Biomedical subjects

Beining Chen

Publications and source records attributed to Beining Chen.

11 recordsLinked to original sources

PubMed2007

Evaluation of machine-learning methods for ligand-based virtual screening.

Machine-learning methods can be used for virtual screening by analysing the structural characteristics of molecules of known (in)activity, and we here discuss the use of kernel discrimination and naive Bayesian classifier (NBC) methods for this purpose. We report a kernel method that allows the processing of molecules represented by binary, integer and real-valued descriptors, and show that it is little different in screening performance from a previously described kernel that had been developed specifically for the analysis of binary fingerprint representations of molecular structure. We then evaluate the performance of an NBC when the training-set contains only a very few active molecules. In such cases, a simpler approach based on group fusion would appear to provide superior screening performance, especially when structurally heterogeneous datasets are to be processed.

Artificial Intelligence↗

PubMed2006

Library design, synthesis, and screening: pyridine dicarbonitriles as potential prion disease therapeutics.

Transmissible spongiform encephalopathies (TSEs) or prion diseases are a family of invariably fatal neurodegenerative disorders, and there are no effective therapeutics currently available. In this paper, we report on the design, synthesis, and screening of a series of pyridine dicarbonitriles as potential novel prion disease therapeutics. A virtual reaction-based library of 1050 compounds was constructed. Docking and evaluation using GOLD scores assisted the initial selection of compounds for synthesis. The selection was augmented with further compounds to increase structural diversity. A total of 45 compounds were synthesized via a one-pot three-component coupling reaction. The mechanism of the three-component coupling reaction was investigated, and it was discovered that chemical oxidation is required for the last step, forming the pyridine ring (aromatization). A total of 19 compounds were identified as binders to one or more forms of prion protein by in vitro screening using surface plasmon resonance (SPR). A selection of compounds were investigated for activity in cells, resulting in the discovery of a new inhibitor of PrP(Sc) formation.

Combinatorial Chemistry Techniques↗

PubMed2005

Screening a library of potential prion therapeutics against cellular prion proteins and insights into their mode of biological activities by surface plasmon resonance.

The conversion of cellular prion protein (PrP(C)) to the protease resistant isoform (PrP(Sc)) is considered essential for the progression of transmissible spongiform encephalopathies (TSEs). A potential therapeutic strategy for preventing the accumulation of PrP(Sc) is to stabilize PrP(C) through the direct binding of a small molecule to make conversion less energetically favourable. Using surface plasmon resonance (SPR)-based technology we have developed a procedure, based on direct binding, for the screening of small molecules against PrP(C) immobilized on a sensor chip. In this paper we report some problems associated with the immobilization of PrP(C) onto the sensor surface for conducting drug screening and how these problems were overcome. We demonstrated that the conformational change of PrP(C) on the chip surface leads to increased exposure of the C-terminal which was observed by the increase in quinacrine binding over time, and loss of heparin binding to the N-terminal. In addition, we also report the results of the successful screening of a library of 47 compounds of known activity in cell line or cell free conversion studies for direct binding to three forms of PrP(C) (huPrP(C), t-huPrP(C) and moPrP(C)). These results show the usefulness of this technique for the identification of PrP(C) binding ligands and to gain some insight as to their potential mode of action.

Biosensing Techniques↗

PubMed2005

Predicted consequences of site-directed mutagenesis and the impact of species variation on prion protein misfolding through the N-terminal domain.

Variant Creutzfeldt-Jacob disease (vCJD) is considered to afflict humans through the acquisition of variant isomers and misfolding of the normal cellular prion polypeptide, PrP(C). Although the exact mechanism of the misfolding is not been yet clearly understood, this paper provides four additional pieces of evidence in support of the hypothesis that misfolding within PrP(C) involves N-terminal residues, up to and including Asn178. Structural predictions for N-terminal residues between Leu4 and Gly124 revealed that Leu4-Leu19 might adopt a helical conformation. Furthermore, measurement of C(alpha) distance variations, as determined from available NMR solution structures of wild type, as well as the biologically significant Val166, Asn170 and Lys220 variants of PrP(C), revealed previously unreported global and local conformational differences may occur in PrP(C) as a result of these amino-acid substitutions. Notably, three regions, His140-Tyr150 and Met166-Phe175 showed deviations greater than 3 A in their C(alpha)-coordinates (cf wild type) indicating that the majority of the N-terminal domain is likely to contribute to the misfolding of PrP(C). Minor variations in the orientation of amino acids Thr193-Glu200, located towards the C terminus of the protein, were also noted. This most likely indicates the presence of a hinge mechanism, inherent to a Helix-Loop-helix (HLH) motif formed by amino acids within alpha2, LIII and alpha3, in order to accommodate reorientation of the motif in response to misalignment of the N-terminal domain. An unexpected 3 angstroms deviation from the coordinates of the wild type polypeptide, absent from either Val166, Asn170 variants was observed over the region Arg154-Tyr155 within the Val166 form of PrP(C). This may contribute to the explanation as to why patients carrying the Val166 isoform of PrP(C) may be more susceptible to vCJD.

