Target binding and residence: a new determinant of DNA double-strand break repair pathway choice in CRISPR/Cas9 genome editing / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms, and holds tremendous promise in clinical applications. The efficiency and accuracy of the technology are partly determined by the target binding affinity and residence time of Cas9-single-guide RNA (sgRNA) at a given site. However, little attention has been paid to the effect of target binding affinity and residence duration on the repair of Cas9-induced DNA double-strand breaks (DSBs). We propose that the choice of DSB repair pathway may be altered by variation in the binding affinity and residence duration of Cas9-sgRNA at the cleaved target, contributing to significantly heterogeneous mutations in CRISPR/Cas9 genome editing. Here, we discuss the effect of Cas9-sgRNA target binding and residence on the choice of DSB repair pathway in CRISPR/Cas9 genome editing, and the opportunity this presents to optimize Cas9-based technology.

Angiotensin-converting enzyme inhibitory activity of polyphenolic compounds from Peperomia pellucida (L) Kunth: An in silico molecular docking study

This study aimed to predict the potential activity and interaction conformation of polyphenolic compounds fromPeperomia pellucida (L) Kunth (nine compounds) with angiotensin-converting enzyme (ACE) macromolecule by insilico molecular docking study. The crystal structure of ACE as a molecular target was obtained from the PDB database(PDB ID: 1UZF) with captopril as a native ligand. Molecular docking analysis was performed using AutoDockZn (100docking runs) based on the active site of Zn2+, the central grid was placed on Zn2+ with a box size of 40Á × 40Á ×40Á and a center of 40.835Á × 34.382Á × 44.607Á for selective inhibitors (MCO702) with a spacing of 0.375Á.Based on the docking results demonstrated that the prediction of each polyphenol compounds from P. pellucida hasthe potential of active as ACE inhibitors, it was indicated that docking results of each compound has lower affinitycompared to captopril (with binding affinity of −6.36 kcal/mol and the inhibition constant 21.81 μM), where themost moderate binding affinity (the most potential) was tetrahydrofuran lignin ((1R,2S,3S,5R)-3,5-bis(4-hydroxy3,5-dimethoxyphenyl)cyclopentane-1,2-diyl)bis-(methylene) diacetate) of −8.66 kcal/mol and the highest bindingaffinity (the less potential) was dillapiole (6-allyl-4,5-dimethoxybenzo[d][1,3]dioxole) of −4.99 kcal/mol, althoughwith different forms of interaction, bond, and constant inhibition. Based on the interaction of ACE binding site,5,6,7-trimethoxy-4-(2,4,5-trimethoxyphenyl)-3,4-dihydronaphthalen-1(2H)-one showed the most similar interactionwith the captopril ligand. These results are preliminary data for further research with predictions of target compoundbiological activity and interaction quickly, accurately, and inexpensively

Investigation of Non-covalent Interactions of 18-Crown-6 with Amino Acids in Gas Phase by Mass Spectrometry / 分析化学

The non-covalent interactions between 18-crown-6 (18c6) and 20 common types of protonated amino acids were explored by electrospray ionization mass spectrometry (ESI-MS).The mass spectra showed the formation of 1:1 stoichiometric non-covalent complexes between 18c6 and amino acids.The calibration curves and linear equations for the complexes of L-Phe,L-Tyr,L-Lys and L-Asp with 18c6 were established by mass spectrometric titration and used as reference values for competitive ESI-MS.Through competitive equilibrium,the binding constants for the complexes of 18c6 with other L-amino acids and their D-isomers were derived.It was found,as a general trend,lgKa for the complexes of 18c6 with the basic amino acid and the amino acid with alkyl side chain were larger than other complexes,and among the amino acids with alkyl side chain,Gly and Ala exhibited greater 18c6 binding affinities.As for Ser and Thr,the intramolecular hydrogen bond between the nitrogen atom from terminal NH2and the oxygen atom from carboxyl may impede their protonated amino-group to attack the 18c6.Furthermore,Gln and Asn exhibited lower 18c6 binding affinities probably due to effects of electron-withdrawing group of acylamide.Finally,the chiral selectivity of 18c6 for 19 L-,or D-amino acids was measured by ESI-MS,indicating 18c6 could only recognize some neutral amino acid isomers.

