Molecular docking

Molecular docking

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  Molecular Docking • S.Shahriar Arab
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  Presented by VIVEK K RAHULBS
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  Drug discovery Take yearsto decade for discovering a new drug and very costly  To cut down the research timeline and cost by reducing wet-lab experiment use computer modeling softwares Drugs interact with their receptors in a highly specific and complementary manner. Core of the (target-based) structure-based drug design (SBDD) is lead generation and optimization
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   Pharmacophore- theatoms and functional groups required for a specific pharmacological activity, and their relative position in space.  3D arrangement of functional groups that enable a compound to exert a particular biological effect.
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  In silico design In-silicodesign Receptor based Denovo based In silico Ligand design based Combinatorial
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  Receptor/structure based approach Activesite identification No Complex growing Ligand fragments grouping yes Fit for receptor No yes Potential drug Change receptor
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  Ligand based approach Pharmacophoreidentification Pharmacophore modification No Fit to receptor Yes Potential drug
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  Combinatorial based approach • Automated or semiautomated process of synthesisinglarge quantity of compounds in small scale Denovo based approach • Purely based on molecular modelling study of binding site. • Searching large data bases to identify proper ligand.
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  Different terms usedin in-silico design  Receptor/Host/Lock – receiving molecule (protein) – large.  Ligand/ Guest/ Key – molecule bind to receptor –small.  Docking – Computational simulation of a candidate – preffered orientation of ligand binding site to a receptor.  Binding mode – conformation of ligand-receptor bound to each other.  Pose – a candidate binding mode.  Scoring – evaluating a particular pose by counting the number of favourable intermolecular interactions.
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   Ranking –classify ligands most likely to interact favourably to a particular relation based on ∆G of binding.  Hit – Ligand with high rank.  Lead – hit with biological activity.  Pharmacophore – spacial arrangement of atoms or groups believed to be responsible for biological activity.  Rational drug design – Modulation of specific biological target may have therapeutic value.  QSAR – Study of physico chemical properties of a compound with its biological/pharmacological activity.  Drug design – design of ligands.
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  Docking Docking attempts tofind the “best” matching between two molecules
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  ....a more seriousdefinition…. Docking is a method which predicts the preffered orientation of one molecule to a second when bound to form a stable complex with overall minimum energy. • Docking is used to predict both strength & type of signal produced.
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  • Aim of moleculardocking is to achieve an optimized conformation & relative orientation between protein ligand such that ∆G is minimized. It is to study. . . . .  Whether the two molecules interact with each other  If so what is the orientation that maximizes the interaction which minimizing the total energy of the complex Goal. . . Given a protein structure and predict its ligand bindings.
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  Why is dockingimportant? It is of extreme relevance in cellular biology It is the key to rational drug design
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  Docking approaches i. Uses amatching technique – describes the protein and ligand as complementary surfaces. ii. Simulates the actual docking process in which ligandprotein pairwise interaction energies are calculated
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  a) Shape complementarity  Receptor’smolecular surface – solvent accessible surface area.  Ligand’s molecular surface – matching surface description. Advantage  Fast & robust Disadvantage  Can't model the dynamic changes in the ligand / protein conformations accurately.
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  b) Simulation  Proteinand ligands are separated by a physical distance  Binding takes place only after certain moves (translations, rotations,& internal changes like torsional angle rotations) in its conformational space.  In every move total energy of the system is calculated. Disadvantage  It take longer time for evaluation (overcome by using grid based technique & fast optimization methods)
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  Factors affecting docking Intramolecularforces. . . . bond length bond angle dihedral angle Intermolecular forces. . . . electrostatic dipolar H-bonding hydrophobicity Vander waals forces
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  Different type ofinteractions Interactions between particles can be defined as a consequence of forces between molecules connected by particles. Drug + receptor Kf Kr Complex Kf – rate constant for association of the complex Kr – rate constant of dissociation of the complex Affinity, Kas = Kf / Kr Biological activity of a drug is related to its affinity Kas for the receptor
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  Electrostatic energy  Involvesintegration of overall electron clouds of the two molecule.  Longest range. Ion-ion (1/R) Dipoledipole Iondipole (1/R3) (1/R2)
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  Electrodynamic forces  Attractiveforces existing between all pairs of atoms,even between rare gas atoms.  Depends on polarizability & number of valence electrons of interacting molecule.  Polarization energy involves the interaction of a molecule that is already polar with another polar/non polar molecule.  Eg. London or Vander waals forces.
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  Steric forces  Eachatom wthin the molecule occupies a certain amount of space.  If atoms are too closer there is an associated lost in energy due to overlapping electron cloud – may affect molecules preferred shape, reactivity and activation energies of most chemical reaction.  Steric effect will determine how & at what rate a drug will interact with its target biomolecule.