Amino Acid Sequence↗

PubMed2005

Identification of mammalian species using genosensors.

This work reports the development of DNA biosensors for the identification of mammalian species in real samples based on specific oligonucleotide probes. The oligonucleotide sequences (the probes) of each species studied were selected starting from the sequence of satellites DNA. Two inosine-modified (guanine-free) DNA sequences of 21 and 25 bases have been immobilised on screen printed electrodes (SPEs) as capturing agent and the detection of the duplex formation, via guanine oxidation of the target, was examined and optimised. The duplex formation was detected using the square-wave voltammetry. The developed sensors were applied on bovine and porcine DNA extract samples without polymerase chain reaction (PCR), after a restriction enzyme digestion to avoid steric hindrance. Using standard solutions the hybridisation event was identified when 3 microg/mL of complementary oligonucleotide were presented in solution with a coefficient of variation (CV) of 15%. Using total genomic DNA extracts a clear discrimination of the species with a detection limit of less than 30 microg/ml of total genomic bovine DNA was obtained (CV < 20%). The sensors were able to discriminate among the species indicating that the approach is suitable for the identification of mammalian species.

Animals↗

PubMed2002

Rational design of a polymer specific for microcystin-LR using a computational approach.

A computational approach for the design of a molecularly imprinted polymer (MIP) specific for Cyanobacterial toxin microcystin-LR is presented. By using molecular modeling software, a virtual library of functional monomers was designed and screened against the target toxin, employed as a template. The monomers giving the highest binding energy were selected and used in a simulated annealing (molecular dynamics) process to investigate their interaction with the template. The stoichiometric ratio observed from the simulated annealing study was used in MIP preparation for microcystin-LR. The monomers were copolymerized with a cross-linker in the presence of the template. A control (blank) polymer was prepared under the same conditions but in the absence of template. A competitive assay with microcystin-horseradish peroxidase conjugate was optimized and used to evaluate the affinity and cross-reactivity of the polymer. The performance of the artificial receptor was compared to the performance of monoclonal and polyclonal antibodies raised against the toxin. The results indicate that imprinted polymer has affinity and sensitivity comparable to those of polyclonal antibodies (the detection limit for microcystin-LR using the MIP-based assay was found to be 0.1 microg L-1), while superior chemical and thermal stabilities were obtained. Moreover, cross-reactivity to other toxin analogues was very low for the imprinted polymer, in contrast to the results achieved for antibodies. It is anticipated that the polymer designed could be used in assays, sensors, and solid-phase extraction.

Computer Simulation↗

PubMed2002

High molecular recognition: design of "Keys".

Molecular recognition between molecules is one of the most fundamental processes in biology and chemistry. The recognition process is largely driven by non-covalent forces such as hydrogen bonding, electrostatics, van der Waals forces, pi-pi interactions, and conformational energy. The complementarity between the receptor and substrate is very similar to the "lock and key" function, first described by Emil Fischer over 100 years ago, - the lock being the molecular receptor such as a protein or enzyme and the key being the substrate such as a drug, that is recognized to give a defined receptor-substrate complex. This review focuses on the design of specific ligand systems as "Keys" to enable the induced fit of these keys into the target macromolecules, protein/enzyme (Locks) with particular emphasis on protein recognition.

Animals↗

PubMedDate not supplied

Retrospective docking study of PDE4B ligands and an analysis of the behavior of selected scoring functions.

