Biomedical subjects

Shaomeng Wang

Publications and source records attributed to Shaomeng Wang.

At least 55 records · Page 3Linked to original sources

PubMed2004

Design, synthesis, and evaluation of hexahydrobenz[f]isoquinolines as a novel class of dopamine 3 receptor ligands.

We previously identified hexahydrobenz[f]isoquinoline (4a) as a new class of dopamine 3 receptor (D(3)) ligand. Herein, we described the design, synthesis, and preliminary structure-activity relationships of new analogues of 4a as a novel class of D(3) ligands. Among these new analogues, compound 4 h is a potent D(3) ligand (K(i)=6.1 nM) and has a selectivity of 133-fold between D(3)- and D(2)-like receptors, and of 163-fold between D(3)- and D(1)-like receptors, respectively. Thus, compound 4 h represents a promising new lead compound for further design and optimization toward achieving highly potent and selective D(3) ligands.

Animals↗

PubMed2004

In vitro effects of the BH3 mimetic, (-)-gossypol, on head and neck squamous cell carcinoma cells.

PURPOSE: Bcl-xL overexpression is common in head and neck squamous cell carcinomas (HNSCC) and correlates with resistance to chemotherapy. Thus, a nonpeptidic, cell-permeable small molecule that mimics the BH3 domain of proapoptotic proteins may inhibit Bcl-xL function and have therapeutic potential for HNSCC by overcoming drug-resistance. (-)-Gossypol, the levorotatory isomer of a natural product isolated from cottonseeds and roots, was recently discovered to bind to the BH3 binding groove of Bcl-xL and Bcl-2. EXPERIMENTAL DESIGN: We investigated the in vitro effects of (-)-gossypol on HNSCC cell lines as well as on fibroblast and keratinocyte cultures by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cell survival assays and assessed the results with respect to Bcl-2 family protein expression. RESULTS: We observed dose-dependent growth inhibition of 10 HNSCC cell lines at biologically achievable doses (2.5-10 micromol/L). (-)-Gossypol doses required to inhibit the growth of human fibroblast cell lines by 50% were 2- to 10-fold higher than for HNSCC cell lines. To inhibit human oral keratinocyte growth by 50%, (-)-gossypol concentrations were 2-to 3-fold higher than for HNSCC cell lines. CONCLUSIONS: There is a direct correlation between Bcl-xL-to-Bcl-xS ratios and sensitivity to (-)-gossypol. This agent induced apoptosis in a much higher proportion of cells with wild-type p53. Importantly, cell lines resistant to cisplatin were very sensitive to (-)-gossypol. These results demonstrate that (-)-gossypol has potent antitumor activity in HNSCC in vitro. This agent may be developed as a novel therapeutic agent for HNSCC, either alone or in combination with existing chemotherapeutic agents.

Apoptosis↗

PubMed2004

Breast cancer cells can evade apoptosis-mediated selective killing by a novel small molecule inhibitor of Bcl-2.

Proteins of the Bcl-2 family are key regulators of caspase activation and apoptosis. Some members of this family, notably Bcl-2 and Bcl-x(L), are overexpressed in cancer cells, which have been associated with chemoresistance. We have designed and synthesized a small molecule inhibitor of Bcl-2, named YC137, and studied its role in cancer cells. In vitro studies showed that YC137 inhibits the binding of the Bid BH3 peptide to Bcl-2, thus disrupting an interaction essential for the antiapoptotic activity of Bcl-2. This inhibitor induces apoptosis of hematopoietic progenitors overexpressing Bcl-2 but not Bcl-x(L) and breast cancer cells that express high levels of Bcl-2. On the contrary, a variety of normal primary cells, including CD34(+) progenitors, myoblasts, and peripheral blood mononuclear cells, do not respond to the inhibitor. A breast cancer cell line resistant to YC137 was generated. Analysis of resistant cells revealed a reduced expression of Bcl-2, which correlated with low activation of signal transducer and activator of transcription-3 (Stat3) and reduced expression of the human epidermal growth factor receptor-2 (HER2). Of note, YC137-resistant cells were more sensitive to apoptosis induced by chemotherapy. Because HER2 has not been linked previously to the Stat3-Bcl-2 transcriptional pathway, we additionally confirmed that specific blockade of HER2 in breast cancer cells resulted in down-regulation of Stat3 activity and reduced levels of Bcl-2. Consistently, HER2 blockade led to YC137 resistance. These data provide evidence for the selective killing of tumor cells by YC137 and represent the first example of in vitro selection of cancer cells refractory to a Bcl-2 inhibitor.

