Biology subjects

Chang, C.-e.

Publications and source records attributed to Chang, C.-e..

6 recordsLinked to original sources

bioRxiv2018

Discovery of New CDK8 ligands with a Novel Virtual Drug Screening Tool

Selective inhibition of CDK8 could be a promising strategy for reducing mitogenic signals in cancer cells with reduced toxic effects on normal cells. As compared with type I ligands, binding of a type II compound often achieves longer residence time. We developed a novel virtual drug screening package which takes advantage of two energy evaluation methods: Superposition and Single-Point Energy Evaluation, and VM2 free energy calculation, and applied it to the discovery of new CDK8 type II ligands. In this research we analyzed binding thermodynamics of 11 published CDK8 type II ligands, and extracted the key binding information to assist virtual drug screening for new ligands. The free energy and MD calculations on the reference CDK8-ligand complexes revealed the important factors in the binding. The urea moiety was found to be the critical structural contributor of the reference ligands. Starting with the urea moiety we implemented virtual drug screening and singled out three compounds for bio-assay testing. The ranking from the experimental result for the three compounds is completely consistent with the predicted rankings by both energy evaluation methods. A potent drug-like compound was discovered to have a Kd value of 42.5 nM with CDK8, which is comparable to the most potent reference ligands and provided a good starting point to design and synthesize a series of highly selective and potent CDK8 ligands. Therefore, our novel virtual drug screening package is accurate and efficient enough to be used in drug design projects. We believe this work has significant impact to the field of drug discovery.

bioinformatics↗

bioRxiv2017

Evaluating the accuracy of the umbrella sampling plots with different dissociation paths, conformational changes, and structure preparation

The kinetics of ligand dissociation has been found to be crucial for a good drug candidate. Therefore, examining the underlying free energy profile of the dissociation that governs the kinetics becomes important. Umbrella sampling (US), a widely used free energy calculation method, has long been used to explore the dissociation process of ligand-receptor systems. The potential of mean force (PMF) computed from US seems to always produce binding affinity and energy barriers that more or less agree with experiments. However, such PMFs are influenced by many practical aspects, like the method used to generate the initial dissociation pathway, collective variables (CVs) that used to describe the reaction coordinate (RC), and how intensive the sampling is in the conformational space restrained by the CVs. These critical factors were rarely studied. Here we applied US to study the dissociation processes of {beta}-cyclodextrin ({beta}-CD) and p38 complex systems. For {beta}-CD, we used three different {beta}-CD conformations to generate the dissociation path manually. For p38, we generated the dissociation pathway using accelerated molecular dynamics (AMD) followed by conformational relaxing with short conventional molecular dynamics (MD), steered molecular dynamics (SMD) and manual pulling. We found that even for small {beta}-CD complexes, different {beta}-CD conformations will alter the height of the PMF and different dissociation directions result in appearance/disappearance of local minima. SMD poorly samples the residue sidechain movement, leading to overestimated height of PMF. On the other hand, the AMD pathway relaxed by short conventional MD sampled more accurate structures, resulting in reasonable PMF.

biophysics↗

bioRxiv2017

A QM/MM Study of Biomimetic Catalysis of Diels-Adler reactions Using Cyclodextrins

We performed computational research to investigate the mechanism by which cyclodextrins (CDs) catalyze Diels-Alder reactions between 9-anthracenemethanol and N-cyclohexylmaleimide. Hydrogen bonds (Hbonds) between N-cyclohexylmaleimide and the hydroxyl groups of cyclodextrins were suggested to play an important role in the catalysis.However, our free energy calculations and molecular dynamics simulations showed that these Hbonds are not stable, and quantum mechanics calculations suggested that the reaction is not promoted by these Hbonds. The binding of 9-anthracenemethanol and N-cyclohexylmaleimide to cyclodextrins was the key to the catalysis. Cyclodextrins act as a container to hold the two reactants in the cavity, pre-organizes them for the reactions, and thus reduces the entropy penalty to the activation free energy. Dimethyl-{beta}-CD was a better catalyst for this specific reaction than {beta}-CD because of its stronger van der Waals interaction with the pre-organized reactants and better performance in reducing the activation energy. This computational work sheds light on the mechanism of the catalytic reaction by cyclodextrins and introduces new perspectives of supramolecular catalysis.

