Yingyi Chen

ASD: a comprehensive database of allosteric proteins and modulators.

Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloSteric Database (ASD), the first online database that provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Currently, ASD contains 336 allosteric proteins from 101 species and 8095 modulators in three categories (activators, inhibitors and regulators). Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area. Integrating the information of allosteric proteins in ASD should allow for the identification of specific allosteric sites of a given subtype among proteins of the same family that can potentially serve as ideal targets for experimental validation. In addition, modulators curated in ASD can be used to investigate potent allosteric targets for the query compound, and also help chemists to implement structure modifications for novel allosteric drug design. Therefore, ASD could be a platform and a starting point for biologists and medicinal chemists for furthering allosteric research. ASD is freely available at http://mdl.shsmu.edu.cn/ASD/.

Crystal Structures of PI3Kα Complexed with PI103 and Its Derivatives: New Directions for Inhibitors Design

The phosphatidylinositol 3-kinase (PI3K) signaling pathway plays important roles in cell proliferation, growth, and survival. Hyperactivated PI3K is frequently found in a wide variety of human cancers, validating it as a promising target for cancer therapy. We determined the crystal structure of the human PI3Kα-PI103 complex to unravel molecular interactions. Based on the structure, substitution at the R1 position of the phenol portion of PI103 was demonstrated to improve binding affinity via forming a new H-bond with Lys802 at the bottom of the ATP catalytic site. Interestingly, the crystal structure of the PI3Kα-9d complex revealed that the flexibility of Lys802 can also induce additional space at the catalytic site for further modification. Thus, these crystal structures provide a molecular basis for the strong and specific interactions and demonstrate the important role of Lys802 in the design of novel PI3Kα inhibitors.

Insights into the role of magnesium triad in myo-inositol monophosphatase: metal mechanism, substrate binding, and lithium therapy.

myo-Inositol monophosphatase (IMPase) plays a pivotal role in the intracellular phosphatidylinositol cell signaling pathway. It has attracted considerable attention as a putative therapeutic target for lithium therapy in the treatment of bipolar disorder. A trio of activated cofactor Mg²⁺ ions is required for inositol monophosphate hydrolysis by IMPase. In the present study, computational studies, including two-layered ONIOM-based quantum mechanics/mechanical mechanics (QM/MM) calculations, molecular modeling, and molecular dynamics (MD) simulations, were performed to ascertain the role of the Mg²⁺ triad in the IMPase active site. The QM/MM calculations show that the structural identity of the nucleophilic water molecule W1 shared by Mg²⁺-1 and Mg²⁺-3, activated by Thr95/Asp47 dyad, is a hydroxide ion. Moreover, Mg²⁺-3 needs to be conjugated with Mg²⁺-1 in the binding site to create the activated nucleophilic hydroxide ion in accordance with the three-metal ion catalytic mechanism. The MD simulation of the IMPase-substrate-Mg²⁺ complex shows that the three Mg²⁺ ions promote substrate binding and help fix the phosphate moiety of the substrate for nucleophilic attack by the hydroxide ion. When Mg²⁺-2 is displaced with Li⁺, the MD simulations of the postreaction complex indicate that the conformation of the catalytic loop (residues 33 to 44) is disrupted and water molecule W2 does not coordinate with Li⁺. This disruption traps the inorganic phosphate and inositolate in the active site, which lead to IMPase inhibition. By contrast, in the native Mg²⁺ system, the W2 ligated by Mg²⁺-2 and Asp200 aids in protonation of the leaving inositolate moiety.

How calcium inhibits the magnesium‐dependent kinase gsk3β: A molecular simulation study

