• Bulletin of the Korean Chemical Society
• /
• v.13 no.2
• /
• pp.119-122
• /
• 1992

The affinity chromatographic technique was applied to the isolation of Thromboxane Synthase, with a variety of imidazolyl alkanoic acids coupled Sepharose 2B including a gel (G in Table 4) which has one free COOH group in the bound affinity ligand. The effect of ligand structure on the "affinity" and "selectivity" for thromboxane synthase isolation is described.

• Microbiology and Biotechnology Letters
• /
• v.21 no.4
• /
• pp.336-341
• /
• 1993

In metal-affinify aqueous two-phase systems, protein partitioning is affected by a variety of parameters such as pH, the number of surface-accessible histidines, and the amount and partition coefficient of metallated polythylene glyco(PEG) ligand. To enhance partitioning of proteins with surface-accessible histidines, we have synthesized and used a (Cu(II)-ininodiacetic acid)$_2$-PEG20,000($Cu(II)_2IDA_2$-PEG20,000) as well as Cu(II)IDA-PEG5,000 as an affinity ligand. The partition coefficient of $Cu(II)_2-IDA_2$-PEG20,000 in a PEG5,000/dextran two-phase system was 30.1, which corresponded to a 3.8-fold increase over that of Cu(II)IDA-PEG5,000. The partitioning experiments were performed on four proteins, horse cytochrome c, S. cerevisiae cytochrome c, horse myoglobin, and sheep myoglobin. Partitioning of proteins which convey surface-accessible histidines was enhanced dramatically by the addition of $Cu(II)_2IDA_2$-PEG20,000 ligand. These results demonstrate that enhanced partitioning of metal-binding proteins in an aqueous two -phase system can by achieved by using an appropriate metallated PEG ligand.

• Proceedings of the Membrane Society of Korea Conference
• /
• 1993.04a
• /
• pp.12-15
• /
• 1993

방사선 graft 중합법을 이용하여, microfiltration hollow fiber(MF)에 affinity ligand로서 소수성 아미노산 (tryptophan)을 고정하였다. affinity막에 압력차를 주어 막의 안쪽으로 부터 바깥쪽으로 단백질 용액을 투과시키면서, 단백질의 흡착 성능을 알아보았다. affinity막이 확산이동 저항이 없는 우수한 분리 기능 재료인 것을 나타내었다.

• BMB Reports
• /
• v.31 no.2
• /
• pp.135-138
• /
• 1998

A previous study on a yeast protein tyrosine phosphatase, YPTP1, using synthetic phosphotyrosine-containing peptides with various sequences as substrates revealed that DADEpYDA exhibits high affinity ($K_m=4{\mu}M$) toward the enzyme. A modified version of this peptide, GDADEpmFDA, immobilized on a resin, was used in this study as an affinity ligand for the purification of YPTP1. Phosphonomethyl-phenylalanine (pmF) was used as a nonhydrolyzable analog of the phosphotyrosine (pY) residue, with properties similar to pY. A protected form of pmF, $Fmoc-pmF(^{t}Bu)_{2}-OH$, was chemically synthesized and introduced during solid-phase peptide sythesis. YPTP1 was onrexpressed in an E. coli strain carrying a plasmid pT7-7-ptpl. Affinity chromatography of the crude lysate afforded PTPI (39 kDa) of about 50% purity.

• Journal of Microbiology and Biotechnology
• /
• v.3 no.3
• /
• pp.161-167
• /
• 1993

Immobilized metal ion affinity chromatography (IMAC) was used to separate various types of recombinant hirudins from the culture broth. The wild type hirudin exhibited a retention in Cu(II)-chelated affinity chromatgoraphy since it contained a single exposed histidine at position 51. To obtain a stronger retention on an IDA-Cu(II) column, the hirudin variants were genetically engineered to contain one or two histidine (s) more than the wild type. While the affinity of the variants for IDA-Cu(II) ligand increased in comparison to that of the wild type, the antithrombin activities reduced to a certain degree. Cu(II), Ni(II) and Zn(II) ions were applied separately to the metal chelate column to investigate ligand specificity with respect to protein retention. As a result, the Cu(II) chelated chromatography gave the best resolution for all the hirudins tested and appeared to be the only IMAC that could be used generally for the purification of hirudins with a decreasing pH gradient.

