Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.

Quantifying intrinsic specificity: A potential complement to affinity in drug screening

We report here the investigation of a novel description of specificity in protein-ligand binding based on energy landscape theory. We define a new term, intrinsic specificity ratio (ISR), which describes the level of discrimination in binding free energies of the native basin for a protein-ligand complex from the weaker binding states of the same ligand. We discuss the relationship between the intrinsic specificity we defined here and the conventional definition of specificity. In a docking study of molecules with the enzyme COX-2, we demonstrate a statistical correspondence between ISR value and geometrical shapes of the small molecules binding to COX-2. We further observe that the known selective (nonselective) inhibitors of COX-2 have higher (lower) ISR values. We suggest that intrinsic specificity ratio may be a useful new criterion and a complement to affinity in drug screening and in searching for potential drug lead compounds.

Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Computational Methods in Biophysics and Medicinal Chemistry: Applications and Challenges

In this thesis I described the theory and application of several computational methods in solving medicinal chemistry and biophysical tasks. I pointed out to the valuable information which could be achieved by means of computer simulations and to the possibility to predict the outcome of traditional experiments. Nowadays, computer represents an invaluable tool for chemists. In particular, the main topics of my research consisted in the development of an automated docking protocol for the voltage-gated hERG potassium channel blockers, and the investigation of the catalytic mechanism of the human peptidyl-prolyl cis-trans isomerase Pin1.

Proceedings of the Twenty-Fifth Annual Biochemical Engineering Symposium

The Annual Biochemical Engineering Symposium Series started in 1970 when Professors Larry E. Erickson (Kansas State University) and Peter J. Reilly (then with University of Nebraska-Lincoln) got together in Manhattan, KS along with their students for a half-day powwow and technical presentation by their students. Ever since then, it has been a forum for Biochemical Engineering students in the heartland of USA to present their research to their colleagues in the form of talks and posters. The institutions actively involved with this annual symposium include Colorado State University, Kansas State University, Iowa State University, University of Colorado, University of Kansas, University of Missouri-Columbia, and University of Oklahoma. The University of lowa and University of Nebraska-Lincoln have also participated in the conference in recent years. The host institutions for the different symposia have been: Kansas State University (1, 3, 5, 9, 12, 16, 20), Iowa State University (6, 7, 10, 13, 17, 22), University of Missouri-Columbia (8, 14, 19, 25), Colorado State University (II, 15, 21), University of Colorado (18, 24), University of Nebraska-Lincoln (2, 4), University of Oklahoma (23). The next symposium will be held at Kansas State University. Proceedings of the Symposium are edited by faculty of the host institution and include manuscripts written and submitted by the presenters (students). These often include works-in-progress and final publication usually takes place in refereed journals. ContentsPatrick C. Gilcrease and Vincent G. Murphy, Colorado State University. Use of 2,4,6-Trinitrotoluene (TNT) As A Nitrogen Source By A Pseudomonas florescens Species Under Aerobic Conditions. Marulidharan Narayanan, Lawrence C. Davis, and Larry E. Erickson, Kansas State University. Biodegradation Studies of Chlorinated Organic Pollutants in a Chamber in the Presence of Alfalfa Plants. S.K. Santharam, L.E. Erickson, and L.T. Fan, Kansas State University.Surfactant-Enhanced Remediation of a Non-Aqueous Phase Contaminant in Soil. Barry Vant-Hull, Larry Gold, and Robert H. Davis, University of Colorado.The Binding of T7 RNA Polymerase to Double-Stranded RNA. Jeffrey A. Kern and Robert H. Davis, University of Colorado.Improvement of RNA Transcription Yield Using a Fed-Batch Enzyme Reactor. G. Szakacs, M. Pecs, J. Sipocz, I. Kaszas, S.R. Deecker, J.C. Linden, R.P. Tengerdy, Colorado State University.Bioprocessing of Sweet Sorghum With In Situ Produced Enzymes. Brad Forlow and Matthias Nollert, University of Oklahoma.The Effect of Shear Stress ad P-selectin Site Density on the Rolling Velocity of White Blood Cells. Martin C. Heller and Theodore W. Randolph, University of Colorado.The Effects of Plyethylene Glycol and Dextran on the Lyophilization of Human Hemoglobin. LaToya S. Jones and Theodore W. Randolph, University of Colorado.Purification of Recombinant Hepatitis B Vaccine: Effect of Virus/Surfactant Interactions. Ching-Yuan Lee, Michael G. Sportiello, Stephen Cape, Sean Ferree, Paul Todd, Craig E. Kundrot, and Cindy Barnes, University of Colorado.Application of Osmotic Dewatering to the Crystallization of Oligonucleotides for Crystallography. Xueou Deng, L.E. Erickson, and D.Y.C. Fung, Kansas State University.Production of Protein-Rich Beverages from Cheese Whey and Soybean by rapid Hydration Hydrothermal Cooking. Pedro M. Coutinho, Michael K. Dowd, and Peter J. Reilly, Iowa State University.Automated Docking of Glucoamylase Substrates and Inhibitors. J. Johansson and R.K. Bajpai, University of Missouri.Adsorption of Albumin on Polymeric Microporous Membranes.

Automated Feedback for 'Fill in the Gap' Programming Exercises

Timely feedback is a vital component in the learning process. It is especially important for beginner students in Information Technology since many have not yet formed an effective internal model of a computer that they can use to construct viable knowledge. Research has shown that learning efficiency is increased if immediate feedback is provided for students. Automatic analysis of student programs has the potential to provide immediate feedback for students and to assist teaching staff in the marking process. This paper describes a “fill in the gap” programming analysis framework which tests students’ solutions and gives feedback on their correctness, detects logic errors and provides hints on how to fix these errors. Currently, the framework is being used with the Environment for Learning to Programming (ELP) system at Queensland University of Technology (QUT); however, the framework can be integrated into any existing online learning environment or programming Integrated Development Environment (IDE)

Automated code checking

Most buildings constructed in Australia must comply with the Building Code of Australia (BCA). Checking for compliance against the BCA is a major task for both designers and building surveyors. This project carries out a prototype research using the EDM Model Checker and the SMC Model Checker for automated design checking against the Building Codes of Australia for use in professional practice. In this project, we develop a means of encoding design requirements and domain specific knowledge for building codes and investigate the flexibility of building models to contain design information. After assessing two implementations of EDM and SMC that check compliance against deemed-to-satisfy provision of building codes relevant to access by people with disabilities, an approach to automated code checking using a shared object-oriented database is established. This project can be applied in other potential areas – including checking a building design for non-compliance of many types of design requirements. Recommendations for future development and use in other potential areas in construction industries are discussed

Test architecture for prototyping automated dynamic airspace control

The automation of various aspects of air traffic management has many wide-reaching benefits including: reducing the workload for Air Traffic Controllers; increasing the flexibility of operations (both civil and military) within the airspace system through facilitating automated dynamic changes to en-route flight plans; ensuring safe aircraft separation for a complex mix of airspace users within a highly complex and dynamic airspace management system architecture. These benefits accumulate to increase the efficiency and flexibility of airspace use(1). Such functions are critical for the anticipated increase in volume of manned and unmanned aircraft traffic. One significant challenge facing the advancement of airspace automation lies in convincing air traffic regulatory authorities that the level of safety achievable through the use of automation concepts is comparable to, or exceeds, the accepted safety performance of the current system.

Automated Scheduler

Automated Scheduler is a prototype software tool that automatically prepares a construction schedule together with a 4D simulation of the construction process from a 3D CAD building model.