Biomedical subjects

Jung-Hsin Lin

Publications and source records attributed to Jung-Hsin Lin.

11 recordsLinked to original sources

PubMed2006

Preparation of secolycorines against acetylcholinesterase.

5,6-Secolycorines possessing a 5,6-dihydrophenanthridine skeleton were facilely prepared from lycorine through chemical transformations, mainly including N-alkylation, Hofmann degradation type reaction, reductive cleavage of trichloroethylcarbonyl moiety, and hydrogenation. Several secolycorine derivatives showed potent inhibitory activity against acetylcholinesterase with the IC(50) value at micromolar range and are more potent than galanthamine.

Acetylcholinesterase↗

PubMed2006

Protemot: prediction of protein binding sites with automatically extracted geometrical templates.

UNLABELLED: Geometrical analysis of protein tertiary substructures has been an effective approach employed to predict protein binding sites. This article presents the Protemot web server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the crystal structures of protein-ligand complexes in the PDB (Protein Data Bank). The automatic extraction mechanism is essential for creating and maintaining a comprehensive template library that timely accommodates to the new release of PDB as the number of entries continues to grow rapidly. The design of Protemot is also distinctive by the mechanism employed to expedite the analysis process that matches the tertiary substructures on the contour of the query protein with the templates in the library. This expediting mechanism is essential for providing reasonable response time to the user as the number of entries in the template library continues to grow rapidly due to rapid growth of the number of entries in PDB. This article also reports the experiments conducted to evaluate the prediction power delivered by the Protemot web server. Experimental results show that Protemot can deliver a superior prediction power than a web server based on a manually curated template library with insufficient quantity of entries. AVAILABILITY: http://protemot.csie.ntu.edu.tw/step1.cgi http://bioinfo.mc.ntu.edu.tw/protemot/step1.cgi.

Binding Sites↗

PubMed2006

Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design.

To test the anticorrelated relationship that was recently displayed in conventional molecular dynamics (MD) simulations, several different restrained MD simulations on a wild type and on the V82F/I84V drug-resistant mutant of HIV-1 protease were performed. This anticorrelated relationship refers to the observation that compression of the peripheral ear-to-cheek region of HIV protease (i.e., the elbow of the flap to the fulcrum and the cantilever) occurred as the active site flaps were opening, and, conversely, expansion of that ear-to-cheek region occurred as both flaps were closing. An additional examination of this anticorrelated relationship was necessary to determine whether it can be harnessed in a useful manner. Consequently, six different MD experiments were performed that incorporated pairwise distance restraints in that ear-to-cheek region (i.e., the distance between the alpha-carbons of Gly40 and Gln61 was restrained to either 7.7 or 10.5 A, in both monomers). Pushing the backbones of the ear and the cheek regions away from each other slightly did force the flaps that guard the active site to remain closed in both the wild type and the mutant systems-even though there were no ligands in the active sites. Thus, these restrained MD simulations provided evidence that the anticorrelated relationship can be exploited to affect the dynamic behavior of the flaps that guard the active site of HIV-1 protease. These simulations supported our hypothesis of the mechanism governing flap motion, and they are the first step towards validating that peripheral surface as a new target for drug design.

Binding Sites↗

PubMed2006

Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design.

The Relaxed Complex method, an approach to structure-based drug design that incorporates the flexibilities of both the ligand and target protein, was applied to the immunodeficiency virus protease system. The control cases used AutoDock3.0.5 to dock a fully flexible version of the prospective drug JE-2147 (aka SM-319777 or KNI-764) to large ensembles of conformations extracted from conventional, all atom, explicitly solvated molecular dynamic simulations of the wild type, and the V82F/I84V drug-resistant mutant of HIV-1 protease. The best set of run parameters from the control cases produced robust results when used against 2200 different conformations of the wild-type HIV-1 protease or against 2200 conformations of the mutant. The results of the control cases, the published advice from experts, and structural intuition were used to design a new series of 23 potential active site inhibitors. The compounds were evaluated by docking them against 700 different conformations of the V82F/I84V mutant. The results of this first round of lead optimization were quite promising. Approximately one-third of that series performed at least slightly better than the parent compound, and four of those compounds displayed significantly better binding affinities against that drug-resistant mutant (within our computational model).

Amino Acid Substitution↗

PubMed2005

A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP.

Cyclic AMP activates protein kinase A by binding to an inhibitory regulatory (R) subunit and releasing inhibition of the catalytic (C) subunit. Even though crystal structures of regulatory and catalytic subunits have been solved, the precise molecular mechanism by which cyclic AMP activates the kinase remains unknown. The dynamic properties of the cAMP binding domain in the absence of cAMP or C-subunit are also unknown. Here we report molecular-dynamics simulations and mutational studies of the RIalpha R-subunit that identify the C-helix as a highly dynamic switch which relays cAMP binding to the helical C-subunit binding regions. Furthermore, we identify an important salt bridge which links cAMP binding directly to the C-helix that is necessary for normal activation. Additional mutations show that a hydrophobic "hinge" region is not as critical for the cross-talk in PKA as it is in the homologous EPAC protein, illustrating how cAMP can control diverse functions using the evolutionarily conserved cAMP-binding domains.

Animals↗

PubMed2005

Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment.