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  Solvent related forces these are forces generated due to chemical reaction between the solvent & protein or ligand. Eg. Hydrogen bonds (hydrophyllic interactions) Hydrophobic interactions
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  Mechanics of docking Methodsto derive 3D structures
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  X – raycrystallography Protein + precipitating medium individual protein molecule data collection using Computer controlled detector phase & amplitude of diffracted waves calculated & combined with experimentally observed structural functions Protein structure arrange to form a crystalline entity (single crystalline x ray diffraction) image of electron diffracting cloud (electron density map) model building & refinement (electron density fitting program FRODO, TNT)
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  Proton detected heteronuclearNMR Protein + drug spectrum re run Drug fail to combine with protein NMR still be detected drug bind to protein nuclei will have shorter relaxation time no NMR spectrum
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  Homologous modelling  Alignthe amino acid sequence of protein with unknown structural agent, the sequence of a homologous protein whose 3D structure has already been determined.  By converting structurally conserved region & structural variable region, the core of the molecule can be identified.
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  Prepared protein structure Input to docking program Database of potential ligands Search algorithm Scoring function Successof docking program
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  a) Search algorithm Determine all possible optimal conformation for a given complex (protein-ligand/ protein-protein)  Calculate the energy of resulting complex & of each individual interactions. Conformational search strategies include • Systematic/ stochastic torsional searches about rotatable bonds. • Molecular dynamic simulations • Genetic algorithms to evolve new low energy conformations
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  Ligand flexibility  Conformationof the ligand may be generated in the absence of receptor or in the presence of receptor binding activity. Force field energy evaluation Knowledge based method Receptor flexibility  Large number of degrees of freedom experimentally determined multiple steric structures Rotamer libraries of aminoacid side chain surrounds the binding cavity
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  b) Scoring function
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  Types of docking a)Lock and key/ rigid docking b) b) Induced fitting/ flexible docking
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  MOLECULAR DOCKING • Docking-the process by which molecular modeling software fits a molecule into target binding sites. • Used for finding binding modes of protein with ligands/inhibitors • In molecular docking, attempt to predict the structure of the intermolecular complex formed between two or more molecules
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  MANUAL DOCKING Dock orfit a molecule in the binding site Binding group on the ligand and binding site are known, defined by the operator. Ideal bonding distance for potential interaction is defined. Binding group in the ligand is paired with its complementary group in the binding site Docking procedure is started The program try to get best fit, as defined by the operator
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  The paired groupsare not directly overlaid, they are fitted within preferred bonding distance. Both ligand and protein remain same conformation throughout the process Same as in energy minimization. So this is a rigid fit, once a molecule successfully docked fit optimization is carried out. Different conformation of molecule can be docked to in same way Identify the best fit
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  FLEXIBLE DOCKING Rigid docking-the protein and the ligand as rigid bodies. The drawback of rigid docking is, since it neglects the conformational degrees of freedom of ligands. It fails to give satisfactory answer for flexible ligand, will form different conformations.
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  To solve this,dock different conformations of ligand as possible in order to get the best result. FLOG (flexible ligand oriented on grid) is a program that generates conformational libraries called flexibose, contain 10-20 conformations for each ligand studied.
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  DOCKING OF FLEXIBLELIGANDS Various programs are for generate different ligand conformations The popular method is to fragment the ligand , identify a rigid anchor fragment which can be docked Examples of programs Then reconstruct or grow the molecule back onto the anchor.
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  Direct dock anddock 4.0 The algorithm identifies the rotatable bonds present In the ligand Identification of flexible and rigid region Molecule is split into fragments
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  The most rigid fragmentis termed as anchor Torison angle is varied for each addition This increases the partially build structures(contructs) Docked by shape complimentarity Flexible parts then added sequentially to the anchor. Selection of limited number constructs based on binding and difference in their structures
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  The segments areadded in layers working outwards The segments in the layer 1 are added sequentially before the segments in layer 2 . FLEX The software also uses the anchor and grow method The anchor is docked according to chemical complementarity.
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  Docking is determinedby the intermolecular interactions formed between the anchor and binding site. Docking the anchor by chemical complementarity rather than steric complementarity has the advantage to cut down the number of possible binding orientation for the anchor. An interaction surface consisting interaction points
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  Matching process occurs,it matches atoms on the anchor to interaction points in the binding sites The distance between atoms on the anchor must match the distance between interaction points in the binding site The anchor atom and corresponding interaction point must have binding compatibility Docking requires identification of 3 matched pairs of anchor atoms, equal to identifying complimentary pharmacophore triangles for the anchor & binding site
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  Matching process -Comparisonof pharmacophore triangles for the ligand and binding site For a match a triangle for the ligand have same dimensions as a triangle for the binding site, but also the corners of the triangle must have binding compatibility The docking is now carried out such that anchor atoms are overlaid with their matched interaction point in the binding site.
