3d qsar

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1 WELCOME

3D QSAR APPROACHES STRUCTURE AIDED AND COMPUTER AIDED DRUG DESIGNMETHODS TO OBTAIN THREE DIMENSIONAL STRUCTURES : 

2 3D QSAR APPROACHES STRUCTURE AIDED AND COMPUTER AIDED DRUG DESIGNMETHODS TO OBTAIN THREE DIMENSIONAL STRUCTURES MEERA PAUL FIRST YEAR MPHARM Department of Pharmaceutical Chemistry University college of pharmacy, Kottayam

CONTENTS : 

3 CONTENTS 3D QSAR APPROACHES STEREOCHEMISTRY ACTIVE SITE INTERACTION COMPARITIVE MOLECULAR FIELD ANALYSIS STRUCTURE AIDED &COMPUTER AIDED DRUG DESIGN METHODS TO OBTAIN 3 DIMENSIONAL STRUCTURES CRYSTALLOGRAPHY 2D,3D-NMR

3D QSAR : 

4 3D QSAR In 3 D QSAR, 3D properties of a molecule are considered. 3D-QSAR involve the analysis of the quantitative relationship between the biological activity of a set of compounds and their three-dimensional properties using statistical correlation methods. 3 D QSAR revolves around the important features of a molecule, its overall size and shape, and its electronic properties.

3D QSAR- ADVANTAGES : 

5 3D QSAR- ADVANTAGES Useful in the design of new drugs. The necessary software and hardware are readily affordable and relatively easy to use. Favorable and unfavorable interaction are represented by 3 D contours around a representative molecule. Graphical representation of beneficial and non beneficial interactions help to define a new structure. In 3 D QSAR, the properties of test molecule are calculated individually by computer program.

3D QSAR -APPROACHES : 

6 3D QSAR -APPROACHES STEREOCHEMISTRY ACTIVE SITE INTERACTION COMPARITIVE MOLECULAR FIELD ANALYSIS (CoMFA)

STEREOCHEMISTRY AND DRUG ACTION : 

7 STEREOCHEMISTRY AND DRUG ACTION plays an important role for the biological activity. According to Ariens and Lehman, chirality has an important influence on biological activity. This situation is even worse in diastereomeric mixtures for two reasons.٭ 2n species are involved.٭ the relative amounts of the different racemate in the mixture vary largely.

STEREOCHEMISTRY AND DRUG ACTION : 

8 STEREOCHEMISTRY AND DRUG ACTION Eg:Labetalol, a β anti adrenergic drug having two centers of optical asymmetry shows different pharmacological actions for its enantiomers.

STEREOCHEMISTRY AND DRUG ACTION : 

9 STEREOCHEMISTRY AND DRUG ACTION According to Pfeiffer’s, the activity ratio of the active Vs the less active enantiomer increases with increasing activity of more active one. Schaper derived quantitative as well as qualitative models for the dependence of the biological activity of a racemate on the activity of pure enantiomers.

ACTIVE SITE INTERACTION : 

10 ACTIVE SITE INTERACTION Pharmacophore pattern searching and receptor mapping use information from the QSAR’s in the different positions of the ligand and also from the ligand with restricted internal rotations (rigid analogs) Thus derive the pharmacophore and to conclude on the properties at the different sites of the receptor surface (the receptor map) .

ACTIVE SITE INTERACTION : 

11 ACTIVE SITE INTERACTION The interaction energies of ligand to hypothetical receptor sites have been performed by Holtje. Simple organic molecules are models of different amino acid side chains. E g: n-propane for aliphatic amino acids, acetamide for amide side chains, methanol for serine, toluene for aromatic amino acids etc.

ACTIVE SITE INTERACTION : 

12 ACTIVE SITE INTERACTION The interaction energies of each molecule are calculated using several of these probes All analogs of a series are placed in standard geometries and in certain distances to the hypothetical amino acid side chains. The resulting energies are then correlated to receptor affinities or to biological activities

ACTIVE SITE INTERACTION MODELS : 

13 ACTIVE SITE INTERACTION MODELS GRID Good Ford A new computer program. It calculates interaction energies of probe atoms around a protein surface of known three dimensional structure Gives contour maps of energy value. Negative contour value –attraction between the probe atom & the protein.

