the potency of NECA (EC₅₀) in an impedance-based cell-morphology assay was mostly correlated with the binding affinity for the different mutants. Moreover, S132L and H278N were found to shift the A_2AAR towards the inactive state. Importantly, we found that ZM241385 could not inhibit the activation of V275A and P285L stimulated by NECA. Taken together, the cancer-associated mutations of A_2AAR modulated ligand binding and receptor functions. This study provides fundamental insights into the structure–activity relationship of the A_2AAR and provides insights for A_2AAR-related personalized treatment in cancer.     

Irreversible Antagonists for the Adenosine A2B Receptor

Blockade of the adenosine A_2B receptor (A_2BAR) represents a potential novel strategy for the immunotherapy of cancer. In the present study, we designed, synthesized, and characterized irreversible A_2BAR antagonists based on an 8-p-sulfophenylxanthine scaffold. Irreversible binding was confirmed in radioligand binding and bioluminescence resonance energy transfer(BRET)-based Gα₁₅ protein activation assays by performing ligand wash-out and kinetic experiments. p-(1-Propylxanthin-8-yl)benzene sulfonyl fluoride (6a, PSB-21500) was the most potent and selective irreversible A_2BAR antagonist of the present series with an apparent K_i value of 10.6 nM at the human A_2BAR and >38-fold selectivity versus the other AR subtypes. The corresponding 3-cyclopropyl-substituted xanthine derivative 6c (PSB-21502) was similarly potent, but was non-selective versus A₁- and A_2AARs. Attachment of a reactive sulfonyl fluoride group to an elongated xanthine 8-substituent (12, K_i 7.37 nM) resulted in a potent, selective, reversibly binding antagonist. Based on previous docking studies, the lysine residue K269^7.32 was proposed to react with the covalent antagonists. However, the mutant K269L behaved similarly to the wildtype A_2BAR, indicating that 6a and related irreversible A_2BAR antagonists do not interact with K269^7.32. The new irreversible A_2BAR antagonists will be useful tools and have the potential to be further developed as therapeutic drugs.     

An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor

The binding free energy calculation of protein–ligand complexes is necessary for research into virus–host interactions and the relevant applications in drug discovery. However, many current computational methods of such calculations are either inefficient or inaccurate in practice. Utilizing implicit solvent models in the molecular mechanics generalized Born surface area (MM/GBSA) framework allows for efficient calculations without significant loss of accuracy. Here, GBNSR6, a new flavor of the generalized Born model, is employed in the MM/GBSA framework for measuring the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor. A computational protocol is developed based on the widely studied Ras–Raf complex, which has similar binding free energy to SARS-CoV-2/ACE2. Two options for representing the dielectric boundary of the complexes are evaluated: one based on the standard Bondi radii and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein–ligand binding. Predictions based on the two radii sets provide upper and lower bounds on the experimental references: −14.7(ΔGbindBondi)<−10.6(ΔGbindExp.)<−4.1(ΔGbindOPT1) kcal/mol. The consensus estimates of the two bounds show quantitative agreement with the experiment values. This work also presents a novel truncation method and computational strategies for efficient entropy calculations with normal mode analysis. Interestingly, it is observed that a significant decrease in the number of snapshots does not affect the accuracy of entropy calculation, while it does lower computation time appreciably. The proposed MM/GBSA protocol can be used to study the binding mechanism of new variants of SARS-CoV-2, as well as other relevant structures.     

Non-Peptide Opioids Differ in Effects on Mu-Opioid (MOP) and Serotonin 1A (5-HT1A) Receptors Heterodimerization and Cellular Effectors (Ca2+, ERK1/2 and p38) Activation