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  The procedure ensuresthat the angle requirements for hydrogen bonding are fine with respect to the interaction points in the binding site .
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  Problems The anchor hasto be chosen manually, becomes difficult when large number of structures Vast number of different pharmacophore triangles constructed to represent the binding site.
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  HAMMERHEAD PROGRAM Anchor andgrow program Probes are placed into the binding site in order to identify locations of binding interactions The probes used are hydrogen atoms as well as c=o and NH fragments
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  Each probes canbe scored as high scoring or low scoring based on No. of hydrogen bonds it can form. Once the probe has positioned, they act as the targets for docking procedure.
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  Matching of atomsof a molecular fragment with probes, docking must involve at least one of the high scoring probes. Both steric and chemical complementarity is used in the matching process. Once the match has been identified the docking operation is carried out. Since the ligand is split into fragments, have limited number of rotatable bonds
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  All fragments thatare formed contain an atom or bond that is shared with another fragment. For each fragment, a number of conformations are generated.
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  The fragments aredocked and scored Fragments that are particularly high scoring are defined as head and act as an anchors The remaining fragments are defined as tails The reconstruction phase is carried out for each fragment that has been identified as potential anchor.
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  The tails arethen docked The first fragments share an atom or bond with the anchor and is docked like that it is aligned both to the relevant atom or bond on the anchor. Two fragments are then merged by overlaying the shared bonds or atoms. The tail fragments moves to the anchor
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  Advantages Anchors are chosenautomatically Different anchors possible and investigated
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  Docking Of FlexibleLigands, By Simulated Annealing And Genetic Algorithm  This method is viable for docking of the flexible ligands.  It involves use of metropolis method by using montecarlo algorithms for conformational analysis.  The ligand is placed randomly in the space close to the binding site.
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   Montecarlo algorithmsare used to generate different conformations  The molecules are translated and rotated such that it tumbles within the binding site.  Different conformations are generated at different position and orientation with in the binding site.  Binding energy of each structure is measured as it is formed and compared with the previous structure.
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  Docking Programs UsingMonte Carlo Algorithms For Docking  Auto dock  Mcdock  Prodock and pro-lead. Disadvantage The quality of result is often depends on how the initial structure s placed in the binding site. This can be over come by using combination of programs Eg; DOCK and Montecarlo based programs
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  Docking programs Docking programs DOCK(I. D. Kuntz, UCSF) AutoDock (Arthur Olson, The Scripps Research Institute) AutoDock was designed to dock flexible ligands into receptor binding sites The strongest feature of AutoDock is the range of powerful optimization algorithms available RosettaDOCK (Baker, Washington Univ., Gray, Johns Hopkins Univ.)
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  Overall steps indocking 1) Get the complex from P.D.B 2) Clean the complex 3) Add the missing hydrogens/side chain atoms & minimized the complex 4) Clean the minimized complex 5) Separate the minimized complex in macromolecule (lock) & ligand (key) 6) Prepare the docking suitable files for lock & key 7) Prepare all the needing files for docking 8) Run the docking 9) Analyze the docking results
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  Working methodology ofSchrodinger i.     ii.  Protein preparation (protein preparation wizard) Prepare co crystallized ligands – correctly define multiple bonds & adding hydrogen Neutralize residues that do not participate in the salt bridge Preprocess the receptor before grid generation Optimization of the protein Ligand preparation (ligprep) Generate energy minimized 3D structures – tautomeric, stereochemical and ionization variations as well as energy minimizations
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  iii. Docking  Generatereceptor grid around the site using glide  Docking conducted using XP GLIDE (Extra precision) iv. Visual inspection  Images were obtained using Glide XP Vsualiser panel
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  Applications  Hit identification Lead optimization  Bio remediation  virtual screening of large databases
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  References i. Introduction tomolecular docking; Edelmiromomen; Pharmaceutical & Medicinal chemistry; Saarland university. ii. Protein-ligand docking methods; Thomas Funkhouser;Princeton university iii.Introduction to molecular docking; Carlos. P.Sosa; university of Minnesofa iv. Molecular docking tutorial; Khuled.H.Brakat; Pharma matrix work shopin, Computational biophysics. v. Principles of Docking: An overview of search Algorithm & a guide to scoring functions; Inbal Halperin,Buyon Ma. vi. An introduction to medicinal chemistry; 4th edition; Graham.L.Patrick; Pg no. 352-361 vii. The organic chemistry of drug design & drug action. 2nd edition; Richard.B.Silverman
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  All informations inthis presentation is collected from various sources available on internet and text books…. This presentation is only for educational purpose…. we sincerely saying thanks to all