On‐Bead Screens Sample Narrower Affinity Ranges of Protein–Ligand Interactions Compared to Equivalent Solution Assays

Conceptually, on‐bead screening is one of the most efficient high‐throughput screening (HTS) methods. One of its inherent advantages is that the solid support has a dual function: it serves as a synthesis platform and as a screening compartment. Compound purification, cleavage and storage and extensive liquid handling are not necessary in bead‐based HTS. Since the establishment of one‐bead one‐compound library synthesis, the properties of polymer beads in chemical reactions have been thoroughly investigated. However, the characterization of the kinetics and thermodynamics of protein–ligand interactions on the beads used for screening has received much less attention. Consequently, the majority of reported on‐bead screens are based on empirically derived procedures, independent of measured equilibrium constants and rate constants of protein binding to ligands on beads. More often than not, on‐bead screens reveal apparent high affinity binders through strong protein complexation on the matrix of the solid support. After decoding, resynthesis, and solution testing the primary hits turn out to be unexpectedly weak binders, or may even fall out of the detection limit of the solution assay. Only a quantitative comparison of on‐bead binding and solution binding events will allow systematically investigating affinity differences as function of protein and small molecule properties. This will open up routes for optimized bead materials, blocking conditions and other improved assay procedures. By making use of the unique features of our previously introduced confocal nanoscanning (CONA) method, we investigated the kinetic and thermodynamic properties of protein–ligand interactions on TentaGel beads, a popular solid support for on‐bead screening. The data obtained from these experiments allowed us to determine dissociation constants for the interaction of bead‐immobilized ligands with soluble proteins. Our results therefore provide, for the first time, a comparison of on‐bead versus solution binding thermodynamics. Our data indicate that affinity ranges found in on‐bead screening are indeed narrower compared to equivalent interactions in homogeneous solution. A thorough physico‐chemical understanding of the molecular recognition between proteins and surface bound ligands will further strengthen the role of on‐bead screening as an ultimately cost‐effective method in hit and lead finding.     

Fast Epitope Mapping for the Anti‐MUC1 Monoclonal Antibody by Combining a One‐Bead‐One‐Glycopeptide Library and a Microarray Platform

Anti‐MUC1 monoclonal antibodies (mAbs) are powerful tools that can be used to recognize cancer‐related MUC1 molecules, the O‐glycosylation status of which is believed to affect binding affinity. We demonstrate the feasibility of using a rapid screening methodology to elucidate those effects. The approach involves i) “one‐bead‐one‐compound”‐based preparation of bilayer resins carrying glycopeptides on the shell and mass‐tag tripeptides coding O‐glycan patterns in the core, ii) on‐resin screening with an anti‐MUC1 mAb, iii) separating positive resins by utilizing secondary antibody conjugation with magnetic beads, and (iv) decoding the mass‐tag that is detached from the positive resins pool by using mass spectrometric analysis. We tested a small library consisting of 27 MUC1 glycopeptides with different O‐glycosylations against anti‐MUC1 mAb clone VU‐3C6. Qualitative mass‐tag analysis showed that increasing the number of glycans leads to an increase in the binding affinity. Six glycopeptides selected from the library were validated by using a microarray‐based assay. Our screening provides valuable information on O‐glycosylations of epitopes leading to high affinity with mAb.     

高压芒刺静电场对小鼠LFA-1和ICAM-1表达的影响

采用不同电压高压芒刺静电场对小鼠进行全身辐射,荧光免疫流式细胞术检测蛋白表达量的变化.通过时程/量效研究不同电压高压芒刺静电场对细胞表面分子LFA-1和ICAM-1的影响.剂量效应结果表明,LFA-1和ICAM-1在10～20 kV之间处理组的表达量明显高于对照组（P＜0.01）;在30 kV以上电压表达量明显降低（P＜0.05）;时间进程研究结果表明,处理后2 h开始实验组表达量与对照组相比差异显著,一直持续到24 h.不同电压高压芒刺静电场可引起ICAM-1和LFA-1不同的生物效应,二者的相互作用在免疫调节反应中发挥重要功能.     

