Protein encapsulation: a new approach for improving the capability of small-molecule fluorogenic probes

Herein, we report a protein-based hybridization strategy that exploits the host-guest chemistry of HSA (human serum albumin) to solubilize the otherwise cell impermeable ONOO⁻ fluorescent probe Pinkment-OAc. Formation of a HSA/Pinkment-OAc supramolecular hybrid was confirmed by SAXS and solution-state analyses. This HSA/Pinkment-OAc hybrid provided an enhanced fluorescence response towards ONOO⁻versusPinkment-OAc alone, as determined by in vitro experiments. The HSA/Pinkment-OAc hybrid was also evaluated in RAW 264.7 macrophages and HeLa cancer cell lines, which displayed an enhanced cell permeability enabling the detection of SIN-1 and LPS generated ONOO⁻ and the in vivo imaging of acute inflammation in LPS-treated mice. A remarkable 5.6 fold (RAW 264.7), 8.7-fold (HeLa) and 2.7-fold increased response was seen relative to Pinkment-OAc alone at the cellular level and in vivo, respectively. We anticipate that HSA/fluorescent probe hybrids will soon become ubiquitous and routinely applied to overcome solubility issues associated with hydrophobic fluorescent imaging agents designed to detect disease related biomarkers.

Herein, we report a protein-based hybridization strategy that exploits the host–guest chemistry of HSA (human serum albumin) to solubilize the otherwise cell impermeable ONOO⁻ fluorescent probe Pinkment-OAc.     

Discovery of a novel CCR5 antagonist lead compound through fragment assembly

CCR5, as the major co-receptor for HIV-1 entry, is an attractive novel target for the pharmaceutical industry in the HIV-1 therapeutic area. In this study, based on the structures of maraviroc and 1,4-bis(4-(7-chloroquinolin-4-yl)piperazin-1-yl)butane-1,4-dione (1), which was identified using structure-based virtual screening in conjunction with a calcium mobilization assay, a series of novel small molecule CCR5 antagonists have been designed and synthesized through fragment assembly. Preliminary SARs were obtained, which are in good agreement with the molecular binding model and should prove helpful for future antagonist design. The novel scaffold presented here might also be useful in the development of maraviroc-derived second generation CCR5 antagonists.     

Quantifying the protein core flexibility through analysis of cavity formation

We present an extensive analysis of cavity statistics in the interior of three different proteins, in liquid n-hexane, and in water performed using molecular-dynamics simulations. The heterogeneity of packing density over atomic length scales in different parts of proteins is evident in the wide range of values observed for the average cavity size, the probability of cavity formation, and the corresponding free energy of hard-sphere insertion. More interestingly, however, the distribution of cavity sizes observed at various points in the protein interior is surprisingly homogeneous in width. That width is significantly smaller than that measured for similar distributions in liquid n-hexane or water, indicating that protein interior is much less flexible than liquid hexane. The width of the cavity size distribution correlates well with the experimental isothermal compressibility data for liquids and proteins. An analysis of cavity statistics thus provides an efficient method to quantify local properties, such as packing, stiffness, or compressibility in heterogeneous condensed media.     

Crystallographic and biophysical analysis of the fusion core from SARS-CoV-2 spike protein

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a newly emerging infectious pathogen causing coronavirus disease 2019 (COVID-19). The virus primarily infects cells via its spike glycoprotein, which is cleaved into S1 and S2 subunits to aid in cell attachment and membrane fusion, respectively. Heptad repeat 1 (HR1) and heptad repeat 2 (HR2) of the S2 subunit are essential for membrane fusion, culminating in an expected six-helix bundle termed fusion core. To better understand the structural and biophysical features of the SARS-CoV-2 fusion core, we designed, constructed, and bacterially produced a recombinant single-chain HR1-L6-HR2 protein and conducted a series of biochemical and biophysical experiments. Our findings demonstrate that the HR1-L6-HR2 protein spontaneously assembles into a highly stable trimeric complex, further confirmed by x-ray crystallographic analysis. The crystal structure of the fusion core reveals a trimeric coiled-coil structure of HR1 antiparallelly surrounded by three HR2 to form a six-helical bundle. Additionally, four residues of HR1 that contribute to binding with HR2 through the formation of hydrogen bonds and salt bridges were observed. These results indicate that the SARS-CoV-2 fusion core exhibits similar characteristics to other class I viral glycoproteins, suggesting potential for drug repurposing as an alternative strategy to combat COVID-19.     

Chemical probes for the recognition of cannabinoid receptors in native systems

Receptors made visible: The described biotin-tagged small-molecule probes with excellent affinities for the CB(1) and CB(2) cannabinoid receptors (CB(1)R and CB(2)R) enable direct visualization of these receptors in native cellular systems, including neurons, microglia, and immune cells. This method could overcome some of the limitations of current methodologies and may help to dissect the complexity of the endogenous cannabinoid system.     

