Protein docking is used to check the structure, position and orientation of a protein when it interacts with small molecules like ligands. Protein receptor-ligand motifs fit together tightly, and are often referred to as a lock and key mechanism. There are both high specificity and induced fit within these interfaces with specificity increasing with rigidity. The foremost thing that we need to start with a docking search is the sequence of our protein of interest. (Halperin et al., 2002). Protein-protein interactions occur between two proteins that are similar in size. The interface between the two molecules tends to be flatter and smoother than those in interfaces of these interactions do not have the ability to alter protein-ligand interactions. Protein-protein interactions are usually more rigid, the conformation in order to improve binding and ease movement. (Smith and Sternberg, 2002). The process of drug development has revolved around a screening approach, as nobody knows which compound or approach could serve as a drug or therapy. Such almost blind screening approach is very time-consuming and laborious. The goal of structure-based drug design is to find chemical structures fitting in the binding pocket of the receptor. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them (Weil et al., 2004). A homology model of the housefly voltage-gated sodium channel was developed to predict the location of binding sites for the insecticides fenvalerate, a synthetic pyrethroid, and DDT, an early generation organochlorine. The model successfully addresses the state-dependent affinity of pyrethroid insecticides. (O’Reilly et al., 2006).

1. Protein Docking
Rajendra Kumar

2. Proteins Are…
 The functional units of the cell
 Polymers of amino acids
 Maintain a key role in intra and intercellular processes
 Maintain the control functions as Enzymes
 Characteristic elements are :
carbon,hydrogen,oxygen,nitrogen

3. Definition
 To place a ligand into the binding site of a protein in the
appropriate manner for optimal interactions with a
receptor protein
Goal:
 To be able to search a database of molecular structures and
retrieve all molecules that can interact with the query
structure

4. Protein-protein Docking
 Aim: predict the structure of a protein complex from
its partners
+
Complex
Monomers
(James meiler,2007)

5. Types of Docking studies
 Protein-Protein Docking
Both molecules usually considered rigid
 6 degrees of freedom
 Search space and the energetics of possible binding
conformations
 Protein-Ligand Docking
 Flexible ligand, rigid-receptor
 Reduce flexible ligand to rigid fragments connected
by one or several hinges, or search the
conformational space using molecular dynamics

6. Rigid Vs Flexible docking
 Rigid Body Docking:
 No modification in bond angles, lengths & torsion
angles of the components
 Flexible Docking :
 Takes in to the conformational changes

7. Protein docking is the computational determination of protein complex
structure from individual protein structures.
(Smith and Sternberg, 2002)

8. Interactions lead to …
Ligand binds to the active site of protein
 Binding leads to conformational changes in protein
 Conformational changes thermodynamically most stable
 Lowest Gibb’s energy

9. Protein –Protein interaction Thermodynamics
(Smith and Sternberg, 2002)

10. Why docking is important?
 It is of extreme relevance in cellular biology, where
function is accomplished by proteins interacting with
themselves and with other molecular components
 It is the key to rational drug design: The results of
docking can be used to find inhibitors for specific target
proteins and thus to design new drugs.

11. Basic Requirements For Docking
 Structure of protein of interest should be known
 X-ray Crystallography
 NMR Spectroscopy

12. X-Ray Diffraction
 The spacing of atoms in a crystal lattice can be determined
by measuring the locations and intensities of spots
produced on photographic film.
 x-ray analysis of sodium chloride crystals shows that Na
and Cl ions are arranged in a simple cubic lattice.
 X – rays, wavelengths in the range of 0.7 to 1.5 Å (0.07 to
0.15 nm).
( Hubbard, 2006)

13. cont..
( Hubbard, 2006)

14. ( Hubbard, 2006)

15. Nuclear Magnetic Resonance
 Modern NMR techniques are being used to determine the
structures of larger macromolecules.
 NMR is based on nuclear spin angular momentum.
 Only certain atoms, including 1H, 13C, 15N, 19F,and 31P,
possess the kind of nuclear spin that gives rise to an NMR
signal.
(James,1998)