Apoptosis↗

PubMed2004

Structure-based discovery of nonpeptidic small organic compounds to block the T cell response to myelin basic protein.

We have utilized a computational structure-based approach to identify nonpeptidic small organic compounds that bind to a human leukocyte antigen (HLA) DR1301 molecule (HLA-DR1301 or DR1301) and block the presentation of myelin basic protein peptide 152-165 (MBP 152-165) to T cells. A three-dimensional (3D) structure of DR1301 was derived by homology modeling followed by extensive molecular dynamics simulation for structural refinement. Computational structure-based database searching was performed to identify nonpeptidic small-molecule candidates from the National Cancer Institute (NCI) database containing over 150 000 compounds that can effectively interact with the peptide-binding groove of the HLA molecule. By in vitro testing of 106 candidate small molecules, two lead compounds were confirmed to specifically block IL-2 secretion by DR1301-restricted T cells in a dose-dependent and reversible manner. The specificity of blocking DR1301-restricted MBP presentation was further validated in a binding assay using an analogue of the most potent lead compound. Computational docking was performed to predict the three-dimensional binding model of these confirmed small molecule blockers to the DR1301 molecule and to gain structural insight into their interactions. Our results suggest that computational structure-based searching is an effective approach to discover nonpeptidic small organic compounds to block the interaction between DR1301 and T cells. The nonpeptidic small organic compounds identified in this study are useful pharmacological tools to study the interactions between HLA molecules and T cells and a starting point for the development of a novel therapeutic strategy for the treatment of multiple sclerosis (MS) or other immune-related disorders.

Animals↗

PubMed2004

Formation of a novel reversible cytochrome P450 spectral intermediate: role of threonine 303 in P450 2E1 inactivation.

tert-Butyl acetylene (tBA) is a mechanism-based inactivator of cytochromes P450 2E1 and 2E1 T303A; however, the inactivation of the T303A mutant could be reversed by overnight dialysis. The inactivation of P450 2E1 T303A, but not the wild-type 2E1 enzyme, by tBA resulted in the formation of a novel reversible acetylene-iron spectral intermediate with an absorption maximum at 485 nm. The formation of this intermediate required oxygen and could be monitored spectrally with time. Although the alternate oxidants tert-butyl hydroperoxide (tBHP) and cumene hydroperoxide (CHP) supported the inactivation of wild-type P450 2E1 by tBA in a reductase- and NADPH-free system, only tBHP supported the inactivation of the 2E1 T303A mutant. The losses in enzymatic activity occurred concomitantly with losses in the native P450 heme, which were accompanied by the formation of tBA-adducted heme products. The inactivations supported by tBHP and CHP were completely irreversible with overnight dialysis. Spectral binding constants (K(s)) for the binding of tBA to the 2E1 P450s together with models of the enzymes with the acetylenic inactivator bound in the active site suggest that the T303A mutation results in increased hydrophobic interactions between tBA and nearby P450 residues, leading to a higher binding affinity for the acetylene compound in the mutant enzyme. Together, these data support a role for the highly conserved T303 residue in proton delivery to the active site of P450 2E1 and in the inactivation of the 2E1 P450s by small acetylenic compounds.

Alkynes↗

PubMed2004

Development and optimization of a binding assay for the XIAP BIR3 domain using fluorescence polarization.

