Lupei Du

Selecting aptamers for a glycoprotein through the incorporation of the boronic acid moiety.

The first general method for the selection of boronic acid-based aptamers (boronolectins) that allows for glycan substructure focusing is described. Using fibrinogen as a model glycoprotein, we have selected boronic acid-modified DNA aptamers that have high affinities (low nM Kd) and the ability to recognize changes in the glycosylation site. The method developed should also be applicable to the development of aptamers for other glycoproducts, such as glycolipids and glycopeptides.

Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor

The 14-3-3 family of phosphoserine/threonine-recognition proteins engage multiple nodes in signaling networks that control diverse physiological and pathophysiological functions and have emerged as promising therapeutic targets for such diseases as cancer and neurodegenerative disorders. Thus, small molecule modulators of 14-3-3 are much needed agents for chemical biology investigations and therapeutic development. To analyze 14-3-3 function and modulate its activity, we conducted a chemical screen and identified 4-[(2Z)-2-[4-formyl-6-methyl-5-oxo-3-(phosphonatooxymethyl)pyridin-2-ylidene]hydrazinyl]benzoate as a 14-3-3 inhibitor, which we termed FOBISIN (FOurteen-three-three BInding Small molecule INhibitor) 101. FOBISIN101 effectively blocked the binding of 14-3-3 with Raf-1 and proline-rich AKT substrate, 40 kDa and neutralized the ability of 14-3-3 to activate exoenzyme S ADP-ribosyltransferase. To provide a mechanistic basis for 14-3-3 inhibition, the crystal structure of 14-3-3ζ in complex with FOBISIN101 was solved. Unexpectedly, the double bond linking the pyridoxal-phosphate and benzoate moieties was reduced by X-rays to create a covalent linkage of the pyridoxal-phosphate moiety to lysine 120 in the binding groove of 14-3-3, leading to persistent 14-3-3 inactivation. We suggest that FOBISIN101-like molecules could be developed as an entirely unique class of 14-3-3 inhibitors, which may serve as radiation-triggered therapeutic agents for the treatment of 14-3-3-mediated diseases, such as cancer.

Bioluminescent Probe for Hydrogen Peroxide Imaging in Vitro and in Vivo

Reactive oxygen species (ROS) often have significant roles in mediating redox modifications and other essential physiological processes, such as biological process regulation and signal transduction. Considering that H2O2 is a substantial member of ROS, detection and quantitation of H2O2 undertakes important but urgent responsibility. In this report, a bioluminescent probe for detecting H2O2 was well designed, synthesized, and evaluated. This probe was designed into three parts: a H2O2-sensitive aryl boronic acid, a bioluminescent aminoluciferin moiety, and a self-immolative linker. After extensive evaluation, this probe can selectively and sensitively react with H2O2 to release aminoluciferin. It should be pointed out that this probe is a potential bioluminescent sensor for H2O2 since it can provide a promising toolkit for real-time detection of the H2O2 level in vitro, in cellulo, and in vivo.

Coumarin-based fluorescent probes for H2S detection.

Although hydrogen sulfide (H2S) has been known as a toxic gas with unpleasant rotten egg smell, the correlation between H2S and physiological processes has attracted scientists to develop brand new methods to monitor such a gaseous molecule in vitro and in vivo. Herein, we described a couple of coumarin-based fluorescent probes (1a and 1b) that can be activated by reduction of azide to amine in the presence of H2S. It should be emphasized that probe 1b demonstrated high selectivity and sensitivity for H2S over other relevant reactive sulfur species in vitro, as well as identified exogenous H2S in living cells.

How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials

Molecular docking, which is the indispensable emphasis in predicting binding conformations and energies of ligands to receptors, constructs the high-throughput virtual screening available. So far, increasingly numerous molecular docking programs have been released, and among them, AutoDock 4.2 is a widely used docking program with exceptional accuracy. It has heretofore been substantiated that the calculation of partial charge is very fundamental for the accurate conformation search and binding energy estimation. However, no systematic comparison of the significances of electrostatic potentials on docking accuracy of AutoDock 4.2 has been determined. In this paper, nine different charge-assigning methods, including AM1-BCC, Del-Re, formal, Gasteiger-Hückel, Gasteiger-Marsili, Hückel, Merck molecular force field (MMFF), and Pullman, as well as the ab initio Hartree-Fock charge, were sufficiently explored for their molecular docking performance by using AutoDock4.2. The results clearly demonstrated that the empirical Gasteiger-Hückel charge is the most applicable in virtual screening for large database; meanwhile, the semiempirical AM1-BCC charge is practicable in lead compound optimization as well as accurate virtual screening for small databases.