Scoring forms a major obstacle to the success of any docking study. In general, fast scoring functions perform poorly when used to determine the relative affinity of ligands for their receptors. In this study, the objective was not to rank compounds with confidence but simply to identify a scoring method which could provide a 4-fold hit enrichment in a screening sample over random selection. To this end, LigandFit, a fast shape matching docking algorithm, was used to dock a variety of known inhibitors of type 4 phosphodiesterase (PDE4B) into its binding site determined crystallographically for a series of pyrazolopyridine inhibitors. The success of identifying good poses with this technique was explored through RMSD comparisons with 19 known inhibitors for which crystallographic structures were available. The effectiveness of five scoring functions (PMF, JAIN, PLP2, LigScore2, and DockScore) was then evaluated through consideration of the success in enriching the top ranked fractions of nine artificial databases, constructed by seeding 1980 inactive ligands (pIC50 < 5) with 20 randomly selected inhibitors (pIC50 > 6.5). PMF and JAIN showed high average enrichment factors (greater than 4 times) in the top 5-10% of the ranked databases. Rank-based consensus scoring was then investigated, and the rational combination of 3 scoring functions resulted in more robust scoring schemes with (cScore)-DPmJ (consensus score of DockScore, PMF, and JAIN) and (cScore)-PPmJ (PLP2, PMF, and JAIN) yielding particularly good results. These cScores are believed to be of greater general application. Finally, the analysis of the behavior of the scoring functions across different chemotypes uncovered the inherent bias of the docking and scoring toward compounds in the same structural family as that employed for the crystal structure, suggesting the need to use multiple versions of the binding site for more successful virtual screening strategies.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMedDate not supplied

Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions.

A new method for the postprocessing of docking outputs has been developed, based on encoding putative 3D binding modes (docking solutions) as ligand-protein interactions into simple bit strings, a method analogous to the structural interaction fingerprint. Instead of employing traditional scoring functions, the method uses a series of new, knowledge-based scores derived from the similarity of the bit strings for each docking solution to that of a known reference binding mode. A GOLD docking study was carried out using the Bissantz estrogen receptor antagonist set along with the new scoring method. Superior recovery rates, with up to 2-fold enrichments, were observed when the new knowledge-based scoring was compared to the GOLD fitness score. In addition, top ranking sets of molecules (actives and potential actives or decoys) were structurally diverse with low molecular weights and structural complexities. Principal component analysis and clustering of the fingerprints permits the easy separation of active from inactive binding modes and the visualization of diverse binding modes.

Cluster Analysis↗

PubMedDate not supplied

Virtual screening using binary kernel discrimination: effect of noisy training data and the optimization of performance.

Binary kernel discrimination (BKD) uses a training set of compounds, for which structural and qualitative activity data are available, to produce a model that can then be applied to the structures of other compounds in order to predict their likely activity. Experiments with the MDL Drug Data Report database show that the optimal value of the smoothing parameter, and hence the predictive power of BKD, is crucially dependent on the number of false positives in the training set. It is also shown that the best results for BKD are achieved using one particular optimization method for the determination of the smoothing parameter that lies at the heart of the method and using the Jaccard/Tanimoto coefficient in the kernel function that is used to compute the similarity between a test set molecule and the members of the training set.

Algorithms↗

PubMedDate not supplied

Prostate-specific antigen (PSA)-mediated proliferation, androgenic regulation and inhibitory effects of LY312340 in HOS-TE85 (TE85) human osteosarcoma cells.

BACKGROUND: PSA mediates growth factor responses that stimulate proliferation of prostatic and other cellular types. Androgen-sensitive TE85 human osteosarcoma cells were used to study PSA as a potential mediator of prostatic cancer growth and osseous metastasis. MATERIALS AND METHODS: TE85 cells were probed for PSA mRNA and protein levels under testosterone (T)-replete and--depleted conditions. TE85 proliferative responses to PSA were evaluated in the absence and presence of LY312340, a monocyclic beta-lactam inhibitor of PSA enzymatic activity. RESULTS: A 3.1-fold increase in PSA mRNA was observed following T stimulation. Low levels of immunoreactive PSA (iPSA) were detected in media of androgen-stimulated TE85 cells while iPSA was not found in control media. Conversely, iPSA was detected in TE85 cell pellets from control but not in androgen-stimulated cell cultures. Exogenously added enzymatically active PSA stimulated TE85 proliferation in a bi-phasic manner. LY312340 inhibited PSA-induced increases in TE85 cell numbers but had no effect on basal or T- stimulated cellular proliferation. CONCLUSION: While the PSA levels produced by TE-85 cells in response to androgen stimulation are too low to be biologically active, PSA produced by metastatic PCa cells may mediate paracrine stimulation of osteogenic PCa metastasis. Inhibitors of PSA enzymatic activity could be useful therapeutic agents.

Adolescent↗