Conversion of C5 into C6 cyclic species through the formation of C7 intermediates

We have recently proposed that the addition of C2H2 to the cyclopentadienyl radical can lead to the rapid formation of the cycloheptatrienyl radical and, in succession, of the indenyl radical. These reactions represent an interesting and unexplored route for the enlargement of gas-phase cyclic species. In this work we report ab initio calculations we performed with the aim of investigating in detail the gas-phase reactivity of cycloheptatrienyl and indenyl radicals. We found that the reaction of the cycloheptatrienyl radical with atomic hydrogen can lead to its fast conversion into the more stable benzyl radical. This reaction pathway involves the intermediate formation of heptatriene, norcaradiene, and toluene. Successively we investigated whether this reaction mechanism can be extended to polycyclic aromatic hydrocarbons (PAHs). For this purpose we studied the reaction of C2H2 with the indenyl radical, which can be considered as a superior homologue of the cyclopentadienyl radical. This reaction proceeds through a pathway similar to that proposed for C5H5 but with a reaction rate about an order of magnitude smaller. The present calculations extend thus the previously proposed C5-C7-C9 mechanism to bicyclic PAH and suggest a fast route for the conversion of C5 into C6 cyclic radicals, mediated by the formation of C7 cyclic species.     

The development of simple and sensitive small-molecule fluorescent probes for the detection of serum proteins after native polyacrylamide gel electrophoresis

In this paper, a simple and sensitive small-molecule fluorescent probe, 2,5-dihydroxy-4'-dimethylaminochalcone (DHDMAC), was designed and synthesized for the detection of human serum proteins via hydrophobic interactions after polyacrylamide gel electrophoresis (PAGE). This probe produced lower fluorescence emission in the absence of proteins, and the emission intensity was significantly increased after the interaction with serum proteins. To demonstrate the imaging performance of this probe as a fluorescent dye, a series of experiments was conducted that included sensitivity comparison and 2D-PAGE. The results indicated that the sensitivity of DHDMAC staining is comparable to that of the most widely used fluorescent dye, SYPRO Ruby, and more protein spots (including thyroxine-binding globulin, angiotensinogen, afamin, zinc-α-2-glycoprotein and α-1-antichymotrypsin) were detected after 2D-PAGE. Therefore, DHDMAC is a good protein reporter due to its fast staining procedure, low detection limits and high resolution.     

Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a,V2 receptors and with oxytocin receptors

The nonapeptide hormones arginine vasopressin (CYFQNCPRG-NH₂, AVP) and oxytocin (CYIQNCPLG-NH₂, OT), control many essential functions in mammals. Their main activities include the urine concentration (via stimulation of AVP V2 receptors, V2R, in the kidneys), blood pressure regulation (via stimulation of vascular V1a AVP receptors, V1aR), ACTH control (via stimulation of V1b receptors, V1bR, in the pituitary) and labor and lactation control (via stimulation of OT receptors, OTR, in the uterus and nipples, respectively). All four receptor subtypes belong to the GTP-binding (G) protein-coupled receptor (GPCR) family. This work consists of docking of YM087, a potent non-peptide V1aR and V2R – but not OTR – antagonist, into the receptor models based on relatively new theoretical templates of rhodopsin (RD) and opiate receptors, proposed by Mosberg et al. (Univ. of Michigan, Ann Arbor, USA). It is simultaneously demonstrated that this RD template satisfactorily compares with the first historical GPCR structure of bovine rhodopsin (Palczewski et al., 2000) and that homology-modeling of V2R, V1aR and OTR using opiate receptors as templates is rational, based on relatively high (20–60%) sequence homology among the set of 4 neurophyseal and 4 opiate receptors. YM087 was computer-docked to V1aR, V2R and OTR using the AutoDock (Olson et al., Scripps Research Institute, La Jolla, USA) and subsequently relaxed using restrained simulated annealing and molecular dynamics, as implemented in AMBER program (Kollman et al., University of California, San Francisco, USA). From about 80 diverse configurations, sampled for each of the three ligand/receptor systems, 3 best energy-relaxed complexes were selected for mutual comparisons. Similar docking modes were found for the YM087/V1aR and YM087/V2R complexes, diverse from those of the YM087/OTR complexes, in agreement with the molecular affinity data.     

Development of activity-based probes with tunable specificity for protein tyrosine phosphatase subfamilies

Herein we describe the development of activity-based probes toward protein tyrosine phosphatase (PTP) subfamilies. A novel phosphotyrosine analog serving as the latent trapping unit has been designed and explored. It allows addition of various amino acid residues to its C- and N-termini to extend the recognition element. As a proof-of-concept, we have synthesized three tripeptide probes, which carry the phosphotyrosine analog in the middle position and a leucinamide residue at the C-terminus. The three tripeptide probes differed only in their N-terminal amino acid (Glu, Phe, and Lys). The labeling properties of these probes were determined and the results showed the newly synthesized probes could selectively label PTPs in an activity-dependent manner. In addition, the probes’ target specificity was also shown to be influenced by the amino acid residues flanking the phosphotyrosine analog.     