The X-linked inhibitor of apoptosis protein (XIAP) is a potent cellular inhibitor of apoptosis. Designing small-molecule inhibitors that target the BIR3 domain of XIAP, where Smac/DIABLO (second mitochondria-derived activator of caspase/direct IAP-binding protein with low pI) and caspase-9 bind, is a promising strategy for inhibiting the antiapoptotic activity of XIAP and for overcoming apoptosis resistance of cancer cells mediated by XIAP. Herein, we report the development of a homogeneous high-throughput assay based on fluorescence polarization for measuring the binding affinities of small-molecule inhibitors to the BIR3 domain of XIAP. Among four fluorescent probes tested, a mutated N-terminal Smac peptide (AbuRPFK-(5-Fam)-NH(2)) showed the highest affinity (Kd =17.92 nM) and a large dynamic range (deltamP = 231 +/- 0.9), and was selected as the most suitable probe for the binding assay. The binding conditions (DMSO tolerance and stability) have been investigated. Under optimized conditions, a Z' factor of 0.88 was achieved in a 96-well format for high-throughput screening. It was found that the popular Cheng-Prusoff equation is invalid for the calculation of the competitive inhibition constants (Ki values) for inhibitors in the FP-based competitive binding assay conditions, and accordingly, a new mathematical equation was developed, validated, and used to compute the Ki values. An associated Web-based computer program was also developed for this task. Several known Smac peptides with high and low affinities have been evaluated under the assay conditions and the results obtained indicated that the FP-based competitive binding assay performs correctly as designed: it can quantitatively and accurately determine the binding affinities of Smac-based peptide inhibitors with a wide range of affinities, and is suitable for high-throughput screening of inhibitors binding to the XIAP BIR3 domain.

Binding, Competitive↗

PubMed2004

Structure-based design, synthesis, and evaluation of conformationally constrained mimetics of the second mitochondria-derived activator of caspase that target the X-linked inhibitor of apoptosis protein/caspase-9 interaction site.

A successful structure-based design of conformationally constrained second mitochondria-derived activator of caspase (Smac) mimetics that target the XIAP/caspase-9 interaction site is described. The most potent Smac mimetic 12d has a Ki of 350 nM for binding to the XIAP BIR3 domain protein. 12d is found to be effective in enhancing apoptosis induced by cisplatin in PC-3 human prostate cancer cells.

Amino Acid Motifs↗

PubMed2004

The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures.

We have screened the entire Protein Data Bank (Release No. 103, January 2003) and identified 5671 protein-ligand complexes out of 19 621 experimental structures. A systematic examination of the primary references of these entries has led to a collection of binding affinity data (K(d), K(i), and IC(50)) for a total of 1359 complexes. The outcomes of this project have been organized into a Web-accessible database named the PDBbind database.

Databases, Protein↗

PubMed2004

Discovery of embelin as a cell-permeable, small-molecular weight inhibitor of XIAP through structure-based computational screening of a traditional herbal medicine three-dimensional structure database.

The X-linked inhibitor of apoptosis (XIAP) is a promising new molecular target for the design of novel anticancer drugs aiming at overcoming apoptosis-resistance of cancer cells to chemotherapeutic agents and radiation therapy. Recent studies demonstrated that the BIR3 domain of XIAP where caspase-9 and Smac proteins bind is an attractive site for designing small-molecule inhibitors of XIAP. Through computational structure-based screening of an in-house traditional herbal medicine three-dimensional structure database of 8221 individual natural products, followed by biochemical testing of selected candidate compounds, we discovered embelin from the Japanese Ardisia herb as a small-molecular weight inhibitor that binds to the XIAP BIR3 domain. We showed that embelin binds to the XIAP BIR3 protein with an affinity similar to that of the natural Smac peptide using a fluorescence polarization-based binding assay. Our NMR analysis further conclusively confirmed that embelin interacts with several crucial residues in the XIAP BIR3 domain with which Smac and caspsase-9 bind. Embelin inhibits cell growth, induces apoptosis, and activates caspase-9 in prostate cancer cells with high levels of XIAP, but has a minimal effect on normal prostate epithelial and fibroblast cells with low levels of XIAP. In stably XIAP-transfected Jurkat cells, embelin effectively overcomes the protective effect of XIAP to apoptosis and enhances the etoposide-induced apoptosis and has a minimal effect in Jurkat cells transfected with vector control. Taken together, our results showed that embelin is a fairly potent, nonpeptidic, cell-permeable, small-molecule inhibitor of XIAP and represents a promising lead compound for designing an entirely new class of anticancer agents that target the BIR3 domain of XIAP.

