MAYANK_Drug_Designing

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Protein Interactions and Docking : 

Submitted By: MAYANK BEDI M.Tech Bioinformatics Protein Interactions and Docking

What is Docking? : 

What is Docking? Docking attempts to find the “best” match between two molecules

… a more serious definition… : 

… a more serious definition… 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. In short, (Defining Features of CADD - Computer Aided Drug Design)

Why is docking important? : 

Why is docking 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. It is gaining importance as the number of proteins whose structure is known increases

HIV-1 Protease : 

HIV-1 Protease Active Site (Aspartyl groups)

Why is this difficult? : 

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

Types of Docking studies : 

Types of Docking studies Protein-Protein Docking Both molecules usually considered rigid 6 degrees of freedom First apply steric constraints to limit search space and the examine energetics of possible binding conformations Protein-Ligand Docking Flexible ligand, rigid-receptor Search space much larger Either reduce flexible ligand to rigid fragments connected by one or several hinges, or search the conformational space using monte-carlo methods or molecular dynamics

Docking Programs : 

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

DOCK : 

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

DOCK: Example : 

DOCK: Example Aspartyl groups are its active side HIV-1 protease is the target receptor

DOCK : 

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

DOCK: Example : 

DOCK: Example

DOCK : 

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

DOCK : 

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

DOCK : 

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

DOCK: Example : 

DOCK: Example 4 5 Three scoring schemes: Shape scoring, Electrostatic scoring and Force-field scoring Image 5 is a comparison of the top scoring orientation of the molecule thioketal with the orientation found in the crystal structure

Other Docking programs : 

Other Docking programs AutoDock 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 It models physical forces and creates a very large number of decoys It uses degeneracy after clustering as a final criterion in decoy selection

Protein-Protein Docking : 

Protein-Protein Docking Our goal is to try to predict protein-protein complexes from the coordinates of the unbound monomer components. The method is divided in two steps: A low-resolution Monte Carlo search and a final optimization using Monte Carlo minimization. Up to 105 independent simulations are carried out, and the resulting “decoys” are ranked using an energy function. The top-ranking decoys are clustered to select the final predictions.

Conclusions : 

Conclusions The so-called computational molecular docking problem is far from being solved. There are two major bottle-necks: The algorithms can handle only a limited extent of backbone flexibility The availability of selective and efficient scoring functions

Docking programs : 

Docking programs Rigid body DOCK 3.4 Kuntz et al GOLD (Genetic algorithm) Jones et al Auto Dock (Monte Carlo ) Morris et al Fragment Based FlexX Rarely et al LUDI Bohm GROMOL Bohacek & McMartin HOOK Eisen et al

“Drug Designing”Concepts and Methods!! : 

“Drug Designing”Concepts and Methods!!

Introduction : 

Introduction DRUG – derived from an Old French word "drogue“. “Chemical Compound showing activity and generating some therapeutic response.” Drug Designing – An inventive process of finding new chemical compounds having therapeutic value, based on a particular biological target.

Slide 23: 

Drug design is an iterative process. It begins with identification of a compound (target) in the Biochemical pathways of crucial interactions. Conceiving hypothesis regarding chemical feature of the inhibitor/activator molecule (a lead compound), which displays interesting biological properties . It ends with optimizing both the activity profile for the molecule and its chemical synthesis.

Slide 24: 

There is increasing concern in pharmaceutical industry regarding the cost and time of production. About $500 to $700 million and 12-15 years required to discover a new drug. There is also a fierce competition amongst different drug companies There are many unmet therapeutic needs where the treatment is inadequate

Slide 25: 

Ancient times Chemical Era Rationalizing design process Biochemical era Evolutionary drug designing

Drug Discovery & Development : 

Drug Discovery & Development Identify disease Isolate protein involved in disease (2-5 years) Find a drug effective against disease protein (2-5 years) Preclinical testing (1-3 years) Formulation Human clinical trials (2-10 years) Scale-up FDA approval (2-3 years) File IND File NDA IND – Investigational New Drug NDA – New Drug Application

Technology is impacting this process : 

Technology is impacting this process Identify disease Isolate protein Find drug Preclinical testing GENOMICS, PROTEOMICS & BIOPHARM. HIGH THROUGHPUT SCREENING MOLECULAR MODELING VIRTUAL SCREENING COMBINATORIAL CHEMISTRY IN VITRO & IN SILICO ADME MODELS Potentially producing many more targets and “personalized” targets Screening up to 100,000 compounds a day for activity against a target protein Using a computer to predict activity Rapidly producing vast numbers of compounds Computer graphics & models help improve activity Tissue and computer models begin to replace animal testing

How are some of the drugs discovered in past? : 

How are some of the drugs discovered in past? Isolate active substance from natural products: Pennicilin/Quinine Modification of natural products: Thienamycin Broad screening of known synthetic substances: Sulfa drugs Derivation and activation of structure activity data: Cephalosporin Structure directed molecular design: Carbonic anhydrase inhibitor Mechanism based molecular design: Suicide inhibitor

Types of Drug Designing : 

Types of Drug Designing Structure Based Drug Designing Ligand Based Drug Designing

Assumptions : 

Assumptions There is a specific target which can control diseased state There is a specific inhibitor that can fit to that target and block its activity Rational approach succeeds only if there is good understanding of 3D structure of the target molecule.