Glycogen synthase kinase 3β (GSK3β) is a ubiquitous serine/threonine kinase that plays a pivotal role in many biological processes. GSK3β catalyzes the transfer of γ‐phosphate of ATP to the unique substrate Ser/Thr residues with the assistance of two natural activating cofactors Mg2+. Interestingly, the biological observation reveals that a non‐native Ca2+ ion can inhibit the GSK3β catalytic activity. Here, the inhibitory mechanism of GSK3β by the displacement of native Mg2+ at site 1 by Ca2+ was investigated by means of 80 ns comparative molecular dynamics (MD) simulations of the GSK3β···Mg2+‐2/ATP/ Mg2+‐1 and GSK3β···Mg2+‐2/ATP/Ca2+‐1 systems. MD simulation results revealed that using the AMBER point charge model force field for Mg2+ was more appropriate in the reproduction of the active site architectural characteristics of GSK3β than using the magnesium‐cationic dummy atom model force field. Compared with the native Mg2+ bound system, the misalignment of the critical triphosphate moiety of ATP, the erroneous coordination environments around the Mg2+ ion at site 2, and the rupture of the key hydrogen bond between the invariant Lys85 and the ATP Oβ2 atom in the Ca2+ substituted system were observed in the MD simulation due to the Ca2+ ion in active site in order to achieve its preferred sevenfold coordination geometry, which adequately abolish the enzymatic activity. The obtained results are valuable in understanding the possible mechanism by why Ca2+ inhibits the GSK3β activity and also provide insights into the mechanism of Ca2+ inhibition in other structurally related protein kinases. Proteins 2013.

Toward an understanding of the sequence and structural basis of allosteric proteins

Allostery is the most efficient means of regulating protein functions, ranging from the control of metabolic mechanisms to signal transduction pathways. Although allosteric regulation has been recognized for half a century, our knowledge is limited to the characteristics of allosteric proteins and the structural coupling of allosteric sites and modulators. In this paper, we present a comprehensive analysis of allosteric proteins that provides insight into the foundation of allosteric interactions by revealing a series of common features in the allosteric proteins. Allosteric proteins mainly appear in transferases, and phosphorylation is the most common type of modification found in allosteric proteins. Disorders related to allosteric proteins primarily comprise metabolic diseases and cancers. In general, allosteric proteins prefer to exist as monomers or even-numbered multimers. Greater stability and hydrophobicity are observed in allosteric proteins than in general proteins. Further analysis of the allosteric sites reveals a series of buried and compact pockets composed of significantly greater hydrophobic surface area than the corresponding orthosteric sites. The hydrophobicity of the allosteric sites plays a dominant role in the binding of allosteric modulators as observed in the analysis of 106 diverse allosteric protein-modulator pairs. These results may be of great significance in predicting which proteins are allosteric and in designing novel triggers to inhibit or activate proteins of interest.

A Novel Inhibitor of Human La Protein with Anti-HBV Activity Discovered by Structure-Based Virtual Screening and In Vitro Evaluation

Background Over 350 million people worldwide are infected with hepatitis B virus (HBV), a major cause of liver failure and hepatocellular carcinoma. Current therapeutic agents are highly effective, but are also associated with development of viral resistance. Therefore, strategies for identifying other anti-HBV agents with specific, but distinctive mechanisms of action are needed. The human La (hLa) protein, which forms a stabilizing complex with HBV RNA ribonucleoprotein to promote HBV replication, is a promising target of molecular therapy. Aims This study aimed to discover novel inhibitors of hLa that could inhibit HBV replication and expression. Methods A multistage molecular docking approach was used to screen a Specs database and an in-house library against hLa binding sites. Sequential in vitro evaluations were performed to detect potential compounds with high scores in HepG2.2.15 cells. Results Of the 26 potential compounds with high scores chosen for experimental verification, 12 had HBV DNA inhibition ratios of less than 50% with P<0.05. Six had significant inhibition of HBV e antigen (HBeAg) levels, and 13 had significant inhibition of HBV surface antigen (HBsAg) levels by in vitro assays. Compounds HBSC-11, HBSC-15 and HBSC-34 (HBSC is system prefix for active compounds screened by the library) were selected for evaluation. HBSC-11 was found to have an obvious inhibitory effect on hLa transcription and expression. Conclusions Our findings suggest that anti-HBV activity of HBSC-11 may be mediated by a reduction in hLa levels. In addition, our data suggest the potential clinical use of hLa inhibitors, such as HBSC-11, for treating HBV infection.

Identification of novel compounds for human bitter taste receptors.