Aptamer-Based Carbohydrate Recognition

Carbohydrates have been revealed to play fundamental roles in diverse biological phenomena, such as being recognition sites and biomarkers. Recently, ample nucleic acid aptamers guided for carbohydrate recognition have already been isolated and characterized through SELEX methodology. This review would like to present and discuss these aptamers toward recognizing various carbohydrate targets: monosaccharides, oligosaccharides, polysaccharides, aminoglycoside antibiotics and glycans from glycoproteins. High affinity carbohydrate aptamers that we reviewed herein might shed light on the development of a tool to augment drug discovery creations.

Discovery of Bioluminogenic Probes for Aminopeptidase N Imaging

To find an approach that can image the hydrolysis activity of aminopeptidase N (APN) both in vitro and in vivo, three bioluminescent probes have been well designed and synthesized herein. All of them can be recognized and hydrolyzed by APN to produce bioluminescence emission in the presence of firefly luciferase. To the best of our knowledge, they are the first bioluminescent probes for imaging APN in deep tissues and living animals.

How to generate reliable and predictive CoMFA models.

Comparative Molecular Field Analysis (CoMFA) is a mainstream and down-to-earth 3D QSAR technique in the coverage of drug discovery and development. Even though CoMFA is remarkable for high predictive capacity, the intrinsic data-dependent characteristic still makes this methodology certainly be handicapped by noise. Its well known that the default settings in CoMFA can bring about predictive QSAR models, in the meanwhile optimized parameters was proven to provide more predictive results. Accordingly, so far numerous endeavors have been accomplished to ameliorate the CoMFA models robustness and predictive accuracy by considering various factors, including molecular conformation and alignment, field descriptors and grid spacing. Herein, we would like to make a comprehensive survey of the conceivable descriptors and their contribution to the CoMFA models predictive ability.

Modeling the binding modes of Kv1.5 potassium channel and blockers

The ultra-rapid delayed rectifier potassium current (I(Kur)), encoded by Kv1.5 gene, is the critical determinant of Phase I repolarization of action potential duration (APD). The evidences that Kv1.5 gene expresses more extensively in human atrial myocytes than in ventricle and the I(Kur) currents has not been recorded in the human ventricle, suggest Kv1.5 potassium channel as a selective target for the treatment of atrial fibrillation (AF). Recent mutagenesis studies have provided us some evidences that are useful in designing Kv1.5 blockers. In order to further evaluate these molecular biological information, the homology model of Kv1.5 potassium channel was established based on the Kv1.2 crystal structure (PDB entry: 2A79) using MODELLER 9v2 program. After the molecular dynamics refinement, the optimized homology model was assessed as a reliable structure by PROCHECK, ERRAT, WHAT-IF, PROSA2003 and DOPE graph. The results of molecular docking studies on different Kv1.5 inhibitors are in agreement with the published mutagenesis data. Based on the docking conformations, a pharmacophore model was developed by HipHop algorithm in order to probe the common features of blockers. By analyzing the results, active site architecture, certain key residues and pharmacophore common-features that are responsible for substrate specificity were identified on the Kv1.5 potassium channel, which would be very helpful in understanding the blockade mechanism of Kv1.5 potassium channel and providing insights into rational design of novel Kv1.5 blockers.

Toward Fluorescent Probes for G-Protein-Coupled Receptors (GPCRs)

G-protein-coupled receptors (GPCRs), a superfamily of cell-surface receptors that are the targets of about 40% of prescription drugs on the market, can sense numerous critical extracellular signals. Recent breakthroughs in structural biology, especially in holo-form X-ray crystal structures, have contributed to our understanding of GPCR signaling. However, actions of GPCRs at the cellular and molecular level, interactions between GPCRs, and the role of protein dynamics in receptor activities still remain controversial. To overcome these dilemmas, fluorescent probes of GPCRs have been employed, which have advantages of in vivo safety and real-time monitoring. Various probes that depend on specific mechanisms and/or technologies have been used to study GPCRs. The present review focuses on surveying the design and applications of fluorescent probes for GPCRs that are derived from small molecules or using protein-labeling techniques, as well as discussing some design strategies for new probes.