The importance of the dynamic interplay between the opioid and the serotonin neuromodulatory systems in chronic pain is well recognized. In this study, we investigated whether these two signalling pathways can be integrated at the single-cell level via direct interactions between the mu-opioid (MOP) and the serotonin 1A (5-HT_1A) receptors. Using fluorescence cross-correlation spectroscopy (FCCS), a quantitative method with single-molecule sensitivity, we characterized in live cells MOP and 5-HT_1A interactions and the effects of prolonged (18 h) exposure to selected non-peptide opioids: morphine, codeine, oxycodone and fentanyl, on the extent of these interactions. The results indicate that in the plasma membrane, MOP and 5-HT_1A receptors form heterodimers that are characterized with an apparent dissociation constant Kdapp = (440 ± 70) nM). Prolonged exposure to all non-peptide opioids tested facilitated MOP and 5-HT_1A heterodimerization and stabilized the heterodimer complexes, albeit to a different extent: Kd, Fentanylapp = (80 ± 70) nM), Kd,Morphineapp = (200 ± 70) nM, Kd, Codeineapp = (100 ± 70) nM and Kd, Oxycodoneapp = (200 ± 70) nM. The non-peptide opioids differed also in the extent to which they affected the mitogen-activated protein kinases (MAPKs) p38 and the extracellular signal-regulated kinase (Erk1/2), with morphine, codeine and fentanyl activating both pathways, whereas oxycodone activated p38 but not ERK1/2. Acute stimulation with different non-peptide opioids differently affected the intracellular Ca²⁺ levels and signalling dynamics. Hypothetically, targeting MOP–5-HT_1A heterodimer formation could become a new strategy to counteract opioid induced hyperalgesia and help to preserve the analgesic effects of opioids in chronic pain.     

The Pharmacological Potential of Adenosine A2A Receptor Antagonists for Treating Parkinson’s Disease

The adenosine A_2A receptor subtype is recognized as a non-dopaminergic pharmacological target for the treatment of neurodegenerative disorders, notably Parkinson’s disease (PD). The selective A_2A receptor antagonist istradefylline is approved in the US and Japan as an adjunctive treatment to levodopa/decarboxylase inhibitors in adults with PD experiencing OFF episodes or a wearing-off phenomenon; however, the full potential of this drug class remains to be explored. In this article, we review the pharmacology of adenosine A_2A receptor antagonists from the perspective of the treatment of both motor and non-motor symptoms of PD and their potential for disease modification.     

Inhibition Mechanism of Hydroxyproline-like Small Inhibitors to Disorder HIF-VHL Interaction by Molecular Dynamic Simulations and Binding Free Energy Calculations

Protein-protein interactions are vital for a wide range of biological processes. The interactions between the hypoxia-inducible factor and von Hippel Lindau (VHL) are attractive drug targets for ischemic heart disease. In order to disrupt this interaction, the strategy to target VHL binding site using a hydroxyproline-like (pro-like) small molecule has been reported. In this study, we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein, which were investigated via molecular dynamics simulations and binding free energy calculations. It was found that pro-like inhibitors showed a strong binding affinity toward VHL. Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.     

X‐Ray Crystal Structures and Quantum Chemical Calculations of Tetraphenyl‐arsonium Tetraazidoaurate(III) and Azido(triphenylphosphine)Gold(I)

The single crystal X‐ray structure determinations are reported for [Ph₄As][Au(N₃)₄] ( 1 ) and Ph₃PAuN₃ ( 2 ). Compound 1 is an ionic species with a “windmill” shaped anion. It crystallizes in the monoclinic space group C2/c, a = 18.396(2), b = 6.2492(4), c = 23.555(2) Å; β = 107.98(1)°, Z = 4, R1_{(all data)} = 0.0227, wR2 = 0.0374. The lattice parameters of compound 2 , which crystallizes in the orthorhombic space group P2₁2₁2₁, are a = 10.9252(1), b = 11.5642(1), c = 13.0993(1) Å; Z = 4, R1_{(all data)} = 0.0176, wR = 0.0334. The experimentally obtained X‐ray data and vibrational frequencies of both compounds were compared with those calculated at B3LYP/LANL2DZ and B3LYP/SDD level of theory and for 1 also at the MP2/SDD level.     

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     

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC₅₀ values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.     