Simple enrichment of thiol‐containing biomolecules by using zinc(II)–cyclen‐functionalized magnetic beads

A simple and efficient method based on magnetic‐bead technology has been developed for the enrichment of thiol‐containing biomolecules, such as l ‐glutathione and cysteine‐containing peptides. The thiol‐binding site on the bead is a mononuclear complex of zinc(II) with 1,4,7,10‐tetraazacyclododecane (cyclen); this is linked to a hydrophilic cross‐linked agarose coating on a particle that has a magnetic core. All steps for the thiol‐affinity separation are conducted in aqueous buffers with 0.10 mL of the magnetic beads in a 1.5 mL microtube. The entire separation protocol for thiol‐containing compounds, from addition to elution, requires less than one hour per sample, provided the buffers and the zinc(II)–cyclen‐functionalized magnetic beads have been prepared in advance. The thiol‐affinity magnetic beads are reusable at least 15 times without a decrease in their thiol‐binding ability, and they are stable for six months at room temperature.     

An Organometallic Inhibitor for the Human Repair Enzyme 7,8‐Dihydro‐8‐oxoguanosine Triphosphatase

The probe‐based discovery of the first small‐molecule inhibitor of the repair enzyme 8‐oxo‐dGTPase (MTH1) is presented, which is an unconventional cyclometalated ruthenium half‐sandwich complex. The organometallic inhibitor with low‐nanomolar activity displays astonishing specificity, as verified in tests with an extended panel of protein kinases and other ATP binding proteins. The binding of the organometallic inhibitor to MTH1 is investigated by protein crystallography.     

Electrophoretic behavior of DNA‐methyl‐CpG‐binding domain protein complexes revealed by capillary electrophoreses laser‐induced fluorescence

The free solution electrophoretic behavior of DNA‐protein complexes depends on their charge and mass in a certain experimental condition, which are two fundamental properties of DNA‐protein complexes in free solution. Here, we used CE LIF to study the free solution behavior of DNA‐methyl‐CpG‐binding domain protein (MBD2b) complexes through exploring the relationship between the mobilities, charge, and mass of DNA‐protein complexes. This method is based on the effective separation of free DNA and DNA‐protein complexes because of their different electrophoretic mobility in a certain electric field. In order to avoid protein adsorption, a polyacrylamide‐coated capillary was used. Based on the evaluation of the electrophoretic behavior of formed DNA‐MBD2b complexes, we found that the values of (μ₀/μ)‐1 were directly proportional to the charge‐to‐mass ratios of formed complexes, where the μ₀ and μ are the mobility of free DNA probe and DNA‐protein complex, respectively. The models were further validated by the complex mobilities of protein with various lengths of DNA probes. The deviation of experimental and calculated charge‐to‐mass ratios of formed complexes from the theoretical data was less than 10%, suggesting that our models are useful to analyze the DNA‐binding properties of the purified MBD2b protein and help to analyze other DNA‐protein complexes. Additionally, this study enhances the understanding of the influence of the charge‐to‐mass ratios of formed DNA‐protein complexes on their separation and electrophoretic behaviors.     

Biointeraction analysis of carbamazepine binding to α1‐acid glycoprotein by high‐performance affinity chromatography

Interactions of the drug carbamazepine with the serum protein α₁‐acid glycoprotein (AGP) were examined by high‐performance affinity chromatography. Frontal analysis studies with an immobilized AGP column and control column indicated carbamazepine had both low‐affinity interactions with the support and high‐affinity interactions with AGP. When a correction was made for binding to the support, the association equilibrium constant measured at pH 7.4 and 37°C for carbamazepine with AGP was 1.0 (±0.1)×10⁵ M^?1, with values that ranged from 5.1 to 0.58×10⁵ M^?1 in going from 5 to 45°C. It was found in competition studies that these interactions were occurring at the same site that binds propranolol on AGP. Temperature studies indicated that the change in enthalpy was the main driving force for the binding of carbamazepine to AGP. These results provide a more complete picture of how carbamazepine binds to AGP in serum. This report also illustrates how high‐performance affinity chromatography can be used to examine biological interactions and drug–protein binding in situations in which significant interactions for an analyte are present with both the chromatographic support and an immobilized ligand.     

