View
2.659
Download
37
Category
Tags:
Preview:
Citation preview
A
H GB
C
D
E
F
Drug Design(DOCKING)
R
P
By: JAIDEEP SARKAR
High Throughput Screening104 ligands per day
Drug Design
But: Hit Rate 10-6 per ligand
RATIONAL DRUG DESIGN
Compound databases,
Microbial broths,Plants extracts,Combinatorial
Libraries
3-D ligand Databases
DockingLinking orBinding
Receptor-LigandComplex
Randomscreening synthesis
Lead molecule
3-D QSAR
Target EnzymeOR Receptor
3-D structure by Crystallography,NMR, electron microscopy OR
Homology Modeling
Redesign to improve
affinity, specificity etc.
Testing
Structure specific drugs – Act at specific sites (receptor or enzyme)- Activity/potency susceptible to small changes in structure
Ex.- It took Pfizer about 18 years to develop the anti-inflammatory drug Piroxicam, which was launched in 1980 during the “golden age of rational drug discovery
MECHANISM OF DRUG ACTION
Substrate
ProteinLigand
BINDING
REACTION
FUNCTION
STRUCTURAL CHANGE
What is Docking?•Docking attempts to find the “best” matching between two molecules
•It includes finding the Right Key for the Lock
•Given two biological molecules determine:
- Whether the two molecules “interact”
- If so, what is the orientation that maximizes the “interaction” while minimizing the total “energy” of the complex
Goal: To be able to search a database of molecular structures and retrieve all molecules that can interact with the query structure
The Process
Identify disease protein Identify active siteDetermine structure
of Protein
Virtual Screening ofDrug Candidates
Synthesis of LeadCompounds
PharmacologicalTesting
Optimisation Clinical Trials Drug
Docking Protocol
contd...
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
Lead Optimization
Lead Lead OptimizationActive site
Express proteins with changes in amino acid sequencesIdentify amino acids involved in function
Generate molecular surface of protein Cavities in the receptor are used to
define spheres (blue); the centres
are potential locations for ligand atoms.
Sphere centres are matched to ligand
atoms, to determine possible orientations
for the ligand. 104 orientations generated
How DOCK works…….
Virtual screening, to identify potential lead compounds from a large dataset
• Known structures of organic compounds
• Libraries of Virtual Compounds
• Programs calculate affinity for protein
• Narrow down to small number of possiblities
• Surface representation that efficiently represents the docking surface and identifies the regions of interest (cavities and protrusions)
• Surface matching that matches surfaces to optimize a binding score
Pose prediction• If we know exactly
where and how a known ligand binds...
– We can see which parts are important for binding
– We can suggest changes to improve affinity
– Avoid changes that will ‘clash’ with the protein
• Monte Carlo methods (MC)• Molecular Dynamics (MD)• Simulated Annealing (SA)• Genetic Algorithms (GA)
Available in packages: Auto Dock (MC,GA,SA) GOLD (GA) Sybyl (MD)
Rosetta DOCK (Baker , Washington Univ., Gray, Johns Hopkins Univ.)
Introducing flexibility:Whole molecule docking programs
Glide (Schrodinger)
Why is docking important?
• 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. It is gaining importance as the number of proteins whose structure is known increases
• In addition to new drug discovery, it is of extreme relevance in cellular biology, where function is accomplished by proteins interacting with themselves and with other molecular components
Modified Simple Algorithm and 3D Superposition and Alignment
Drug Discovery by Drug DesigningCase Study: Tuberculosis
Crystals & Crystal structure
Lead compound
Virtual Screening
Combinatorial chemistryEnzyme assay
-0.006 -0.004 -0.002 0 0.002 0.004 0.006 0.008 0.010 0.012 0.014-1
0
1
2
3
4
5
6
7AccD5-NCI65828
1/[Malonyl-CoA]um-1
1/V
o (m
in-1
)[I] = 0.00[I] = 2.50[I] = 5.00[I] =10.00
TB ACCase, AccD5
Docking
The Computational Loop - Similarity Search
Structure-Based Drug Design Identified AccD5 Inhibitors
New TB drug lead
HO3S
NH2
N
N
OH
Why is this difficult?• Both molecules are flexible and may alter each other’s
structure as they interact:
• Hundreds to thousands of degrees of freedom (DOF)• Total possible conformations are astronomical
Trypsinogen
Trypsin
Chymotrypsinogen
Chymotrypsin
Duodenal Cell
Enterokinase
USES OF DOCKINGDrug targets Protein- ligand interactions that otherwise may be overlookedBetter understand the Machinery of Life
Enzyme-inhibitor classAntibody-antigen classOthers
Protein Therapies Engineered Protein EnzymesAlthough the reliability of docking methods is not so high, they
can provide new suggestions False positives rates can be reduced using several scoring
functions in a consensus-scoring strategy
Large tomatoes can evolve from wild, blueberry-size tomatoes. The genetic mechanism responsible for this is similar to the one that proliferates cancer cells in mammalians. That's a connection nobody could have made in the past.
Cancer cell growth appears to be related to evolutionary development of plump fruits and vegetables
ADVANCE USE…….
Future Challenges For Docking
• Better Scoring Functions
• High-Throughput Screening
• Tractable Models of Flexibility
• The so-called computational molecular docking problem is far from being solved. There are two major bottle-necks:
1. The algorithms can handle only a limited extent of backbone flexibility
2. The availability of selective and efficient scoring functions
Recommended