Synthesis of Phosphanes Bearing 2‐Imino‐1,3‐thiazolidine Ligands – X‐Ray Analyses and NMR Spectroscopy

Pseudo‐ephedrine derived 2‐imino‐1,3‐thiazolidine 1 reacts with tris(diethylamino)phosphane by stepwise replacement of the diethylamino group to give the mono‐, bis‐ and tris(imino)phosphanes 2 , 3 and 4 , respectively, of which 4 could be isolated in pure state. The analogous reaction with diethylamino‐diphenylphosphane affords the imino‐diphenylphosphane 5 . The iminophosphanes react with sulfur or selenium to give the corresponding phosphorus(V) compounds. In contrast, the reaction of the iminophosphanes with oxygen is very slow; anhydrous trimethylamine N‐oxide reacts in the melt with the phosphanes to give the oxides 4(O) and 5(O) . The molecular structures of 4(O) (in mixture with 4 ), 4(Se) , 5(S) and 5(Se) were determined by X‐ray analysis. In all cases the ring‐sulfur and the phosphorus atoms are in cis‐positions at the C=N bonds. The analogous solution structures were determined by ¹H, ¹³C, ¹⁵N, ³¹P and ⁷⁷Se NMR spectroscopy. In the case of the compounds 5 , 5(O) , 5(S) and 5(Se) the isotope‐induced chemical shifts ¹δ^14/15N(³¹P) were determined, using INEPT‐HEED experiments.     

Docking,Binding Free Energy Calculations and In Vitro Characterization of Pyrazine Linked 2-Aminobenzamides as Novel Class I Histone Deacetylase (HDAC) Inhibitors

Class I histone deacetylases, HDAC1, HDAC2, and HDAC3, represent potential targets for cancer treatment. However, the development of isoform-selective drugs for these enzymes remains challenging due to their high sequence and structural similarity. In the current study, we applied a computational approach to predict the selectivity profile of developed inhibitors. Molecular docking followed by MD simulation and calculation of binding free energy was performed for a dataset of 2-aminobenzamides comprising 30 previously developed inhibitors. For each HDAC isoform, a significant correlation was found between the binding free energy values and in vitro inhibitory activities. The predictive accuracy and reliability of the best preforming models were assessed on an external test set of newly designed and synthesized inhibitors. The developed binding free-energy models are cost-effective methods and help to reduce the time required to prioritize compounds for further studies.     

ChemInform Abstract: Study of Phase Transformation in BaTe2O6 by in situ High‐Pressure X‐Ray Diffraction,Raman Spectroscopy,and First‐Principles Calculations.

The title compound is synthesized by solid state reaction of a stoichiometric mixture of BaCO₃ and TeO₂ (air, 550 °C for 6 h, and 650 °C for 12 h).     

New Open‐Chain and Cyclic Tetrapeptides,Consisting of α‐, β2‐, and β3‐Amino‐Acid Residues,as Somatostatin Mimics – A Survey

Cyclo‐β‐tetrapeptides are known to adopt a conformation with an intramolecular transannular hydrogen bond in solution. Analysis of this structure reveals that incorporation of a β²‐amino‐acid residue should lead to mimics of ‘α‐peptidic β‐turns’ (cf. A, B, C ). It is also known that short‐chain mixed β/α‐peptides with appropriate side chains can be used to mimic interactions between α‐peptidic hairpin turns and G protein‐coupled receptors. Based on these facts, we have now prepared a number of cyclic and open‐chain tetrapeptides, 7 – 20 , consisting of α‐, β²‐, and β³‐amino‐acid residues, which bear the side chains of Trp and Lys, and possess backbone configurations such that they should be capable of mimicking somatostatin in its affinity for the human SRIF receptors (hsst_1–5). All peptides were prepared by solid‐phase coupling by the Fmoc strategy. For the cyclic peptides, the three‐dimensional orthogonal methodology (Scheme 3) was employed with best success. The new compounds were characterized by high‐resolution mass spectrometry, NMR and CD spectroscopy, and, in five cases, by a full NMR‐solution‐structure determination (in MeOH or H₂O; Fig. 4). The affinities of the new compounds for the receptors hsst_1–5 were determined by competition with [¹²⁵I]LTT‐SRIF₂₈ or [¹²⁵I] [Tyr¹⁰]‐CST₁₄. In Table 1, the data are listed, together with corresponding values of all β‐ and γ‐peptidic somatostatin/Sandostatin^® mimics measured previously by our groups. Submicromolar affinities have been achieved for most of the human SRIF receptors hsst_1–5. Especially high, specific binding affinities for receptor hsst₄ (which is highly expressed in lung and brain tissue, although still of unknown function!) was observed with some of the β‐peptidic mimics. In view of the fact that numerous peptide‐activated G protein‐coupled receptors (GPCRs) recognize ligands with turn structure (Table 2), the results reported herein are relevant far beyond the realm of somatostatin: many other peptide GPCRs should be ‘reached’ with β‐ and γ‐peptidic mimics as well, and these compounds are proteolytically and metabolically stable, and do not need to be cell‐penetrating for this purpose (Fig. 5).     