ACTIVE SITE INTERACTION MODELS : 

14 ACTIVE SITE INTERACTION MODELS USE OF GRID For design of new ligands. To calculate fields of CoMFA related 3D-QSAR approaches. To model a receptor map for series of active analogues.

ACTIVE SITE INTERACTION MODELS : 

15 ACTIVE SITE INTERACTION MODELS HINT The program HINT maps hydrophobic fields of molecules for 3D- QSAR. HINT can also be used to calculate the log P values.

ACTIVE SITE INTERACTION MODELS : 

16 ACTIVE SITE INTERACTION MODELS DISTANCE GEOMETRY is an approach to calculate 3D Co-ordinates from a set of distances. used for the calculation of 3D structures of organic compounds, peptides and small proteins from 2D measurements. Approximate 3D structures of the ligands are constructed and low energy conformations are selected.

ACTIVE SITE INTERACTION MODELS : 

17 ACTIVE SITE INTERACTION MODELS REMOTEDISIC Is receptor modeling from the three dimensional structure and physicochemical properties of the ligand molecules. Starts from low energy conformation of a reference compound. Low energy conformations of all other analogues are automatically superimposed to achieve a maximum overlap.

ACTIVE SITE INTERACTION MODELS : 

18 ACTIVE SITE INTERACTION MODELS HASL MODEL Doweyko developed HASL (Hypothetical active site lattice) model. Minimum energy conformations are calculated for similar or dissimilar ligands and all molecules are placed in a three –dimensional grid. A user –selected physico-chemical property, e.g., lipophilicity or electron density, is added to it as the fourth dimension. The resulting multidimensional lattices are automatically superimposed by an iterative fitting.

ACTIVE SITE INTERACTION MODELS : 

19 ACTIVE SITE INTERACTION MODELS In this manner a hypothetical active site lattice is formed to predict the relative orientation and affinities of the ligands. Wiese &Coat modified the HASL method by using P L S analysis, instead of interactive fitting and obtained better results.

ACTIVE SITE INTERACTION MODELS : 

20 ACTIVE SITE INTERACTION MODELS APEX – 3 D - It recognizes pharmacophores in biologically active molecules. - This program compares the descriptors and their distances for active and inactive analogues and stores the results as rules in a knowledge base, which can be used to predict the activity of new compounds.

COMPARITIVE MOLECULAR FIELD ANALYSIS : 

21 COMPARITIVE MOLECULAR FIELD ANALYSIS CoMFA involves placing of molecules in a grid and to correlate field properties of the molecules with biological activities. Dick Crammer in 1988 Steps Group of compounds having a common pharmacophore is selected . The 3-dimensional structures of reasonable conformation must be generated from 2-dimensional structures.

CoMFA : 

22 CoMFA 3.The energy minimized structures are fitted to each other using pharmacophore hypothesis. 4.Molecules are then aligned using active analog approach, distance geometry method

PHARMACOPHORE SELECTION : 

23 PHARMACOPHORE SELECTION PHARMACOPHORE L-LIPOPHILIC SITE D-H- BOND DONOR PD-PROTONATED H- BOND DONOR

Identification Of Pharmacophore : 

24 Identification Of Pharmacophore

CoMFA ALIGNMENT : 

25 CoMFA ALIGNMENT

CoMFA : 

26 CoMFA Once molecules are aligned, a grid or lattice is established which surrounds the sets of analogues in potential receptor space.

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27 Each grid point defines a point in space Place the pharmacophore into a lattice of grid points Each grid point defines a point in space CoMFA

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28 CoMFA Each grid point defines a point in space Position molecule to match the pharmacophore

CoMFA : 

29 CoMFA A Probe atom is placed at each grid point. Steric and electrostatic fields are calculated for each molecule in every grid point. Next step in a CoMFA is a partial least square analysis to determine a minimal set of grid points necessary to explain measured biological activities of the compounds. CoMFA results are often presented in a graphical form ;with contours :favorable and unfavorable regions of different fields.