Protein kinase C (PKC) family members are allosterically activated following membrane recruitment by specific membrane-targeting modules. Conventional PKC isozymes are recruited to membranes by two such modules: a C1 domain, which binds diacylglycerol (DAG), and a C2 domain, which is a Ca2+-triggered phospholipid-binding module. In contrast, novel PKC isozymes respond only to DAG, despite the presence of a C2 domain. Here, we address the molecular mechanism of membrane recruitment of the novel isozyme PKCdelta. We show that PKCdelta and a conventional isozyme, PKCbetaII, bind membranes with comparable affinities. However, dissection of the contribution of individual domains to this binding revealed that, although the C2 domain is a major determinant in driving the interaction of PKCbetaII with membranes, the C2 domain of PKCdelta does not bind membranes. Instead, the C1B domain is the determinant that drives the interaction of PKCdelta with membranes. The C2 domain also does not play any detectable role in the activity or subcellular location of PKCdelta in cells; in vivo imaging studies revealed that deletion of the C2 domain does not affect the stimulus-dependent translocation or activity of PKCdelta. Thus, the increased affinity of the C1 domain of PKCdelta allows this isozyme to respond to DAG alone, whereas conventional PKC isozymes require the coordinated action of Ca2+ binding to the C2 domain and DAG binding to the C1 domain for activation.

Binding Sites↗

PubMed2005

MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm.

The prediction of ligand binding sites is an essential part of the drug discovery process. Knowing the location of binding sites greatly facilitates the search for hits, the lead optimization process, the design of site-directed mutagenesis experiments and the hunt for structural features that influence the selectivity of binding in order to minimize the drug's adverse effects. However, docking is still the rate-limiting step for such predictions; consequently, much more efficient algorithms are required. In this article, the design of the MEDock web server is described. The goal of this sever is to provide an efficient utility for predicting ligand binding sites. The MEDock web server incorporates a global search strategy that exploits the maximum entropy property of the Gaussian probability distribution in the context of information theory. As a result of the global search strategy, the optimization algorithm incorporated in MEDock is significantly superior when dealing with very rugged energy landscapes, which usually have insurmountable barriers. This article describes four different benchmark cases that span a diverse set of different types of ligand binding interactions. These benchmarks were compared with the use of the Lamarckian genetic algorithm (LGA), which is the major workhorse of the well-known AutoDock program. These results demonstrate that MEDock consistently converged to the correct binding modes with significantly smaller numbers of energy evaluations than the LGA required. When judged by a threshold of the number of energy evaluations consumed in the docking simulation, MEDock also greatly elevates the rate of accurate predictions for all benchmark cases. MEDock is available at http://medock.csie.ntu.edu.tw/ and http://bioinfo.mc.ntu.edu.tw/medock/.

Algorithms↗

PubMed2004

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs.

The protease from type 1 human immunodeficiency virus (HIV-1) is a critical drug target against which many therapeutically useful inhibitors have been developed; however, the set of viral strains in the population has been shifting to become more drug-resistant. Because indirect effects are contributing to drug resistance, an examination of the dynamic structures of a wild-type and a mutant could be insightful. Consequently, this study examined structural properties sampled during 22 nsec, all atom molecular dynamics (MD) simulations (in explicit water) of both a wild-type and the drug-resistant V82F/I84V mutant of HIV-1 protease. The V82F/I84V mutation significantly decreases the binding affinity of all HIV-1 protease inhibitors currently used clinically. Simulations have shown that the curling of the tips of the active site flaps immediately results in flap opening. In the 22-nsec MD simulations presented here, more frequent and more rapid curling of the mutant's active site flap tips was observed. The mutant protease's flaps also opened farther than the wild-type's flaps did and displayed more flexibility. This suggests that the effect of the mutations on the equilibrium between the semiopen and closed conformations could be one aspect of the mechanism of drug resistance for this mutant. In addition, correlated fluctuations in the active site and periphery were noted that point to a possible binding site for allosteric inhibitors.

Amino Acid Substitution↗

PubMed2003

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.

An extension of the new computational methodology for drug design, the "relaxed complex" method (J.-H. Lin, A. L. Perryman, J. R. Schames, and J. A. McCammon, Journal of the American Chemical Society, 2002, vol. 24, pp. 5632-5633), which accommodates receptor flexibility, is described. This relaxed complex method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand enzyme complexes. Rapid docking serves as an efficient initial filtering method to screen a myriad of docking modes to a limited set, and it is then followed by more accurate scoring with the MM/PBSA (Molecular Mechanics/Poisson Boltzmann Surface Area) approach to find the best ligand-receptor complexes. The MM/PBSA scorings consistently indicate that the calculated binding modes that are most similar to those observed in the x-ray crystallographic complexes are the ones with the lowest free energies.

Algorithms↗

PubMed2002

Computational drug design accommodating receptor flexibility: the relaxed complex scheme.

A novel computational methodology for drug design that accommodates receptor flexibility is described. This "relaxed-complex" method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand-enzyme complexes. This new method serves as the computational analog of the experimental "SAR by NMR" and "tether" methods, which permit a building block approach for constructing a very potent drug.

Algorithms↗

PubMed2002

Bridging implicit and explicit solvent approaches for membrane electrostatics.

Conformations of a zwitterionic bilayer were sampled from a molecular dynamics simulation and their electrostatic properties analyzed by solution of the Poisson equation. These traditionally implicit electrostatic calculations were performed in the presence of varying amounts of explicit solvent to assess the magnitude of error introduced by a uniform dielectric description of water surrounding the bilayer. It was observed that membrane dipole potential calculations in the presence of explicit water were significantly different than wholly implicit solvent calculations with the calculated dipole potential converging to a reasonable value when four or more hydration layers were included explicitly.

Algorithms↗