g. narahari sastry molecular modeling group organic chemical sciences indian institute of chemical...
TRANSCRIPT
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G. Narahari SastryMolecular Modeling GroupOrganic Chemical Sciences
Indian Institute of Chemical TechnologyHyderabad 500 007
INDIA
Seminar on Systems Approach to Bioinformatics, Feb., 18-20, 2004Bioinformatics centre, Pondicherry University
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Integration of Chemoinformatics and Bioinformatics
Computational chemistry
SmallMolecules
Large MoleculeTargets
Genomic Biology
Bioinformatics Cheminformatics
In silico
HighThroughputScreening
Assays
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MESDAMESETMESSRSMYNAMEISWALTERYALLKINCALLMEWALLYIPREFERDREVILMYSELFIMACENTERDIRATVANDYINTENNESSEEILIKENMRANDDYNAMICSRPADNAPRIMASERADCALCYCLINNDRKINASEMRPCALTRACTINKARKICIPCDPKIQDENVSDETAVSWILLWINITALL
3D structure
Biological Structure
Organism
CellSystem Dynamics
CellStructures
SSBs
polymerase
Assemblies
helicase
primase
Complexes
Sequence
Structural Scales
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Much About Structure
• Structure Function
• Structure Mechanism
• Structure Origins/Evolution
• Structure-based Drug Design
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Bottlenecks in developing Structure – Function Relationships
Structures determined by NMR, computation, or X-ray crystallography are static snapshots of highly dynamic molecular systems
Biological processes (recognition, interaction, chemistry) require molecular motions and are time dependent.
To comprehend and facilitate thinking about the dynamic structure of molecules is crucial.
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What is Molecular Modeling?
• A science that elucidates and validates experimental evidence through imagination, visualization, and rationalization
• Applied in many areas of research (Academic/Industrial)
Caveat: Is the interpolation and extrapolation reliable?
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Capabilities of Molecular Modeling at Ranbaxy
Ligand- basedStructure- based
Lead Optimization
Crystal Structure analysis
Homology Modeling
Computational Analysis of Protein- Ligand Interactions
SAR, 2D- & 3D- QSAR
Lead Identification
I n- SillicoBBB,Solubility,Caco- 2 &Toxicity Predictions
Lead Hopping
Modification of ligands within the active- site for better binding
Pharmacophore Development
Hits fromDatabase Searches
Capabilities of Molecular Modeling
Prioritization of Hits
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Drug Design
Structure based Ligand based
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Ligand (analog)based drug design
Receptor structure is not knownMechanism is known/ unknownLigands and their biological activities are known
Target (structure) based drug design
Receptor structure is knownMechanism is knownLigands and their biological activities are known/ unknown
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High Resolution Structural Biology
Determine atomic structure
Analyze why molecules interact
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Anti-tumor activityDuocarmycin SA
The Reward: UnderstandingControl
Shape
Atomic interactions
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CAUTION….
macromolecular structure
protocols
methods
Structure determination methods
•Don't be a naive user!?!
•When computers are applied to biology, it is vital to understand the difference between mathematical & biological significance
•computers don’t do biology, they do sums quickly
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Receptor Structure
Known Unknown
Structure BasedDrug Design
Analog BasedDrug Design
Docking
Homology ModelingReceptor Mapping
REQUIREMENTLead Compound and
derivatives with biologicaldata
REQUIREMENTA Model Receptor
Molecular DynamicsSimulations
Rigid Docking
FlexiDock
Monte CarloSimulations
Simulated Annealing
Quantum Mechanical(BRABO) ANN
GA
PCA
CoMFACoMSIA
QuantumMechanicalDescriptors
QuantumMechanics forAlignment
SYBYL, INSIGHT II, CERIUS2, MOE, AMBER (CDAC), DOCK, AUTODOCK
SINGLE MOLECULE
QSAR
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Structure Based Drug Design
3D ligand Databases
DockingLinking orBinding
Receptor-LigandComplex
Random screening synthesis
Lead molecule
3D QSAR
Target Enzyme(or) Receptor
3D structure by Crystallography,NMR, electron microscopy (or)
Homology Modeling
Redesign to improve
affinity, specificity etc.
Testing
Compound databases, Microbial broths, Plants extracts,
Combinatorial Libraries
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Drug and Target : Drug and Target : Lock and Key ?Lock and Key ?
Most of the drugs “FIT” well to their targets
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Study of protein crystals give the details of the “lock”. Knowing the “lock” structure, we can DESIGN some “keys”.
“Lock” structure (from experiment)
This is achieved by COMPUTER Algorithms
This is called “STRUCTURE BASED DRUG DESIGN”
“Key”constructed by computer
AlgorithmsAlgorithms
Some “Locks” are known but not all !!
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Variations on the Lock and Key Model
1- Which structure of the lock should be targeted?
2- Is the binding pocket a good target?
3- Is structure-based design relevant for my receptor?