Antineoplastic Agents↗

PubMed2003

Molecular modeling of the three-dimensional structure of dopamine 3 (D3) subtype receptor: discovery of novel and potent D3 ligands through a hybrid pharmacophore- and structure-based database searching approach.

The dopamine 3 (D3) subtype receptor has been implicated in several neurological conditions, and potent and selective D3 ligands may have therapeutic potential for the treatment of drug addiction, Parkinson's disease, and schizophrenia. In this paper, we report computational homology modeling of the D3 receptor based upon the high-resolution X-ray structure of rhodopsin, extensive structural refinement in the presence of explicit lipid bilayer and water environment, and validation of the refined D3 structural models using experimental data. We further describe the development, validation, and application of a hybrid computational screening approach for the discovery of several classes of novel and potent D3 ligands. This computational approach employs stepwise pharmacophore and structure-based searching of a large three-dimensional chemical database for the identification of potential D3 ligands. The obtained hits are then subjected to structural novelty screening, and the most promising compounds are tested in a D3 binding assay. Using this approach we identified four compounds with K(i) values better than 100 nM and eight compounds with K(i) values better than 1 microM out of 20 compounds selected for testing in the D3 receptor binding assay. Our results suggest that the D3 structural models obtained from this study may be useful for the discovery and design of novel and potent D3 ligands. Furthermore, the employed hybrid approach may be more effective for lead discovery from a large chemical database than either pharmacophore-based or structure-based database screening alone.

Algorithms↗

PubMed2003

Molecular mechanism of gossypol-induced cell growth inhibition and cell death of HT-29 human colon carcinoma cells.

Gossypol, a male contraceptive drug, has been demonstrated to have antiproliferative and antimetastatic effects on many kinds of cancer cells in vitro. HT-29 human carcinoma cell line is one of the most susceptible cell lines to gossypol-induced cell death. Here, it is shown that treatment of HT-29 cells with gossypol not only induces cell cycle arrest on the G0/G1 phase, but also induces apoptosis. With a serial of Western blot analysis, it is revealed that gossypol-induced cell cycle arrest is involved in P21 up-regulation and cyclin D1 down-regulation; gossypol-induced apoptosis triggers down-regulation of anti-apoptosis Bcl-2 members: Bcl-X(L), Bag-1 and Mcl-1, up-regulation of pro-apoptosis Bcl-2 member Bak, activation of caspase-3, -6, -7, -8, and -9, up-regulation of Apaf-1, release of cytochrome c (cyto-c) from mitochondria, and activation of both DFF45 and PARP. Taken together, gossypol-induced cell death initiates extensive alterations of cell cycle and apoptosis proteins. Gossypol-induced apoptosis of HT-29 cells is through first the mitochondrial pathway, then the death receptor pathway, and the mitochondria pathway is, at least in part, involved in cyto-c release.

Apoptosis↗

PubMed2003

Comparative evaluation of 11 scoring functions for molecular docking.

Eleven popular scoring functions have been tested on 100 protein-ligand complexes to evaluate their abilities to reproduce experimentally determined structures and binding affinities. They include four scoring functions implemented in the LigFit module in Cerius2 (LigScore, PLP, PMF, and LUDI), four scoring functions implemented in the CScore module in SYBYL (F-Score, G-Score, D-Score, and ChemScore), the scoring function implemented in the AutoDock program, and two stand-alone scoring functions (DrugScore and X-Score). These scoring functions are not tested in the context of a particular docking program. Instead, conformational sampling and scoring are separated into two consecutive steps. First, an exhaustive conformational sampling is performed by using the AutoDock program to generate an ensemble of docked conformations for each ligand molecule. This conformational ensemble is required to cover the entire conformational space as much as possible rather than to focus on a few energy minima. Then, each scoring function is applied to score this conformational ensemble to see if it can identify the experimentally observed conformation from all of the other decoys. Among all of the scoring functions under test, six of them, i.e., PLP, F-Score, LigScore, DrugScore, LUDI, and X-Score, yield success rates higher than the AutoDock scoring function. The success rates of these six scoring functions range from 66% to 76% if using root-mean-square deviation < or =2.0 A as the criterion. Combining any two or three of these six scoring functions into a consensus scoring scheme further improves the success rate to nearly 80% or even higher. However, when applied to reproduce the experimentally determined binding affinities of the 100 protein-ligand complexes, only X-Score, PLP, DrugScore, and G-Score are able to give correlation coefficients over 0.50. All of the 11 scoring functions are further inspected by their abilities to construct a descriptive, funnel-shaped energy surface for protein-ligand complexation. The results indicate that X-Score and DrugScore perform better than the other ones at this aspect.

