MOLECULAR DOCKING.pptx

Molecular Docking

1. MOLECULAR DOCKING PRESENTED BY E.POOVARASAN M.PHARM FIRST YEAR PSG COLLEGE OF PHARMACY

2. MOLECULAR DOCKING 2 Docking is a method which predicts the preferred orientation of one molecule to a second, When a ligand and a target are bound to each other to form a stable complex. Preferred orientation used to predict the strength of association or binding affinity between two molecules using scoring functions

3. Overview Of Molecular Docking: 3

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5. Steps involved in Molecular Docking: 5 Protein Preparation Binding site analysis Ligand Preparation Docking Docking analysis and Scoring functions Validation of docking protocol

6. Protein Preparation 6 3D structure of a protein is downloaded from the data bank ( www.rcsb.org ) Protein data Bank ( PDB) maintained by research collaboratory for Structural Bioinformatics (RCSB) It contains various X-ray crystal structures for Proteins and other biomolecules.

7. 7 Cleaning of Protein: Once, the protein is downloaded, it is to be corrected for missing residues, missing atoms, alternate locations, added water molecules and incorrect bonding types and charges are to be balanced. When , protein has been cleaned , it is then further refined by molecular mechanics calculations to be finally prepared for use in docking purposes.

8. Binding Site Analysis: 8 Binding site is the part of the protein where the ligand binds It is generally a cavity on the protein surface. It can be identified by looking at the crystal structure of the protein bound with a known inhibitor. The binding site can be predicted by Static approach Dyanamic approaches Mixed approaches

9. Ligand Preparations: 9 The type of ligands chosen for docking will depends on goal. For docking the ligand to be prepared in a particular format even after energy minimization and conformational anlalysis , for correct visualization of hydrogen bonds and other interactions. It can be obtained from various data bases ( e.g Zinc or and Pubchem ) or it can Sketched by means of Chemsketch tool or prepared in PRODRG server. It is necessary to apply filters to reduce the number of molecules to be docked. Examples: net charge, molecular weight, polar surface area, solubility, commercial availability, similarity thresholds, pharmacophores, synthetic accessibility, and ADMET properities .

10. Docking : 10 Select a receptor and a ligand from your library Modify advanced parameters during simulation, such as number of runs, number of evaluations, etc,. Where ligand is docked onto the receptor and the interactions are checked. The scoring function generates a score depending on the best selected ligands.

11. Docking analyses and Scoring : 11 Docking is carried out by searching for the correct binding mode of a molecule with a number of trials and keepings the energetically favourable poses. After a certain number of trials have been carried out and a sufficient number of poses have for a molecule – the search Stops The decision to keep a trial pose is based on the computed ligand receptor interaction energy ( score) of that pose.

12. Scoring Function 12 The nature of interactions ( van der waals , hydrogen bonding, electrostatic, etc,.) between the ligands and their protein or nucleic acid targets, termed as “ scoring function”. Scoring refers to evaluation and ranking of all configurations which are generated during a search process. The actual free energy is preferred one. The free energy of binding of complex should be less than the sum of their individual free energy

13. 13 Knowledge of interaction energies and forces flows into an assigned score. Scoring functions have a two – fold task They serve as an objective function to differentiate between diverse poses of a single ligand in the receptor- binding site After docking a compound database, they are required to estimate binding affinities of different receptor- ligand and to rank – order the compounds. Hydrophobic effects, van der waal’s and dispersion interactions , hydrogen bonding, steric, electrostatic interactions and solvation effects are among the factors that contribute to ligand binding, which in turn are governed by kinetic and thermodynamic principles.

14. Types of scoring Function: 14 1.Empirical Based: Empirical scoring functions sum enthalpic and entropic interactions with the relative weights of the terms based on a training set of protein – ligand complexes. The weights are assigned by regression methods that are used to fit the experimentally determined affinities. The interactions terms often include van der waals , electrostatic interactions and hydrogen bonds ▲ G bind = ▲ G solvent + ▲ G conf + ▲ G int + ▲ G rot + ▲ G tran + ▲ G vib Example: PLP , ChemScore , FlexX

15. 2.Force-field based: 15 They predict the binding free energy of protein-ligand complex by adding up individual contributions from different type of interactions. The interaction terms are derived from physical-chemical phenomena as opposed to experimental affinities. E = E stretching + E bending + E torision + E van der waals + E electrostatic + E hydrogen bonding + cross terms Examples : Energy score in DOCK, score function used for single ligand docking in DOCKVISION and that used in GOLD

16. 3.KNOWLEDGE BASED: 16 It relays on statistical means to extract rules on preferred, and non-preferred, atom pair interactions from experimentally determined protein-ligand complexes. The rules are interpreted as pair – potentials that are subsequently used to score ligand binding poses. Examples: PMF score

17. 4. Consensus scoring: 17 This applies a number of score functions to the same docked pose identified by docking to eliminate false positives. Protein- ligand docking is so difficult due to tremendous complexity of the system; one must take into account hundreds of thousands of degrees of freedom in the two molecules, as well as the not-completely – known combination of energetic forces acting on them.

18. Factors affecting the docking score: 18 Orientation of residues Protonation states ( ligand and protein) Tautomeric forms Protein flexibility Involvement energy of ligand De-solvation penalties Crystal packing of initial X-ray structure.