Activation of β2-Adrenergic Receptor Induced by Three Catecholamine Agonists: a Docking and Molecular Dynamics Study

We studied the activation of β₂-adrenergic receptor(β₂AR) by norepinephrine, epinephrine and isoproterenol using docking and molecular dynamics(MD) simulation. The simulation was done on the assumption that β₂AR was surrounded with explicit water and infinite lipid bilayer membrane at body temperature. So the result should be close to that under the physiological conditions. We calculated the structure of binding sites in β₂AR for the three activators. We also simulated the change of the conformation of β₂AR in the transmembrane regions(TMs), in the molecular switches, and in the conserved DRY(Aspartic acid, Arginine and Tyrosine) motif. This study provides detailed information concerning the structure of β₂AR during activation process.     

Ultra-Large-Scale Screening of Natural Compounds and Free Energy Calculations Revealed Potential Inhibitors for the Receptor-Binding Domain (RBD) of SARS-CoV-2

The emergence of immune-evading variants of SARS-CoV-2 further aggravated the ongoing pandemic. Despite the deployments of various vaccines, the acquired mutations are capable of escaping both natural and vaccine-induced immune responses. Therefore, further investigation is needed to design a decisive pharmacological treatment that could efficiently block the entry of this virus into cells. Hence, the current study used structure-based methods to target the RBD of the recombinant variant (Deltacron) of SARS-CoV-2, which was used as a model variant. From the virtual drug screenings of various databases, a total of four hits were identified as potential lead molecules. Key residues were blocked by these molecules with favorable structural dynamic features. The binding free energies further validated the potentials of these molecules. The TBE for MNP was calculated to be −32.86 ± 0.10 kcal/mol, for SANC00222 the TBE was −23.41 ± 0.15 kcal/mol, for Liriodenine the TBE was −34.29 ± 0.07 kcal/mol, while for Carviolin the TBE was calculated to be −27.67 ± 0.12 kcal/mol. Moreover, each complex demonstrated distinct internal motion and a free energy profile, indicating a different strategy for the interaction with and inhibition of the RBD. In conclusion, the current study demands further in vivo and in vitro validation for the possible usage of these compounds as potential drugs against SARS-CoV-2 and its variants.     

Characterization of a Poly(2‐oxazoline) Library by High‐Throughput,Automated Contact‐Angle Measurements and Surface‐Energy Calculations

Summary: The feasibility of automated, high‐throughput contact‐angle measurements is demonstrated using a modified commercial contact‐angle measuring apparatus. Droplets are automatically dispensed, analyzed and aspirated. The system automatically measures more than 100 contact angles per hour using two test liquids, and calculates surface energies using the equation of state method. A library of poly(2‐oxazoline) homo‐ and block copolymers was investigated. Polymers with a 2‐nonyl‐2‐oxazoline block were found to have considerably lower surface energies.

Setup used here for characterization of the surface properties of a library of poly(2‐oxazoline) homo‐ and block copolymers.     

ChemInform Abstract: A Raman Spectroscopic Study of the XeOF4/XeF2 System and the X‐Ray Crystal Structure of α‐XeOF4·XeF2.

The interaction of XeF₂ with excess XeOF₄ leads to the formation of a mixture of α‐XeOF₄·XeF₂ and β‐XeOF₄·XeF₂.