The finely tuned bitter taste sensing in humans is orchestrated by a group of 25 bitter taste receptors (TAS2Rs), which belong to the G‐protein‐coupled receptor superfamily. TAS2Rs are expressed in the specialized taste bud cells of the gustatory system and perceive a plethora of bitter substances with versatile structures. To date, more than one hundred bitter ligands have been matched with their cognate receptors, but the understanding of the molecular mechanisms of TAS2Rs remains limited. Additionally, the extraoral expression of TAS2R genes was found in the gastrointestinal tract and respiratory system, which suggests other important physiological functions for TAS2Rs. To gain insight into the physiological functions of TAS2Rs, we established a heterologous expression system and characterized the response of 24 TAS2Rs against a library of potential bitter compounds. Among these bitter compounds of interest, 18 bitter compounds activated 16 TAS2Rs, representing 42 tastant–receptor pairs. We then calculated 14 descriptor properties for the 18 positive compounds. By comparison with 102 previously annotated bitter compounds in the database, we discovered common descriptor properties that may contribute to the discovery of additional bitter ligands and further expand the known molecular receptive ranges of human TAS2Rs.

HEMD: An Integrated Tool of Human Epigenetic Enzymes and Chemical Modulators for Therapeutics

Background Epigenetic mechanisms mainly include DNA methylation, post-translational modifications of histones, chromatin remodeling and non-coding RNAs. All of these processes are mediated and controlled by enzymes. Abnormalities of the enzymes are involved in a variety of complex human diseases. Recently, potent natural or synthetic chemicals are utilized to establish the quantitative contributions of epigenetic regulation through the enzymes and provide novel insight for developing new therapeutics. However, the development of more specific and effective epigenetic therapeutics requires a more complete understanding of the chemical epigenomic landscape. Description Here, we present a human epigenetic enzyme and modulator database (HEMD), the database which provides a central resource for the display, search, and analysis of the structure, function, and related annotation for human epigenetic enzymes and chemical modulators focused on epigenetic therapeutics. Currently, HEMD contains 269 epigenetic enzymes and 4377 modulators in three categories (activators, inhibitors, and regulators). Enzymes are annotated with detailed description of epigenetic mechanisms, catalytic processes, and related diseases, and chemical modulators with binding sites, pharmacological effect, and therapeutic uses. Integrating the information of epigenetic enzymes in HEMD should allow for the prediction of conserved features for proteins and could potentially classify them as ideal targets for experimental validation. In addition, modulators curated in HEMD can be used to investigate potent epigenetic targets for the query compound and also help chemists to implement structural modifications for the design of novel epigenetic drugs. Conclusions HEMD could be a platform and a starting point for biologists and medicinal chemists for furthering research on epigenetic therapeutics. HEMD is freely available at http://mdl.shsmu.edu.cn/HEMD/.

2-(4-Chlorophenyl)-2-oxoethyl 4-benzamidobenzoate derivatives, a novel class of SENP1 inhibitors: Virtual screening, synthesis and biological evaluation.

Prostate cancer is one of the most prevalent types of malignant cancers in men and has a high mortality rate among all male cancers. Previous studies have demonstrated that Sentrin/SUMO-specific protease 1 (SENP1) plays an important role in the occurrence and development of prostate cancer, and has been identified as a novel drug target for development of small molecule drugs against prostate cancer. In this paper, we used virtual screening and docking to identify compound J5 as a novel lead compound inhibiting SENP1, from SPECS library. We further investigated the SAR (structure-activity relationship) of the benzoate substituent of compound J5, and discovered compounds 8d and 8e as better small molecule inhibitors of SENP1. Both compounds are the high potent SENP1 small molecule inhibitors discovered up to date, and further lead optimization may lead to a series of novel anti-SENP1 agents. Further SAR studies are in process and will be reported in due course.

SPPS: A Sequence-Based Method for Predicting Probability of Protein-Protein Interaction Partners

Background The molecular network sustained by different types of interactions among proteins is widely manifested as the fundamental driving force of cellular operations. Many biological functions are determined by the crosstalk between proteins rather than by the characteristics of their individual components. Thus, the searches for protein partners in global networks are imperative when attempting to address the principles of biology. Results We have developed a web-based tool “Sequence-based Protein Partners Search” (SPPS) to explore interacting partners of proteins, by searching over a large repertoire of proteins across many species. SPPS provides a database containing more than 60,000 protein sequences with annotations and a protein-partner search engine in two modes (Single Query and Multiple Query). Two interacting proteins of human FBXO6 protein have been found using the service in the study. In addition, users can refine potential protein partner hits by using annotations and possible interactive network in the SPPS web server. Conclusions SPPS provides a new type of tool to facilitate the identification of direct or indirect protein partners which may guide scientists on the investigation of new signaling pathways. The SPPS server is available to the public at http://mdl.shsmu.edu.cn/SPPS/.