Purification of supercoiled plasmid DNA from clarified bacterial lysate by arginine‐affinity chromatography: Effects of spacer arms and ligand density

Efficient loading on a chromatographic column is the dilemma of the process development faced by engineers in plasmid DNA purification. In this research, novel arginine‐affinity chromatographic beads were prepared to investigate the effect of spacer arm and ligand density to their chromatographic performance for the purification of plasmid. The result indicated that dynamic binding capacity for plasmid increased with an increasing ligand density and carbon number of spacer arm, and the highest binding capacity for plasmid of 6.32 mg/mL bead was observed in the column of arginine bead with a ligand density of 47 mmol/L and 10‐atom carbon spacer. Furthermore, this arginine bead exhibited better selectivity to supercoiled (sc) plasmid. The evidence of a linear gradient elution suggested further that the binding of plasmid on arginine beads was driven by electrostatic interaction and hydrogen bonding. Hence, sc plasmid could successfully be purified from clarified lysate by two‐stepwise elution of salt concentration. By the refinement of the elution scheme and loading volume of clarified lysate, the column of arginine bead with a ligand density of 47 mmol/L exhibited the highest recovery yield and a much higher productivity among arginine‐affinity columns. Therefore, reshaped arginine beads provided more feasible and practical application in the preparation of sc plasmid from clarified lysate.     

Optimized two‐dimensional gel electrophoresis in an alkaline pH range improves the identification of intracellular CFDA‐cisplatin‐protein adducts in ovarian cancer cells

Intracellular binding of cisplatin to proteins has been associated with acquired resistance to chemotherapy. In our previous study we established an analytical method for the identification of intracellular cisplatin‐binding proteins. The method used a fluorescent carboxyfluorescein‐diacetate‐labeled cisplatin analogue (CFDA‐cisplatin), two‐dimensional gel electrophoresis (2DE) and mass spectrometry, which allows detecting and identifying intracellular CFDA‐cisplatin‐containing protein adducts in the acidic pH range (pH 4–7). Based on this analytical method we extended the identification of intracellular cisplatin‐protein adducts to the alkaline pH range (pH 6–10) giving chance to discover new important binding partners. 2DE analysis of alkaline proteins is challenging due to the difficult separation of basic proteins during the isoelectric focusing (IEF). The establishment of an optimized IEF protocol for basic proteins enabled us to identify several intracellular CFDA‐cisplatin‐binding proteins including enzymes of the glucose and serine metabolism like alpha enolase and D‐3‐phosphoglycerate 1‐dehydrogenase.     

Synthesis of 3‐Aryl‐2‐methoxyinden‐1‐one (Z)‐Phenylhydrazones via Hydrobromic Acid‐Mediated Cyclization of 2‐(1‐Aryl‐2‐methoxyethenyl)benzaldehyde Phenylhydrazones

2‐(1‐Aryl‐2‐methoxyethenyl)benzaldehydes 2 , obtained by successive treatment of 1‐(1‐aryl‐2‐methoxyethenyl)‐2‐bromobenzenes 1 with BuLi and 1‐formylpiperidine, were transformed to the corresponding phenylhydrazones 3 on treatment with PhNHNH₂. When these hydrazones were allowed to react with conc. HBr, cyclization, followed by dehydrogenation with air occurred, furnished 3‐aryl‐2‐methoxyinden‐1‐one (Z)‐phenylhydrazones 4 .     

Tri‐n‐butyltin binding to a low‐affinity site decreases the F1FO‐ATPase sensitivity to oligomycin in mussel mitochondria

In mussel digestive gland mitochondria the environmental pollutant tri‐n‐butyltin (TBT), other than strongly inhibiting ATPase activity at <1.0 μ m , at ≥1.0 μ m concentration was previously found to desensitize F₁F_O‐ATPase to the antibiotic oligomycin. While F₁F_O‐ATPase inhibition is widely known as one of the main mitochondrial damages caused by TBT, the enzyme's desensitization to oligomycin was quite unexpected. The possible mechanisms involved are here stepwise approached, aiming at enlightening the molecular mechanism(s) of TBT toxicity and the still poorly investigated oligomycin interaction with F_O. The findings strongly suggest that the oligomycin desensitization directly stems from the covalent binding of TBT to monothiols of the F₁F_O‐ATPase. This binding implies sulfur oxidation, irrespective of the possible formation of radical species in mitochondria, a mechanism which does not seem to be involved here. It is hypothesized that TBT interacts with the enzyme complex in at least two sites distinguished by different affinities: TBT binding to the high‐affinity site would lead to ATPase inhibition, while TBT binding to monothiols in the low‐affinity site could mirror the decrease in F₁F_O‐ATPase oligomycin sensitivity at ≥1.0 μ m TBT. Experiments carried out on inside‐out submitochondrial particles hint that TBT binding destabilizes the oligomycin‐blocked F_O conformation, allowing proton flux recovery within F_O, without uncoupling the catalytic function from proton channeling. Copyright © 2012 John Wiley & Sons, Ltd.     