-Is the 3D structure reliable?
-Is the binding pocket static enough?
4- Which key fits best?
5- What are the prerequisite physicochemical properties for the key for better binding?
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Ligand Active site
Non-Ligands
The ligand has been identified
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Docking of Ligand to the Active site of Protein
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3D Structure of the Complex
Experimental Information: The active site can be identified based on the position of the ligand in the crystal structures of the protein-ligand complexes
If Active Site is not KNOWN?????
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Building Molecules at the Binding Site
Identify the binding regions Evaluate their disposition in space
Search for molecules in the library of ligands for similarity
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Structure Based Ligand Design
O
NH
O
H
O
NH
?
O
O
O
H
O
NH
NSO
O
H
O
NH
O
H
O
NHS?
?
O
H
O
NH
??
?
OO
H
O
NH
DockingBuilding
Linking
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O
O
O
H
HO
O
O
HH
OO
OH
OO
OH
O
O
OH
OH
O
DB Search
Define PharmacophoreLigandDesign
Structure based drug design
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Molecular Docking
• The process of “docking” a ligand to a binding site mimics the natural course of interaction of the ligand and its receptor via a lowest energy pathway.
• Put a compound in the approximate area where binding occurs and evaluate the following:
– Do the molecules bind to each other?– If yes, how strong is the binding?– How does the molecule (or) the protein-ligand complex
look like. (understand the intermolecular interactions)– Quantify the extent of binding.
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Molecular Docking (contd…)
• Computationally predict the structures of protein-ligand complexes from their conformations and orientations.
• The orientation that maximizes the interaction reveals the most accurate structure of the complex.
• The first approximation is to allow the substrate to do a random walk in the space around the protein to find the lowest energy.
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Algorithms used while docking
• Fast shape matching (e.g., DOCK and Eudock), • Incremental construction (e.g., FlexX,
Hammerhead, and SLIDE), • Tabu search (e.g., PRO_LEADS and SFDock), • Genetic algorithms (e.g., GOLD, AutoDock, and
Gambler), • Monte Carlo simulations (e.g., MCDock and
QXP),
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Some Available Programs to Perform Docking
• Affinity
• AutoDock
• BioMedCAChe
• CAChe for Medicinal Chemists
• DOCK
• DockVision
• FlexX
• Glide
• GOLD
• Hammerhead
• PRO_LEADS
• SLIDE
• VRDD
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Ligand in Active Site Region
Ligand
Active site residuesHistidine 6; Phenylalanine 5; Tyrosine 21; Aspartic acid 91; Aspartic acid 48; Tyrosine 51; Histidine 47; Glycine 29; Leucine 2; Glycine 31; Glycine 22; Alanine 18; Cysteine 28; Valine 20; Lysine 62
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Examples of Docked structures
HIV protease inhibitors COX2 inhibitors
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Approaches to Docking
• Qualitative– Geometric– shape complementarity and fitting
• Quantitative– Energy Calculations– determine minimum energy structures– free energy measure
• Hybrid– Geometric and energy complementarity
– 2 phase process: rigid and flexible docking
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Rigid Docking
• Shape-complementarity method: find binding mode(s) without any steric clashes
• Only 6-degrees of freedom (translations and rotations)
• Move ligand to binding site and monitor the decrease in the energy
• Only non-bonded terms remain in the energy term
• Try to find a good steric match between ligand and receptor
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• Describe binding site as set of overlapping spheres
• Both the macromolecule and the ligand are kept rigid; the ligand is allowed to rotate and translate in space
• In reality, the conformation of the ligand when bound to the complex will not be a minima.
binding site overlapping spheres
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The DOCK algorithm in rigid-ligand mode
.. .
.
..
. .
N
NH
N
SO
F
.. .
N
NH
N
SO
F
.
N
NH
N
SO
F
N
NH
N
SO
F
1. Define the target binding site points.
2. Match the distances.
3. Calculate the transformation matrix for the orientation.
4. Dock the molecule.
5. Score the fit.
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Flexible Docking
• Dock flexible ligands into binding pocket of rigid protein
• Binding site broken down into regions of possible interactions
binding site from X-ray
hydrophobic
H-bonds
parameterised binding site
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• Then dock the molecule into pocket by matching up interactions with ligand
• Uses “random” translation, rotation, and torsion, and look for a better binding mode.
parameterised binding site docked ligand
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• Even though we have considered the ligand to be flexible, the active site was kept as a rigid structure.
• The side chains of the protein in the vicinity of the active site should be flexible, but computationally more expensive.
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Incremental Construction (FlexX)
• A piecewise assembly of ligand within the active site.
• Generate rigid fragments by scissoring the rotatable bonds of known ligands.