biophysics↗

bioRxiv2017

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

The activities of CDK8 with partner Cyclin C (CycC) are a common feature of many diseases, especially cancers. Here we report the study of dynamic behaviors and energy profiles of 13 CDK8/CycC systems, including the DMG-in and DMG-out conformations as well as 5 type I ligands and 5 type II ligands, with all-atom unbiased molecular dynamics (MD) simulations. We observed numerous regional motions within CDK8, which move in concert to form five major protein motions. The motion of the activation loop doesnt appear to influence the binding of both types of ligands. Type I ligands remarkably reduce the motion of the C-terminal tail through the strong cation-{pi} interaction between the ligands and ARG356, and type II ligands stabilize the C helix by forming stable hydrogen bonds with GLU66. The MD calculations also confirmed the importance of CycC to the stability of the CDK8 system as well as the ligand binding. The MMPB/SA results show that van der Waals interaction is the main driving force for the binding of both types of ligands, but electrostatic energy and entropy penalty plays important roles in the binding of type II ligands. The volume analysis results indicate that the induced fitting theory applies in the binding of type I ligands. These results would help to improve the affinities of the existing ligands. Our MD work is complementary to crystal structures and may have implications in the development of new CDK8 inhibitors as well as in the field of drug discovery.

biophysics↗

bioRxiv2017

Energy Barriers, Molecular Motions, and Residence Time in Ligand Dissociation: A Computational Study on Type II Inhibitors Binding to CDK8/CycC

This study applies a novel computational strategy to investigate molecular recognition and binding kinetics using five pyrazolourea ligands dissociating from cyclin-dependent kinase 8 with cyclin C (CDK8/CycC) as an example. The computed free energy barriers guide designing compounds using the transient conformations unavailable in experiments. The intermediates and their free energy profile during ligand association and discussion processes control ligand-protein binding kinetics and bring a more complete picture of ligand-protein binding. We used metadynamics and a pathway search method to sample pathways and applied combined reduced dimensionality, molecular dynamics (MD) simulations and milestoning theory to construct the free energy profile and estimate the residence time. The binding free energy and the trend of binding kinetics agreed with experiments. We explain the why of the barriers and the kinetics and use the information to assist ligand design. Guided by a barrier of a ligand passing an C helix and activation loop, we introduced one hydroxyl group to parent compounds to design our ligands with increased residence time and validated our prediction by experiments. This work provides a novel and robust approach to investigate dissociation kinetics of large and flexible systems for understanding unbinding mechanisms and designing new small molecule drugs with desired binding kinetics.\n\nSignificance StatementThe transient conformations during ligand binding/unbinding control non-covalent binding kinetics. However, the transient structures and their free energy landscape of flexible ligand-protein systems are unavailable in experiments and challenging to model. Due to lack of understanding in binding kinetics, even scientists know that kinetic properties can be important in drug development, calculations using the intermediate states to design ligands with preferred binding kinetics are absent. We overcome these challenges and compute ligand-protein unbinding free energy profile using a novel method with molecular dynamics simulations, reduced dimensionality, and milestoning theory to deepen our understanding in molecular recognition. We also designed compounds based on the computed free energy barriers and experimentally validated that our designed compound can increase residence time.

biophysics↗

bioRxiv2017

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with {beta}-cyclodextrin ({beta}-CD) by using microsecond-timescale molecular dynamics (MD) simulations, post-analysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, {Delta}H, {Delta}S, and {Delta}G using GAFF-CD and q4MD-CD force fields for {beta}-CD could be compared with experimental data directly and agreed reasonably with experiment findings. Both force fields resulted in similar computed {Delta}G from independently computed kinetics rates, {Delta}G=-RTln(kon {middle dot} C{degrees} / k off), and thermodynamics properties, {Delta}G={Delta}H - T{Delta}S. The water entropy calculations show that entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of non-polar attractions between solutes and {beta}-CD as well. Water molecules play a crucial role in guest binding to {beta}-CD. However, collective water/{beta}-CD motions could contribute to different computed kon and {Delta}H values by different force fields, mainly because the parameters of {beta}-CD provide different motions of {beta}-CD, hydrogen-bond networks of water molecules in the cavity of free {beta}-CD and the strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driven force of binding. The study further interprets experiments, deepens our understanding of ligand binding, and suggests strategies for force field parameterization.

biophysics↗