3-D structure of Protein and Ligand : 

3-D structure of Protein and Ligand Docking, Free energy calculation Ligand optimization Denovo design, Library search Builder,lead discovery 2-D and 3-D QSAR Pharmacophor search Active Analog based Drug Design Combinatorial chemistry QSAR, Diverse libraries

Basic Principle of structure based drug designsimilarity/complimentarity : 

Basic Principle of structure based drug designsimilarity/complimentarity 2.Electrostatic 4. H-bonding 1.Shape similarity 3.Hydrophobic

Note of caution : 

Note of caution Sterric complimentarity is necessary but not sufficient. 3D database searching is more appropriate than de-novo designing because our knowledge of receptor ligand recognition is poor. De novo designing is good to modify the existing structure to yield more active analog.

Steps in structure Based Drug design : 

Steps in structure Based Drug design 3D structure of macromolecular targets and the target protein Visualization using graphics tools & structure preparation Active site detection Scoring Optimization

1. 3D- structures of macromolecular targets : 

1. 3D- structures of macromolecular targets X-ray Crystallography Crystallization is required. NMR spectroscopy Size of protein and solubility Protein Modelling

In case 3D structure of target not available one can model the same using Protein modeling Techniques : 

In case 3D structure of target not available one can model the same using Protein modeling Techniques

2. Visualization and Structure preparation : 

2. Visualization and Structure preparation Analyze structural features of the target Arrangement of helices/ sheets etc Preparation of the structure to make it suitable for a docking program

3. Identification of the active site : 

3. Identification of the active site Density difference method Fitting spheres or rectangles . Each method gives scoring on the basis of number of amino acid side chains in the active cavity

Multiple binding sites for the ligand : 

Multiple binding sites for the ligand Most difficult part is possibility of different binding sites. ‘Active site' has to be defined before applying any technique.

Eg. HIV-I protease: Ligand binding site : 

Eg. HIV-I protease: Ligand binding site Binding site has 10 binding pockets and the enzyme cleaves eight different peptide sequences, with wide structural variation. A slight modification in one sequence can produce effective inhibitor.

4. Scoring Methods : 

4. Scoring Methods Scoring methods varies according to the type of application used for docking. But generally all are based on energy functions At each point, interaction energy between the docked structure to ligand molecule is calculated using empirical potential energy function of the type: Etot = Evdw + Eel + Ehb Its form as well as parameters used in it known as FORCE FIELD.

Ligand based drug design : 

Ligand based drug design

Steps... : 

Steps... Take a ligand Move the ligand at different points Calculate ‘score’ at each point Find best position Compare scores by different ligands Select the best

Ligand structural data : 

Ligand structural data Structural data for ligands can be available from the Cambridge Crystallographic Structural Database (CCSD) If the desired structure is not available one can select the ‘scaffold’ and build the rest of molecule. Later, energy minimize the molecule

Energy- based docking programs : 

Energy- based docking programs Many docking programs use an 'energy grid' considering ligand as well as the target molecule 'rigid'. They can allow motional as well as conformational flexibility to the 'ligand'. These, usually handle one ligand at a time. Their main use is to obtain the starting model of ligand-receptor complex, which can be refined further.

Energy-GRID based docking programs : 

Energy-GRID based docking programs Their success depends on the inputs from physicochemical studies. Some of the software packages used are: PCMODEL HYPERCHEM SYBYL LIGAND MOLMOL MOE

GRID SEARCH : 

GRID SEARCH The most important consideration is the method of optimization used to find the optimum geometry and conformation of the ligand. For this, the ligand is moved at different position in the active cavity, and interaction and conformation energy functions are evaluated repetitively. Conformational flexibility of the ligand and the receptor are important. Simplest is to follow a Grid or Systematic search (SS) method

GRID SEARCH : 

GRID SEARCH The basic idea is to create a molecular lattice that spans active site of the protein, Next use the lattice to construct a molecule that fills the active site, but does not overlap or penetrate the protein.

Dynamic perturbations in ligand & receptor structures : 

Dynamic perturbations in ligand & receptor structures Conformational flexibility of the target and the drug is important. The bound conformation of the drug need not be the minimum energy conformation.

Lipnski Rule of ‘5’ : 

Lipnski Rule of ‘5’ The inhibitor or the ligand designed should follow the lipnski parameters. Log P < 5.0 Mol.Wt < 500Da Hydrogen bond donors < 5 Hydrogen bond acceptors < 10

ADMET properties : 

ADMET properties ADMET properties considers those parameters of the ‘ligand’ after it enters the human body i.e. its effects inside the body. Log P Solubility Hepatotoxicity Blood Brain Barrier Plasma protein binding CYP2D inhibition etc..

Idea of Pharmacogenomics...??? : 

Idea of Pharmacogenomics...??? How an individuals genetic makeup responds to drugs. “Tailor made drugs”

Thank You... : 

Thank You...

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