16. (James, 1998)

17. Why this is difficult?
 Both molecules are flexible and may alter each other’s structure
as they interact:
 Hundreds to thousands of degrees of freedom (DOF)

19. Some techniques
 Surface representation, that efficiently represents the
docking surface and identifies the regions of interest
(cavities and protrusions)
 Connolly surface
 Clustered-Spheres
 Alpha shapes
 Surface matching- that matches surfaces to optimize a
binding score:
(Fernandez et al.,2005)

20. Surface Representation
 Each atomic sphere is
given the van der Waals
radius of the atom
 Rolling a Probe Sphere
over the Van der Waals
Surface leads to the
Connolly surface
(Fernandez et al.,2005)

21. Clustered-Spheres
 Uses clustered-spheres to identify cavities on the receptor and
protrusions on the ligand
 Regions where cavities (on the receptor) or protrusions (on the
ligand)
j
i
(Fernandez et al.,2005)

22. Alpha Shapes
 In 2D an “edge” between two points is “alpha-exposed” if there
exists a circle of radius alpha such that the two points lie on the
surface of the circle and the circle contains no other points from
the point set
(Fernandez et al.,2005)

23. Alpha Shapes: Example
(Fernandez et al.,2005)

24. 3-D Representation of a Protein Binding Site
6.7
4.2-4.7
5.2 4.8
5.1-7.1
(Fernandez et al.,2005)

25. Surface Matching
 Find the transformation (rotation + translation) that will
maximize the number of matching surface points from
the receptor and the ligand
First Condition
 Find the best fit of the receptor and ligand
Use energy calculations to refine the docking
 Select the fit that has the minimum energy
(Fernandez et al.,2005)

27. CAPRI
 Critical Assessment of Prediction of Interactions
 launched to:
 To assess & compare current docking algorithms
 To stimulate further developments in the field
(Gray et
al.,2003)

28. CAPRI Challenge (2002)
T h e 7 C A P R I D o c k in g
Ta rg e ts
(Gray et al.,2003)

30. DOCK
DOCK works in 5 steps:
 Step 1 Start with crystal coordinates of target receptor
 Step 2 Generate molecular surface for receptor
 Step 3 Generate spheres to fill the active site of the receptor:
The spheres become potential locations for ligand atoms
 Step 4 Matching: Sphere centers are then matched to the
ligand atoms, to determine possible orientations for the ligand
 Step 5 Scoring: Find the top scoring orientation
(Gray et al.,2003)

31. Docking protocol
(Gray et al.,2003)

32. Docking protocol
RANDOM START POSITION
 Creation of a decoy begins with a random orientation of each
partner and a translation of one partner along the line of protein
centers to create a glancing contact between the proteins
(Gray et al.,2003)

33. Docking protocol
LOW-RESOLUTION MONTE CARLO SEARCH
 One partner is translated and rotated around the surface of
the other
 The score is based in the correctness of each decoy and
residue-residue interactions terms
(Gray et al.,2003)

34. Docking protocol
HIGH-RESOLUTION REFINEMENT
 Side-chains are added to the protein backbones to
changing the energy surface
• A filter is employed to detect inferior decoys and reject
them without further refinement
(Gray et al.,2003)

35. Docking protocol
CLUSTERING & PREDICTIONS
 The search procedure is repeated to create approximately
105 decoys per target
 The 200 best-scoring decoys are then clustered
 The clusters with the most members are selected as the
final predictions and ranked according to cluster sizes
(Gray et al.,2003)

36. Scoring Function
 To evaluate the interactions to discriminate the observed
mode from others
 Binding affinity of the complex to be worked out
 Energetically favorable complexes to be predicted
 Large no: of degrees of freedom to be considered
(Gray et al.,2003)