Establishment and verification of assay method for the receptor binding affinity of a PEGylated Exendin-4 analogue / 中国药科大学学报

@#The assay method of GLP-1 receptor binding affinity for a long-acting hypoglycemic peptide—PEgylated Exendin-4 analogue(PE)was optimized and established based on the luciferase reporter gene approach. CHO-GLP-1R-CRE-Luc+ cells were previously constructed in our lab followed by the verification of methodology. This assay method showed good specificity and robustness as well as high accuracy and precision when PE was incubated with the cell for 4 h, the luminescent substrate reacted with cell lysates for 15 min and the concentration for PE ranged 5. 7×10-3-1. 5×103 nmol/L, on which condition this developed method is in accordance with General Principles of Analytical Method Validation Techniques for Biological Products Quality Control. This study also lays the foundations for rapid evaluation and screening of GLP-1 receptor agonist drugs.

Quantum Chemical Investigation of C12 and C6 Position of Oseltamivir Sialidase Antiviral Inhibitor.

The ab initio and DFT investigation of C12 & C6 position of oseltamivir sialidase inhibitor reveals that the absence of pyranose oxygen ring in the inhibitor structure drastically increases binding affinity of the inhibitor in relation to the pyranose based inhibitors. The investigation further reveals that the methyl and ethyl group at the C12 position have substantial binding affinity due to their inherent hyperconjugative and charge transfer effects between C4 and C13 bond. The analysis at C6 position of oseltamivir inhibitor discloses that the methyl amine group increases the binding affinity due to their strong hydrogen bonding tendency with the vicinity receptors. Hence, the investigation validates that the 12-methyl-oseltamivir, 12-ethyl-oseltamivir and 6-methylamine-oseltamivir inhibitor become the potential candidate for the development effective sialidase antiviral inhibitors.

Binding affinity of asiatic acid derivatives design against Inducible Nitric Oxide Synthase and ADMET Prediction.

Asiatic acid (AA) is a pentacyclic triterpenoid compound isolated from pegagan (Centella asiatica) and is reported to show anti-inflammatory activities by inhibiting inducible nitric oxide synthase (iNOS), an isoenzyme responsible for the catalysis of nitric oxide formation. The aim of this study was to obtain information regarding binding affinity of some potential asiatic acid derivatives to iNOS as well as pharmacokinetic properties including oral absorption, distribution, metabolism, and toxicity (ADME/T) using in silico methods. Twelve AA derivatives that were produced by modeling of AA on A- or C-ring or its carboxylic acid group, were included in this study. The affinities of these compounds were studied using molecular docking methods, while pharmacokinetic properties were studied using the PreADMET online program. The results showed that eight AA derivative designs have lower free energy binding (FEB) in comparison to AA (–9.79 kcal/mol), while four of the compound designs showed higher FEB than AA. 2,3-dioxo-11,13 diene-23-carboxy asiatic acid (7) showed the lowest FEB of -11.33 kcal/mol. This compound has the human intestinal absorption (HIA), Caco-2 cell permeability, and plasma protein binding values of 96.62%, 20.90 (nm/Sec.), and 98.46%, respectively, which are comparable to those of AA and other AA derivatives. It is concluded that 2,3-dioxo-11,13 diene-23-carboxy asiatic acid (7) is an AA derivative with potential to be developed as a potential iNOS inhibitor.