Microwave-accelerated Synthesis of Some (±)-1-Aryl-5-chloroisochromans

Solventless one-pot synthesis of some new (±)-1-aryl-5-chloroisochromans by cyclocondensation of 2-(2-chlorophenyl)ethanol with aromatic aldehydes via an acid catalyzed oxa-Pictet-Spengler reaction under microwave irradiation is described.     

Understanding the basis of I50V‐induced affinity decrease in HIV‐1 protease via molecular dynamics simulations using polarized force field

Human immunodeficiency virus (HIV)‐1 protease is one of the most promising drug target commonly utilized to combat Acquired Immune Deficiency Syndrome (AIDS). However, with the emergence of drug resistance arising from mutations, the efficiency of protease inhibitors (PIs) as a viable treatment for AIDS has been greatly reduced. I50V mutation as one of the most significant mutations occurring in HIV‐1 protease will be investigated in this study. Molecular dynamics (MD) simulation was utilized to examine the effect of I50V mutation on the binding of two PIs namely indinavir and amprenavir to HIV‐1 protease. Prior to the simulations conducted, the electron density distributions of the PI and each residue in HIV‐1 protease are derived by combining quantum fragmentation approach molecular fractionation with conjugate caps and Poisson–Boltzmann solvation model based on polarized protein‐specific charge scheme. The atomic charges of the binding complex are subsequently fitted using delta restrained electrostatic potential (delta‐RESP) method to overcome the poor charge determination of buried atom. This way, both intraprotease polarization and the polarization between protease and the PI are incorporated into partial atomic charges. Through this study, the mutation‐induced affinity variations were calculated and significant agreement between experiments and MD simulations conducted was observed for both HIV‐1 protease‐drug complexes. In addition, the mechanism governing the decrease in the binding affinity of PI in the presence of I50V mutation was also explored to provide insights pertaining to the design of the next generation of anti‐HIV drugs. © 2015 Wiley Periodicals, Inc.     

A Novel and Efficient Synthesis of 3‐[(4,5‐Dihydro‐1H‐pyrrol‐3‐yl)carbonyl]‐2H‐chromen‐2‐ones (=3‐[(4,5‐Dihydro‐1H‐pyrrol‐3‐yl)carbonyl]‐2H‐1‐benzopyran‐2‐ones)

An efficient one‐pot synthesis of 3‐[(4,5‐dihydro‐1H‐pyrrol‐3‐yl)carbonyl]‐2H‐chromen‐2‐one (=3‐[(4,5‐dihydro‐1H‐pyrrol‐3yl)carbonyl]‐2H‐1‐benzopyran‐2‐one) derivatives 4 by a four‐component reaction of a salicylaldehyde 1 , 4‐hydroxy‐6‐methyl‐2H‐pyran‐2‐one, a benzylamine 2 , and a diaroylacetylene (=1,4‐diarylbut‐2‐yne‐1,4‐dione) 3 in EtOH is reported. This new protocol has the advantages of high yields (Table), and convenient operation. The structures of these coumarin (=2H‐1‐benzopyran‐2‐one) derivatives, which are important compounds in organic chemistry, were confirmed spectroscopically (IR, ¹H‐ and ¹³C‐NMR, and EI‐MS) and by elemental analyses. A plausible mechanism for this reaction is proposed (Scheme 2).     

Studies on the Reaction of α‐Chloroformylarylhydrazine Hydrochloride1 with N‐Heterocyclic Compounds

In addition to pyridines, α‐chloroformylarylhydrazine hydrochloride 1 can also react with some N‐heterocyclic compounds. The cycloaddition of 1 with isoquinoline was achieved to obtain 3 . The production of 4, 5, 6 given by cycloaddition of 1 with pyridazine was de pendent on the reaction condition. Some heterocyclic compounds bearing an X‐C=N (X:S, N) group on the ring can react with 1 to gain the derivatives of 2,4‐dihydro‐1,2,4‐triazol‐3‐one. 7, 8, 9 and 10 were given by reaction of 1 with 1,3,5‐triazine, 1,4,5,6‐tetrahydropyrimidine, 1,3‐thiazole and 2‐amino‐1,3‐thiazole, respectively. The reactions for 2‐amino‐1,3,4‐thiadiazole and 3‐amino‐1,2,4‐triazole had the same product 11 .     