Algorithms↗

PubMed2003

2,3-Disubstituted quinuclidines as a novel class of dopamine transporter inhibitors.

There is considerable interest in developing dopamine transporter (DAT) inhibitors as potential therapies for the treatment of cocaine abuse. We report herein our pharmacophore-based discovery and molecular modeling-assisted rational design of 2,3-disubstituted quinuclidines as potent DAT inhibitors with a novel chemical scaffold. Through 3-D-database pharmacophore searching, compound 12 was identified as a very weak DAT inhibitor with K(i) values of 7.3 and 8.9 microM in [3H]mazindol binding and in inhibition of dopamine reuptake, respectively. Molecular modeling-assisted rational design and chemical modifications led to identification of potent analogues (-)-29 and 34 with K(i) values of 14 and 32 nM for both compounds in binding affinity and inhibition of dopamine reuptake, respectively. Behavioral pharmacological evaluations in rodents showed that 34 has a profile very different from cocaine. While 34 is substantially more potent than cocaine as a DAT inhibitor, it is approximately four times less potent than cocaine in mimicking the discriminative stimulus properties of cocaine in rat. On the other hand, 34 (3-30 mg/kg) lacks either the locomotor stimulant or stereotypic properties of cocaine in mice. Importantly, 34 blocks locomotor stimulant activity induced by 20 mg/kg cocaine in mice, with an estimated ED(50) of 19 mg/kg. Taken together, our data suggest that 34 represents a class of potent DAT inhibitors with a novel chemical scaffold and a behavioral pharmacological profile different from that of cocaine in rodents. Thus, 34 may serve as a novel lead compound in the ultimate development of therapeutic entities for cocaine abuse and/or addiction.

Animals↗

PubMed2003

Pharmacophore-based discovery of substituted pyridines as novel dopamine transporter inhibitors.

Abnormal dopamine signaling in brain has been implicated in several conditions such as cocaine abuse, Parkinson's disease and depression. Potent and selective dopamine transporter inhibitors may be useful as pharmacological tools and therapeutic agents. Simple substituted pyridines were discovered as novel dopamine transporter (DAT) inhibitors through pharmacophore-based 3D-database search. The most potent compound 18 has a K(i) value of 79 nM in inhibition of WIN35,248 binding to dopamine transporter and 255 nM in inhibition of dopamine reuptake, respectively, as potent as cocaine. Preliminary structure-activity relationship studies show that the geometry and the nature of the substituents on the pyridine ring determine the inhibitory activity and selectivity toward the three monoamine transporters. The substituted pyridines described herein represent a class of novel DAT inhibitors with simple chemical structures and their discovery provides additional insights into the binding site of DAT.

Binding, Competitive↗

PubMed2003

Targeting Bcl-2 and Bcl-XL with nonpeptidic small-molecule antagonists.

Members of the Bcl-2 family of proteins are crucial regulators of programmed cell death or apoptosis. This family of proteins now includes both anti-apoptotic molecules such as Bcl-2 and Bcl-X(L), and pro-apoptotic molecules such as Bax, Bak, Bid, and Bad. The majority of human cancers are found to have overexpression of Bcl-2, Bcl-X(L), or both. Bcl-2 and Bcl-X(L) may play a critical role in cancer progression. Cancers with high levels of Bcl-2 or Bcl-X(L) or both proteins are resistant to a wide spectrum of chemotherapeutic agents and radiation therapy. Bcl-2 and Bcl-X(L) have become attractive targets for designing new anticancer drugs. Small-molecule inhibitors that are capable of inhibiting the activity of Bcl-2 and Bcl-X(L) may have great therapeutic potential as an entirely new class of anticancer drugs for treating many forms of cancers in which Bcl-2 and/or Bcl-X(L) proteins are overexpressed and for which traditional therapies are ineffective. Design of small-molecule inhibitors of Bcl-2 and Bcl-X(L) is a very new and exciting area for current anticancer drug design and development. In this article we will provide a brief review on the strategy and recent progress in designing small-molecule antagonists targeting Bcl-2 and Bcl-X(L).