• Interdisciplinary Bio Central
• /
• v.2 no.2
• /
• pp.6.1-6.5
• /
• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• Biomolecules & Therapeutics
• /
• v.4 no.1
• /
• pp.97-102
• /
• 1996

To investigate whether human $\beta$$_2$-adrenergic receptor devoid of the C-terminal two transmembrane helices retain its ligand binding activity and specificity, 5'780-bp DNA fragment of the receptor gene which encodes amino acid 1-260 of human $\beta$$_2$-adrenergic receptor was subcloned into the bacterial fusion protein expression vector and expressed as a form of glutathione-S-transferase (GST) fusion protein in E. coli DH5$\alpha$. The receptor fusion protein was expressed as a membrane bound form which was verified by SDS-PAGE and Western blot. The fusion protein expressed in this study specifically bound $\beta$-adrenergic receptor ligand [$^3$H] Dihydroalprenolol. In saturation ligand binding assay, the $K_{d}$ value was 7.6 nM which was similar to that of intact $\beta$$_2$-adrenergic receptor in normal animal tissue ( $K_{d}$=1~2 nM) and the $B_{max}$ value was 266 fmol/mg membrane protein. In competition binding assay, the order of binding affinity of various adrenergic receptor agonists to the fusion protein was isoproterenol》epinephrine norepinephrine, which was similar to that of intact receptor in normal animal tissue. These results suggest that N-terminal five transmembrane helices of the $\beta$$_2$-adrenergic receptor be sufficient to determine the ligand binding activity and specificity, irrespective of the presence or absence of the C-terminal two transmembrane helices.s.s.s.

• Biomolecules & Therapeutics
• /
• v.32 no.4
• /
• pp.442-450
• /
• 2024

The type-1 cannabinoid receptor (CB₁R) is a potential therapeutic target in several pathological conditions, including neuropsychological disorders and neurodegenerative diseases. Owing to their structural diversity, it is not easy to derive general structure-activity relationships (SARs) for CB₁R ligands. In this study, CB₁R ligands were classified into six structural families, and the corresponding SAR was determined for their affinities for CB₁R. In addition, we determined their functional activities for the activation of extracellular signal-regulated kinases (ERKs). Among derivatives of indol-3-yl-methanone, the highest ligand affinity was observed when a pentyl and a naphthalenyl group were attached to the N1 position of the indole ring and the carbon site of the methanone moiety, respectively. In the case of adamantane indazole-3-carboxamide derivatives, the presence of fluorine in the pentyl group, the substituent at the N1 position of the indazole ring, strongly increased the affinity for CB₁R. For (naphthalen-1-yl) methanone derivatives, the presence of 4-alkoxynaphthalene in the methanone moiety was more beneficial for the affinity to CB₁R than that of a heterocyclic ring. The functional activities of the tested compounds, evaluated through ERK assay, were correlated with their affinity for CB₁R, suggesting their agonistic nature. In conclusion, this study provides valuable insight for designing novel ligands for CB₁R, which can be used to control psychiatric disorders and drug abuse.

• Journal of Integrative Natural Science
• /
• v.3 no.3
• /
• pp.162-167
• /
• 2010

A pseudoreceptor combines structure-based and ligand-based techniques to represent a unifying concept for both receptor mapping and ligand matching. In this molecular modeling approach, there are opportunities to construct the pseudoreceptor models using a set of small molecules. To build a reliable pseudoreceptor model, we need a set of ligand molecules with known affinity (biological activity) to generate 3D bioactive conformation for each of these ligand molecules. Several software packages are available to generate a pseudoreceptor model and this can provide an entry point for structure based drug discovery in cases where receptor structure information is not available. In this review, we presented the concept of pseudoreceptor, as well as discussed about various software packages available to generate a pseudoreceptor model.

• Journal of Radiopharmaceuticals and Molecular Probes
• /
• v.4 no.2
• /
• pp.73-79
• /
• 2018

In our previous study, tricarbonyl $^{99m}Tc$-labeled TSPO-binding ligand, named $^{99m}Tc$-CB256, having positively charge (+1) was investigated but did not show promising results in in vivo environment despite of a nanomolar binding affinity for TSPO. Because the overall positively charge of $^{99m}Tc$-CB256 would likely interrupt its target protein uptake, we herein designed the neutral tricarbonyl-$^{99m}Tc$ labeled TSPO-binding ligand ($^{99m}Tc$-CB257, 1). $^{99m}Tc$-CB257 was prepared by the facile incorporation of the $[^{99m}Tc(CO)_3]^+$ into a N-(hydroxycarbonylmethyl)-2-picoly moiety in CB257. The radiochemical yield of $^{99m}Tc$-CB257 after HPLC purification was $54.1{\pm}2.4%$ (decay corrected, n = 3). The authentic Re-CB257 (2) was synthesized by using $(NEt_4)_2[Re(CO)_3Br_3]$ in 69.0% yield. The binding affinity of 2 for TSPO was measured in leukocyte and showed approximately 280 times higher than that observed for the positively charged (+1) ligand, Re-CB256 ($K_i=0.57{\pm}0.06nM$ versus $159.3{\pm}8.7nM$, respectively). Our results indicated that 1 can be considered potentially as a new SPECT radiotracer for TSPO-rich cancer and provides the foundation for further in vivo evaluation related with abnormal TSPO-overexpression environments.