Studies of Interaction between Ergosta‐4,6,8(14),22‐tetraen‐3‐one (Ergone) and Human Serum Albumin by Molecular Spectroscopy and Modeling

Our previous experimental results have shown that ergosta‐4,6,8(14),22‐tetraen‐3‐one (ergone) is one of the main bioactive components of Polyporus umbellatus. The efficacy of ergone binding to human serum albumin (HSA) is critical for pharmacokinetic behavior of ergone. The interactions between ergone and HSA under simulative physiological conditions were investigated by the methods of fluorescence spectroscopy, absorption and circular dichroism spectroscopy. Fluorescence data revealed that the fluorescence quenching of HSA by ergone was the result of the formation of the ergone‐HSA complex. According to the modified Stern‐Volmer equation, the binding constants (K_a) between ergone and HSA were determined. The thermodynamic parameters, enthalpy change (ΔH) and entropy change (ΔS) for the reaction were calculated to be 0.989 kJ mol^‐1 and 11.214 J mol^‐1 K^‐1, indicating that the hydrogen bonds and hydrophobic interactions played a dominant role in the binding of ergone to HSA. The conformational investigation showed that the presence of ergone decreased the α‐helical content of HSA and induced the slight unfolding of the polypeptides of protein. Furthermore, displacement experiments using warfarin and ibuprofen indicated that ergone could bind to site I of HSA, which was also in agreement with the results of the molecular modeling.     

Photocycloaddition Reactions of 5,5‐Dimethyl‐3‐(3‐methylbut‐3‐en‐1‐ynyl)cyclohex‐2‐en‐1‐one

The title cyclohexenone 1d undergoes photodimerization selectively at the exocyclic C?C bond to give a 1 : 1 mixture of 1,2‐dialkynyl‐1,2‐dimethylcyclobutanes 6 and 7 . On irradiation in the presence of 2,3‐dimethylbuta‐1,3‐diene, 1d affords bicyclo[8.4.0]tetradeca‐1,2,3,7‐tetraen‐11‐one 9 . This – formal – (6+4)‐cycloadduct undergoes quantitative isomerization to 3‐cycloheptadienyl‐2,5,5‐trimethylcyclohex‐2‐enone 11 on treatment with basic silica gel.     

A Convenient Synthesis of 2,3‐Dihydro‐3‐methylidene‐1H‐isoindol‐1‐ones by Reaction of 2‐Formylbenzo­nitriles with Dimethyloxosulfonium Methylide

A facile method for the synthesis of 2,3‐dihydro‐3‐methylidene‐1H‐isoindol‐1‐one and its derivatives carrying substituent(s) at C(5) and/or C(6) has been developed. The reaction of 2‐formylbenzonitrile ( 1a ) with dimethyloxosulfonium methylide, generated by the treatment of trimethylsulfoxonium iodide with NaH in DMSO/THF at 0°, resulted in the formation of 2,3‐dihydro‐3‐methylidene‐1H‐isoindol‐1‐one ( 2a ) in 77% yield. Similarly, six 2‐formylbenzonitriles carrying substituent(s) at C(4) and/or C(5), i.e., 1b – 1g , also gave the corresponding expected products 2b – 2g in comparable yields.     

Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexane

Force field parameters for polarizable coarse‐grained (CG) supra‐atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine‐grained (FG) CH₂r united atoms of the cyclohexane ring, and one representing three FG CH₂r united atoms. Electronic polarizability is represented by a massless charge‐on‐spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self‐diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.     

Separation of HIV‐1 gag virus‐like particles from vesicular particles impurities by hydroxyl‐functionalized monoliths

The downstream processing of enveloped virus‐like particles is very challenging because of the biophysical and structural similarity between correctly assembled particles and contaminating vesicular particles present in the feedstock. We used hydroxyl‐functionalized polymethacrylate monoliths, providing hydrophobic and electrostatic binding contributions, for the purification of HIV‐1 gag virus‐like particles. The clarified culture supernatant was conditioned with ammonium sulfate and after membrane filtration loaded onto a 1 mL monolith. The binding capacity was 2 × 10¹²/mL monolith and was only limited by the pressure drop. By applying either a linear or a step gradient elution, to decrease the ammonium sulfate concentration, the majority of double‐stranded DNA (88–90%) and host cell protein impurities (39–61%) could be removed while the particles could be separated into two fractions. Proteomic analysis and evaluation of the p24 concentration showed that one fraction contained majority of the HIV‐1 gag and the other fraction was less contaminated with proteins originated from intracellular compartments. We were able to process up to 92 bed volumes of conditioned loading material within 3 h and eluted in average 7.3 × 10¹¹ particles per particle fraction, which is equivalent to 730 vaccination doses of 1 × 10⁹ particles.