37. PROTEIN-LIGAND DOCKING
# A molecular modeling technique
# Goal is to predict the position and orientation of a ligand
when it is bound to a protein receptor or enzyme
# Pertinent to field of drug design

39. In drug designing…
 Drugs are small molecules of therapeutic importance
 Drug discovery costs are too high [~$800 millions]
 Time consuming [8~14 years]
 Drugs interact with their receptors in a highly specific and
complementary manner.
 Effort  to cut down the research timeline and cost by reducing lab
experiment  use computer modelling.
(Wei et al ., 2004)

40. contd…
 By computational means, screen large databases of
potential drugs against protein targets
 HIV protease inhibitors - Invirase ,Norvir , Crixivan
 Influenza neuraminidase inhibitor - zanamivir
(Wei et al ., 2004)

41. DOCK: Example HIV-1 Protease
Active Site
(Aspartyl groups)
(Wei et al ., 2004)

42. TRADITIONAL DRUG DESIGN
Natural ligand /
Screening
Biological Testing
Drug Design Cycle
If promising
Synthesis of New Compounds
Pre-Clinical Studies
(Wei et al ., 2004)

43. SBDD
 drug targets (usually proteins)
 binding of ligands to the target (docking)
↓
“rational” drug design
(benefits = saved time and $$$)
(Wei et al ., 2004)

44. Structure-based Drug Design (SBDD)
Natural ligand / Screening
Molecular Biology & Protein Chemistry
3D Structure Determination of Target
and Target-Ligand Complex
Modelling
Drug Design Cycle
Structure Analysis
Biological Testing
and Compound Design
If promising
Synthesis of New Compounds
Pre-Clinical
Studies
(Wei et al ., 2004)

45. contd…
Ligand Target
database Protein
Molecular
docking
Ligand docked into (Wei et al ., 2004)
protein’s active site

46. Molecular Docking Introduction Page

47. Molecular Docking Page
 Introduction Page

48.  Input Page

49. Input Page (cont..)

50. Submitting Job

51. Results

52. Results (in visualization form)

54. Introduction
 The voltage-gated sodium channel underlies the propagation of action
potentials in neuronal cells of both vertebrates and invertebrates.
 During an action potential of the sodium channel undergoes
transitions between activated and inactivated functional states, and
toxins binding to specific sites on the channel and the channel pore.
(Andrias et al .,2006)

55. Transmembrane topology of the voltage- gated sodium
channel
(Andrias et al .,2006)

56. Model of voltage- gated sodium channel
(Andrias et al .,2006)

57. Chemical structure
(Andrias et al .,2006)

58. Fenvalerate
(Andrias et al .,2006)

59. Acrinathrin
(Andrias et al .,2006)

60. Docking Programs
More information in: http://www.bmm.icnet.uk/~smithgr/soft.html
The programmes are:
 DOCK (I. D. Kuntz, UCSF)
 AutoDOCK (Arthur Olson, The Scripps Research
Institute)
 RosettaDOCK (Baker, Washington Univ., Gray, Johns
Hopkins Univ.)
(Smith and Michael , 2002)

61. PROTEIN-LIGAND DOCKING
 Affinity- (Accelrys Inc.)
 AutoDock- (The Scripps Research institute)
 FlexX -(BioSolve IT)
 GLIDE- (Schrödinger )
 GOLD - (CCDC)
 LIGPLOT -(University College of London)
 FlexiDOCK -(Tripos)
(Smith and Michael , 2002)

62. Protein-Legand & Protein-Protein
Docking
 DOCK -(UCSF Molecular Design Institute )
 GRAMM- (SUNY)
 ICM-Dock- (MolSoft LIC)
(Smith and Michael ,2002)

63. CONCLUSION
 Protein docking is important in :
 Understanding / predicting interactions
 Developing drugs and cures
 The field continuous to progress & is developed by
CAPRI

64. Discussion

65. Have a Nice
Day !