19. Validation of the docking Protocol: 19 Validation requires that the co-crystallized ligand should be extracted from protein, corrected and redocked to the same protein. The redocked conformer is then compared with the original one by superimposition or by visualization as well as the RMSD ( Root mean square deviation) is calculated. RMSD provides deviation between conformer and the original conformer and original co-crystallized ligand with protein. RMSD is acceptable upto 3A , it always better less than 1A 0.

20. SOFTWARES FOR DOCKING: 20 FREEWARES INCLUDE: DOCK 6.1 – http://dock.compbio.ucsf.edu/ AUTODOCK – http://autodock.scripps.edu/ HEX - http://www.csd.abdn.ac.uk/hex/ ( protein-protein docking) SLIDE – http://www.bch.msu.edu/~Kuhn/ projects/slide/home.html COMMERCIAL: GOLD- Cambridge Crystallographic data centre FLEXX – Tripos, Inc GLIDE – schrodinger , Inc ICM- molsoft , Inc LIGANDFIT – Accelrys , Inc OPEN EYE

21. DOCKING TYPES: 21 Manual Docking Automatic Docking Rigid ligand and rigid receptor docking( Rigid docking) Flexible ligand and rigid protein( Flexible Ligand docking) Rigid ligand and Flexible protein ( flexible protein docking) Flexible protein and Flexible Ligand ( Flexible Docking) Most commonly used docking algorithms use the rigid receptor/ flexible ligand model

22. MANUAL DOCKING: 22 Molecules may be docked manually with the aid of computer graphics or automatically by using computer algorithms. Manual docking is done using molecular visualization software, Here bindings groups on the ligand and the active site are known, in which the binding group in ligand is paired with its complimentary group in binding stie. The user manually moves, rotates, translates the compound inside the protein cavity. A new association energy is recorded… etc.

23. 23 Advantages: Quick Can be very efficient if the user knows well the interacting site Disadvantages: Users dependant You can really obtain stupid results.

24. Automatic Docking: 24 It is an unbiased type of docking in which the user does not specify the active site, neither has to direct a ligand to an active and can place a ligand randomly. The system automatically finds an optimal position in which ligand and receptor bind , auto dock is used . Depending upon the flexibility, a docking algorithm may be, Ligand and protein rigid Flexible ligand and rigid protein Rigid ligand and flexible protein Both ligand and protein flexible.

25. 25 Based on the search algorithms, the principal methods are Molecular dynamics Monte Carlo methods Genetic algorithms Fragment based methods Point complementary methods Distance geometry methods Tabu searches Systematic searches

26. RIGID DOCKING: 26 Here the molecules are rigid, in 3D space of one of the molecule which brings it to an optimal fit with the other molecules in terms of a scoring function. Rigid Ligand and Rigid Receptor Docking: when the ligand and receptor are both treated as rigid bodies , the search space is very limited considering only 3 translational and 3 rotational degrees of freedom . In this case, ligand flexibility could be addressed by using a precomputed a set ligand conformations or by allowing for a degree of atom-atom overlap between the protein and ligand.

27. 27 DOCK: It is the first automated procedure for docking a molecule into a receptor site and is being continuously developed FLOG- It generates ligand conformations on the basis of distance geometry and uses a clique – finding algorithm to calculate the sets of distances. This approach is useful if an important interaction is already known before docking.

28. Flexible ligand and rigid receptor docking ( semiflexible induced fit) 28 For systems whose behaviour follows the induced fit paradigm, it is of vital importance to consider the flexibilities of both the ligand and receptor since in that case both the ligand and receptor change their conformations to form a minimum energy perfect fit complex. But, the cost is very high when the receptor is also flexible. Thus the common approach is treating the ligand as flexible while the receptor is kept is rigid docking Example; AutoDock , Flex

29. Flexible docking: 29 In flexible docking molecules are flexible, confirmations of the receptor and the ligand molecules, as they appear in complex. Protein – ligand docking Flexible ligand, rigid receptor Search space much larger Either reduce flexible ligand An enumeration on the rotations of one of the molecules ( usually smaller one ) is performed. Every rotation the energy is calculated , the most optimum pose is selected

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31. APPLICATIONS OF MOLECULAR DOCKING: 31 Hit identification : Docking combined with a scoring function can be used to quickly screen large databases of potential drugs in silico to identify molecules that are likely to bind to protein target of interest In reverse pharmacology docking used target identification. Lead optimization: Docking can be used to predict in where and in which relative orientation a ligand binds to a protein

32. 32 DRUG-DNA INTERACTIONS: This information establishes the correlation between drug’s molecular structure and its cytotoxicity So it is aid in the development of anticancer drugs. Knowledge of molecular associations aids in understanding a variety of pathways taking place in the living and in revealing of the possible pharmacological targets Identification of haloperidol as lead compound in a structure based design for non-peptide inhibitor of HIV Dihydrofolate reductase ( anitbacterial0 Carbonic anhydrase inhibitor( treatment of glaucoma) Renin ( treatment of hypertension)

33. REFERENCES: 33 Molecular modelling and Drug Design by K Anand Solomon Drug Design by Balkishen Razdan www. Google.com

34. 34 THANK YOU