Dependence Potential of the Synthetic Cannabinoids JWH-073, JWH-081, and JWH-210: In Vivo and In Vitro Approaches

Synthetic cannabinoids (CBs) such as the JWH series have caused social problems concerning their abuse liability. Because the JWH series produces euphoric and hallucinogenic effects, they have been distributed illegally under street names such as "Spice" and "Smoke". Many countries including Korea have started to schedule some of the JWH series compounds as controlled substances, but there are a number of JWH series chemicals that remain uncontrolled by law. In this study, three synthetic CBs with different binding affinities to the CB1 receptor (JWH-073, 081, and 210) and Delta9-tetrahydrocannabinol (Delta9-THC) were evaluated for their potential for psychological dependence. The conditioned place preference test (unbiased method) and self-administration test (fixed ratio of 1) using rodents were conducted. Ki values of the three synthetic cannabinoids were calculated as supplementary data using a receptor binding assay and overexpressed CB1 protein membranes to compare dependence potential with CB1 receptor binding affinity. All mice administered JWH-073, 081, or 210 showed significantly increased time spent at unpreferred space in a dose-dependence manner in the conditioned place preference test. In contrast, all tested substances except Delta9-THC showed aversion phenomenon at high doses in the conditioned place preference test. The order of affinity to the CB1 receptor in the receptor binding assay was JWH-210 > JWH-081 >> JWH-073, which was in agreement with the results from the conditioned place preference test. However, no change in self-administration was observed. These findings suggest the possibility to predict dependence potential of synthetic CBs through a receptor binding assay at the screening level.

Exploring the binding affinities of p300 enzyme activators CTPB and CTB using docking method.

CREB binding protein (CBP) and E1A binding protein p300, also known as p300 are functionally related transcriptional co-activators (CoAs) and histone acetyltransferases (HATs). Some small molecules, which target HATs can activate or inhibit the p300 enzyme potently. Here, we report the binding affinities of two small molecules CTPB [N-(4-chloro- 3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide] and CTB [N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide] with p300 using docking method to obtain the insight of their interaction with p300. These small molecules bind to the enzyme, subsequently causing a structural change in the enzyme, which is responsible for the HAT activation. CTB exhibits higher binding affinity than CTPB, and their lowest docked energies are -7.72, -1.18 kcal/mol, respectively. In CTPB molecule, phenolic hydroxyl of Tyr1397 interacts with the non-polar atoms C(5E) and C(5F), and forms polar-non polar interactions. Similar interactions have also been observed in CTB. The residues Tyr1446 and Cys1438 interact with the non-pentadecyl atoms. Further, the docking study predicts a N-HO hydrogen bonding interaction between CTB and Leu1398, in which the HO contact distance is 2.06 Å. The long pentadecyl chain of CTPB reduces the formation of hydrogen bond with the p300. The H-bond interaction could be the key factor for the better activation of CTB.

Studies on the Biological Behaviors of Taxol Derivatives / 대한핵의학회잡지

This study was designed to prospect the 'In-labelled paclitaxel as tumor imaging agent. In order to provide a taxol molecule with a functional group which is able to chelate In-lll, taxol-DTPA conjugate and 2-hemisuccinyltaxol were synthesized by esterification of taxol at C-2 on C-13 carbon with DTPA anhydride and succinic anhydride, respectively. Synthesis yield of the taxol derivatives was 34% for taxol- DTPA and 80% for 2'-hemisuccinyltaxol. Cytotoxicity of the taxol derivatives were measured by MTT method toward cell lines HT29, B16, P388, and CT26. The cytotoxic activities of the taxol derivatives were maintained, although less active than taxol. Radiolabelling of the taxol derivatives were proceeded directly with 111InCh or indirectly with 111In-citrate(ligand-exchange method). The ligand-exchane methocl was not suitable because some precipitat:es appeared during the reaction. On the contrary, by direct radiolabelling methnd, we were able to obtain taxol DTPA-111In in 100% radiochemical yield. However, 2'-hemisuccinyltaxol was not labellecl by both methods. Yield and radiochemiral purity of the radiolabelled com- pound were determined by HPI.C, paper chromatography and instant thin layer chromatography. Taxol-DTPA-111In was characterized to be hydrophilic by lipophi- licity test, and nearly non-adhesive to HT29, E316, P388, and CT26 by cell hinding affinity test. Binding affinity of the taxol-DTPA-111In complex to serum proteins was also examined by protein precipitation with 30% trichloroacetic acid. The results showed that 309o of the taxol-DTPA-111In complex binds with serum proteins.