• Dock the fragments one by one starting from the larger fragment
• Assemble the whole ligand by reconnecting them and repeat the docking process
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Free Energy of Binding
• Dock ligand into pseudo-intercalation site– Manual, automatic, and
flexible ligand docking
• Energy minimize to determine G complex
• Determine Gligand
_=interaction energy of ligand with surroundings when explicitly solvated
Gbinding = Hinteraction - T Sconformation+ Gsolvent
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Detailed calculations on all possibilities would be very expensive
The major challenge in structure based drug design to identify the best position and orientation of the ligand in the binding site of the target.
This is done by scoring or ranking of the various possibilities, which are based on empirical parameters, knowledge based on using rigorous calculations
Need for Scoring
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Exact Receptor Structure is not always known
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• Receptor Mapping
The volume of the binding cavity is felt from the ligands which are active or inactive. This receptor map is derived by looking at the localized charges on the active ligands and hence assigning the active site.
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Receptor Map Proposed for
Opiate Narcotics(Morphine, Codeine, Heroin, etc.)
*6.5Å
7.5-8.5Å
Flat surface for aromatic ring
Cavity for part of piperidine ring
Focus of charge
Anionic site
R1R2
R3
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Homology modeling
Predicting the tertiary structure of an unknown protein using a known 3D structure of a homologous protein(s) (i.e. same family).
Assumption that structure is more conserved than sequence
Can be used in understanding function, activity, specificity, etc.
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Structure modeling (Structure vs. Sequence)
- Homology modeling
- Fold recognition/ Threading
The 3D structures are used to understand protein function and to design new drugs
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•Alignment–Multiple possible alignments
•Build model•Refine loops
–Database methods–Random conformation–Score: best using a real force field
•Refine sidechains–Works best in core residues
Key step in Homology Modeling
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Structure Prediction by Homology Modeling
Structural Databases
Reference Proteins
Conserved Regions Protein Sequence
Predicted Conserved Regions
Initial Model
Structure Analysis
Refined Model
SeqFold,Profiles-3D, PSI-BLAST, BLAST & FASTA
C Matrix Matching
Sequence Alignment
Coordinate Assignment
Loop Searching/generation
WHAT IF, PROCHECK, PROSAII,..
Sidechain Rotamersand/or MM/MD
MODELER
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Framework for just the target backbone is shown in yellow against the template structures
Fragments which have the right conformation to properly connect the stems without colliding with anything else in the structure
Generating a framework
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Typical Contributions of CADD to Drug Discovery Projects
Suggestions of structures which, when retrieved from a compound collection or synthesized, were found upon testing to be active or inactive as predicted
Development of structure-activity relationships
Visualization of receptor models, pharmacophoric models, molecular alignments, or data models
Reanalyzing available data to achieve new insights
Creative search of available structures to find new leads
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Identification of preferred sites for structure elaboration
Development of models to improve drug transport, specificity, safety or stability
Development of mechanistic insights
Use of leads in one area to derive new leads in a related assay
Establishment of useful databases of project structures and properties
Computation of physical or chemical properties to correlate with activities
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Kinds of Computational approaches for the discovery of new ligands
•The search in 3D databases of known small molecules
•De novo design
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Structure Searching
2D Substructure searches
3D Substructure searches
3D Conformationally flexible searches
2D Substructure searches
[
F
,
C
l
,
B
r
,
I
]
O
O
Functional groups
Connectivity
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De Novo Design
1) Define Interacting Sites
HB donor/acceptor regions, Hydrophobic domain,
Exclusion volumes
2) Select Sites
3) Satisfy Sites
4) Join Functional Groups
5) Refine Structure
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Protein-ligand docking
o The most promising route available for determining which molecules are capable of fitting within the very strict structural constraints of the receptor binding site and to find structurally novel leads.
o The most valuable source of data for understanding the nature of ligand binding in a given receptor
Active site-directed pharmacophores
o A Pharmacophore based method along with the utilisation of the geometry of the active site for enzyme inhibitors, represented by 'excluded volumes' features,
o Produces an optimised pharmacophore with improved predictivity compared with the corresponding pharmacophore derived without receptor information
Pharmacophore
Excluded volumesGreenidge et. al. J Med Chem. 1998, 41, 2503
Virtual screening: Target structure based approaches
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Pharmacokinetics play an extremely important role in drug development
ADMET
•Absorption•Distribution•Metabolism•Excretion•Toxicity
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Outlook
• Molecular modeling first introduced in the pharmaceutical industries in the early 70’s have raised probably unrealistic hopes such as it can “do it all”. But it took quite a while before it could deliver
• No doubt, with the ever-expanding new powerful methods available, today’s modelers have the requisite potential to bring real benefits to pharmaceutical industry.
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• Molecular Modeling and Computational Chemistry are essential to understand the molecular basis for biological activity and has Tremendous Potential to aid Drug Discovery
• A healthy interaction between computational chemists and pharmaceutical industry seem indispensable.
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• Structure Based Drug Design is an extremely important tool in the computer aided drug design.
• I Hope that you are convince!
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January, 04