Antineoplastic Agents↗

PubMed2002

Molecular modeling of the interactions of glutamate carboxypeptidase II with its potent NAAG-based inhibitors.

Glutamate carboxypeptidase II (GCPII, NAALADase, or NAAG peptidase) is a catalytic zinc metallopeptidase. Its extracellular domain hydrolyzes the abundant neuropeptide, N-acetyl-L-aspartyl-L-glutamate (NAAG), to produce N-acetylaspartate and glutamate following the synaptic release of this transmitter. Thus, GCPII influences the extracellular concentrations of both glutamate and NAAG. NAAG activates group II metabotropic glutamate receptors, and activation of this receptor has been found to protect against anoxia-induced excitotoxic nerve cell death. In contrast, high levels of glutamate can be neurotoxic. Thus, GCPII is a potential therapeutic target for the reduction of excitotoxic levels of glutamate and enhancement of extracellular NAAG. To explore the structural basis of the interaction between GCPII and its inhibitors, we modeled the three-dimensional structure of the GCPII extracellular domain using a homology modeling approach. On the basis of the GCPII model, the structures of GCPII in complex with its potent inhibitors 2-(phosphonomethyl)pentanedioic acid (PMPA) and 4,4'-phosphinicobis(butane-1,3-dicarboxylic acid) (PBDA) were built by a computational docking method. The model of GCPII mainly consists of two alpha/beta/alpha sandwiches, between which two zinc ions are quadrivalently coordinated by the His379-Asp389-Asp455-H(2)O and the Asp389-Glu427-His555-H(2)O clusters, respectively. The ligand binding pocket is situated between these two sandwiches and is comprised of two subpockets: one is a surface-exposed highly positively charged subpocket; the other is a buried hydrophobic subpocket. The positively charged subpocket can accommodate the pharmacophore groups of inhibitor molecules (PMPA and PBDA) through the coordination of Zn(2+) with their phosphorus functionality and hydrogen-bonding interactions with Arg536, Arg538, and Ser456 (or Asn521), while the hydrophobic subpocket is engaged in hydrophobic and hydrogen-bonding interactions with the nonpharmacophore groups of PBDA. The predicted binding mode is consistent with the experimental data obtained from site-directed mutagenesis. On the basis of the predicted interaction mode, our structure-based design has led to a series of highly potent GCPII inhibitors.

Amino Acid Sequence↗

PubMed2002

Discovery of substituted 3,4-diphenyl-thiazoles as a novel class of monoamine transporter inhibitors through 3-D pharmacophore search using a new pharmacophore model derived from mazindol.

Substituted 3,4-diphenyl-1,3-thiazols were identified as a class of novel and potent monoamine transporter inhibitors through a 3-D pharmacophore search using a new pharmacophore model derived from mazindol. The most potent compound (13) has K(i) values of 24 and 23 nM in binding to dopamine transporter and inhibition of dopamine reuptake, respectively.

Binding Sites↗

PubMed2002

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.

The cooperative folding and unfolding of a beta-hairpin structure are observed in explicit water at native folding conditions through self-guided molecular dynamics simulation. The folded structure agrees excellently with the NMR NOE data. After going through a fully hydrated state, the peptide folds into a beta-hairpin structure in a highly cooperative process. During the folding process it is observed that side chain interaction occurs first, while intrapeptide hydrogen bonds only form at the final stage. On the contrary, the unfolding process starts with the breaking of interstrand hydrogen bonds. Energetic analysis indicates that the driving force of the folding is the intrapeptide interaction, while the solvent interaction opposes the folding.

Amino Acid Sequence↗