Synthesis and characterization of star polyfluorenes with a C60 core

C60‐cored star polyfluorenes were synthesized and fully characterized. A high yield (81%) hexakisaddition of C60 was developed by using Prato reaction and bulky fluorene addends. Suzuki polycondensation of the hexakisadducts of C60 carrying six 2‐bromofluorene addends and AB‐type monomer (2‐bromo‐9,9‐dioctylfluorenyl‐4,4,5,5‐tetramethyl‐ [1,3,2]‐dioxaborane) with Pd(PPh₃)₄ as the catalyst precursor afforded the desired C60‐cored star polyfluorenes. Their three‐dimensional structure can effectively reduce the aggregation of the polyfluorene chains. Annealing studies indicated that the C60‐cored star polyfluorenes are of good color stability. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4696–4706, 2007     

Design and synthesis of C5 methylated L-arginine analogues as active site probes for nitric oxide synthase

The role of nitric oxide (NO) as a biological signaling molecule is well established. NO is produced by the nitric oxide synthases (NOSs, EC 1.14.13.39), a class of heme proteins capable of converting l-arginine to NO and l-citrulline. Despite the large body of knowledge associated with the NOSs, mechanistic details relating to the unique oxidative chemistry performed by these enzymes remain to be fully elucidated. Furthermore, a number of disease states are associated with either the over- or underproduction of NO, making the NOS pathway an attractive target for the development of therapeutics. For these reasons, molecular tools capable of providing mechanistic insights into the production of NO and/or the inhibition of the NOSs remain of interest. We report here the stereospecific synthesis and testing of a number of new l-arginine analogues bearing a minimal substitution, methylation at position 5 of the amino acid side chain (such analogues have not been previously reported). The synthetic approach employed a modified photolysis procedure whereby irradiation of the appropriate diacylperoxide precursors at 254 nm gave access to the required unnatural amino acids in good yields. A heme domain construct of the inducible NOS isoform (iNOSheme) was used to assess the binding of each compound to the enzyme active site. The compounds were also investigated as either inhibitors of, or alternate substrates for, the inducible NOS isoform. The results obtained provide new insight into the steric and stereochemical tolerance of the enzyme active site. These findings also further support the role of a conserved active site water molecule previously proposed to be necessary for NOS catalysis.     

Synthesis and properties of star polymers with a C5‐symmetric bowl‐shaped aromatic core

We report the synthesis and properties of star polymers with a C₅‐symmetric aromatic core. For this, corannulene‐based penta‐substituted polymerization initiators were synthesized. These initiators were then used to polymerize cyclic ester and styrenic monomers via ring opening polymerization and free radical polymerization methods, respectively. Preliminary results suggest that these novel polymers can interact with fullerene, C₆₀, and the degree of interaction can be tuned by the chemical nature of the solvent. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Synthesis of the gymnodimine tetrahydrofuran core through a Ueno-Stork radical cyclization

A straightforward access to the C10-C20 skeleton of gymnodimine, incorporating a tetrahydrofuran fragment, is described. The elaboration of the THF moiety is based on a stereocontrolled Ueno-Stork cyclization. A Lewis-acid mediated allylation of the resulting acetal at C13 and a Horner-Wadsworth-Emmons olefination on the ketone at C17 complete the synthesis.     

Synthesis of novel amphiphilic spin probes with the paramagnetic doxyl group in the polar region

The use of ESR and specially designed spin probes has led to major breakthroughs in understanding the complexity of biological membranes. Research has been focused mainly on molecular events within the lipid bilayer, and few probes have been designed for studying events in the extracellular space near the membrane surface. We have prepared a series of amphiphilic spin probes in which an ethylene glycol type hydrophilic spacer was introduced between a hydrophobic anchor and the doxyl group, placing the latter above the membrane in the extracellular space. Furthermore, the 2pπ orbital, containing the unpaired electron of the nitroxide group, would be orientated perpendicular to the membrane surface, making it more useful for ESR investigations of structural and dynamic properties close to the membrane surface in different situations of the cell life.     

11C-methiodide quinuclidinyl benzilate a muscarinic antagonist for in vivo studies of myocardial muscarinic receptors

A method for labeling MQNB (Methiodide quinuclidinyl benzilate) with carbon-11 using¹¹C-methyl iodide is reported. Injectable labeled product (100 mCi; max. 200 mCi) radiochemically and chemically pure is obtained in a 30 minute synthesis time with a specific activity of 1 Ci/μmol, (max. 2.3 Ci/μmol).     

Thermal degradation of a heteroarm starlike polymer with fullerene C60 core

The mechanism of thermal degradation of a 12-arm starlike polymer with fullerene C₆₀ core and equal number of polystyrene and poly(tert-butyl methacrylate) arms was studied by thermal desorption mass spectrometry. Thermal characteristics of the heteroarm stars were compared with those of six-arm starlike fullerene-containing polystyrenes and linear poly(tert-butyl methacrylate).