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Computational Analyses of Protein-Ligand Interactions

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Computational Analyses of Protein-Ligand Interactions Computational Analyses of Protein-Ligand Interactions Muhammad Kamran Haider Submitted for the Degree of Doctor of Philosophy University of York Department of Chemistry September 2010 Abstract Protein-ligand interactions have a central role in all processes in living systems. A comprehensive understanding of protein interactions with small molecules is of great interest as it provides opportunities for understanding protein function and therapeutic intervention. The major aims of this thesis were to characterise protein- ligand interactions from databases of crystal structures and to apply molecular modelling techniques for accurate prediction of binding modes of molecular fragments in protein binding sites. The first aspect of the project was the analysis of hydrogen bond donors and acceptors in 187 protein-ligand complexes of resolution 2.5Å or better. The results showed that an extremely small fraction of them were not explicitly hydrogen bonded, with the hydrogen bond criterion of donor-acceptor distance ≤ 3.5 Å and H- bond angle of ≥ 90°. It was also noticed that a vast majority of such cases were explicable on the basis of weak interactions and weak donor/acceptor strength. The results were consistent with reported observations for buried protein regions. In a series of docking calculations, the fraction of lost hydrogen bonds was evaluated as a discriminator of good versus bad docking poses. Docking and scoring with a standard program, rDock, did not create incorrect poses with missing hydrogen bonds to an extent that would make lost hydrogen bonds a strong discriminator. The second aspect of the research is related to weak (CH-π and XH-π, X=N,O,S) interactions. In a survey of IsoStar, a database of protein-ligand interactions, subtle differences were noticed in geometric parameters of π interactions involving different types of ligand aromatic rings with strong and weak donor groups in binding sites. The results supported the hypothesis that energetically favourable interaction patterns are more frequent when there are electron-donating substituents attached to the aromatic ring. Finally, the applicability of a modelling technique, multiple copy simultaneous search, in terms of predicting energetically favourable poses of solvents and fragments in target binding sites, was explored in detail. Several factors such as re-scoring with a better scoring function, use of multiple receptor structures and good quality prediction of water binding sites led to a robust protocol for high quality predictions of fragment binding in test datasets. 2 Acknowledgements I am extremely grateful to my supervisor, Prof. Rod. Hubbard, for his guidance and encouragement throughout this project. I am very thankful for his support in academic matters in the university during last four years and for training towards long term goals, especially related to working in Pakistan at the end of PhD. I would like to thank Dr. Hugues-Olivier Bertrand for his support, guidance and stimulating discussions during molecular modelling work. I am particularly thankful to my friends in YSBL, Marcus Fischer, Javier Garcia, Yuan He, Justyna Korczynska and Rob Nicholls for providing me continuous support, encouragement and for enjoyable time in YSBL. Special thanks to my very special friends Vikas Dangi, Chitvan Bochiwal and Hasan Basarir who made my stay in York a wonderful experience. I would like to thank my parents for enabling me to think for myself and providing me an ideal environment for leaning. I am hugely grateful to Higher Education Commission for providing financial support over last four years for my PhD studies. 1 Author’s Declaration Chapter 1, 2, 3 in this thesis is my own work. Chapter 4 and 6 were done in collaboration with Dr. Hugues-Olivier Bertrand of Accelrys, who performed docking calculations with GOLD and validated my MCSS calculations by re-running them. Chapter 5 in this thesis is my own work. 2 Table of Contents Title Page .............................................................................................................. 1 Abstract ................................................................................................................ 2 Acknowledgements .............................................................................................. 3 Author’s Declaration ............................................................................................. 4 Table of Contents .................................................................................................. 5 List of Figures ........................................................................................................ 8 List of Tables ........................................................................................................ 11 Chapter 1 Introduction ......................................................................................... 14 1.1. Protein-ligand binding – Chemical and thermodynamic basis ..................... 14 1.2. Experimental methods for measuring binding affinity ................................. 17 1.3. Protein-Ligand Interactions ........................................................................... 18 1.3.1. Electrostatic Interactions ....................................................................... 18 1.3.2. Hydrophobic Interactions ...................................................................... 21 1.4. Factors affecting protein-ligand binding affinity .......................................... 22 1.4.1. Binding site water molecules ................................................................. 22 1.4.2. Solvation and Desolvation ..................................................................... 24 1.4.3. Flexibility ................................................................................................ 25 1.5. Modelling and Prediction of Protein-Ligand Interactions ............................. 27 1.5.1. Methods based on Free Energy Calculations ........................................ 28 1.5.2. MM-PBSA/GBSA Methods ..................................................................... 28 1.5.3. Docking and Scoring ............................................................................... 29 1.6. Protein-Ligand Interactions in Drug Discovery ............................................. 32 1.6.1. Introduction to Fragment-based Lead discovery................................... 32 1.6.2. Predicting functional group position in binding sites – GRID and MCSS 33 1.6.3. Alternative computational approaches for solvent mapping and fragment docking ................................................................................................. 36 1.6.4. Treatment of desolvation in solvent mapping/fragment docking ........ 38 1.7. Aims ............................................................................................................... 42 1.7.1. Unsatisfied Hydrogen Bonds .................................................................. 42 1.7.2. Weak Hydrogen Bonds .......................................................................... 43 1.7.3. Prediction of fragment positions in binding site ................................... 43 Chapter 2 Unsatisfied Hydrogen Bond Donors and Acceptors at Buried Protein- Ligand Interfaces.................................................................................................. 45 2.1. Introduction................................................................................................... 45 2.2. Aims ............................................................................................................... 48 2.3. Methods ........................................................................................................ 48 2.3.1. Dataset and Programs............................................................................ 48 2.3.2. Atom Typing ........................................................................................... 49 2.3.3. Solvent Accessibility Calculations .......................................................... 50 5 2.3.4. Optimization of side-chain orientations ................................................ 51 2.3.5. Identification of hydrogen bonds .......................................................... 52 2.3.6. Calculation of Normalized B factors ...................................................... 52 2.3.7. Ligand Docking ....................................................................................... 53 2.4. Results ........................................................................................................... 54 2.4.1. Correlation with resolution .................................................................... 54 2.4.2. The percentage of unsatisfied buried donors/acceptors ...................... 55 2.4.3. Normalized B factor profiles .................................................................. 57 2.4.4. Docking Results ...................................................................................... 58 2.5. Discussion ...................................................................................................... 59 2.5.1. Energetics of Lost hydrogen bonds ........................................................ 59 2.5.2. Identification of lost hydrogen bonds ................................................... 61 2.5.3. Types of unsatisfied donors and acceptors ........................................... 62 2.5.4. Unsatisfied buried donors/acceptors in protein-ligand docking ........... 65 Chapter 3 Weak
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