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30 A probe atom is placed at each grid point in turn Measure the steric or electrostatic interaction of the probe atom with the molecule at each grid point

CONTOUR PLOTS : 

31 CONTOUR PLOTS

Slide 32: 

32 QSAR equation Activity = aS001 + bS002 +……..mS998 + nE001 +…….+yE998 + z

STRUCTURE AIDED DRUG DESIGN : 

33 STRUCTURE AIDED DRUG DESIGN Uses the idea of medicinal chemistry with X-ray crystallography, nuclear magnetic resonance, molecular modelling, computational chemistry etc. Possible to: 1) design inhibitors based on the architecture of an enzyme active site, 2) design agonists or antagonists based on the bioactivity of proteins engineered by site directed mutagenesis and

STRUCTURE AIDED DRUG DESIGN : 

34 STRUCTURE AIDED DRUG DESIGN design small molecular agonists or antagonist based on the interfaces of hormone and receptor binding epitopes. In the design of inhibitors based on the architectures of an enzyme active site: helpful to determine the three dimensional structure of the enzyme and of the enzyme in complex with an inhibitor at high resolution.

STRUCTURE AIDED DRUG DESIGN : 

35 STRUCTURE AIDED DRUG DESIGN To define precisely all the molecular interactions that are necessary for a drug to bind to its target site. Thus possible to design a new ligand with better binding affinity & with a shape that fit better into the active site and having charge distribution suitable for increased interaction energy.

STRUCTURE AIDED DRUG DESIGN : 

36 STRUCTURE AIDED DRUG DESIGN The second type drug design process is applied when proteins such as monoclonal antibodies or hormones and growth factors are used as drugs. The genes encoding these proteins can be cloned, mutated by site directed mutagenesis and expressed. The modified proteins thus obtained can be purified, kinetically characterized and assayed to evaluate their biological functions.

STRUCTURE AIDED DRUG DESIGN : 

37 STRUCTURE AIDED DRUG DESIGN This cycle of mutagenesis, expression and evaluation of the engineered protein is repeated to obtain a better agonists or an antagonist. The structure of the protein and / or its target molecule gives an idea about which mutation is to be introduced in the engineered protein to obtain the desired functional modifications.

STRUCTURE AIDED DRUG DESIGN : 

38 STRUCTURE AIDED DRUG DESIGN Structure aided drug design has already resulted in drugs that are in clinical trials: carbonic anhydrase inhibitors to treat glaucoma; rennin inhibitors to treat hypertension; HIV protease inhibitors to treat AIDS etc

COMPUTER AIDED DRUG DESIGN : 

39 COMPUTER AIDED DRUG DESIGN Useful for searching for epitopes which can act as drug binding regions in the surface of the target molecule. Possible for docking small molecules into these binding regions by automated or investigator aided procedures. The basic condition in docking procedure is that the selected ligands should possess the appropriate geometry to fit in to binding site of the target molecule with minimal steric clashes.

COMPUTER AIDED DRUG DESIGN : 

40 COMPUTER AIDED DRUG DESIGN Many programs generate structures which can be fitted in to the binding sites of the target molecule, by displacing solvent molecules and maximizing the drug receptor interactions. Software DOCK creates a complementary image of the target site . DIRECTED DOCK is a modification of the above procedure in which hydrogen bonding information is used and conformational flexibility is allowed.

COMPUTER AIDED DRUG DESIGN : 

41 COMPUTER AIDED DRUG DESIGN To orient the functional groups of the ligand in to the binding site, Multiple Copy Simultaneous Search (MCSS) Method can be used. A range of small functional groups are placed inside the site and by using the program CHARMM ,it results in the migration of the introduced groups in to preferred orientations within the cavity of the binding site. The preferred orientations of the functional groups of a pharmacophore in the receptor site is identified.

COMPUTER AIDED DRUG DESIGN : 

42 COMPUTER AIDED DRUG DESIGN The program HOOK is then used to construct new ligands by linking the bound fragments with skeletons obtained from database searches. Another procedure uses least square fitting method in which the ligand is allowed to rotate in the available space within the binding site to maximize steric contacts.

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43

METHODS TO OBTAIN THREE DIMENSIONAL STRUCTURES : 

44 METHODS TO OBTAIN THREE DIMENSIONAL STRUCTURES Crystallography 2D & 3D NMR

CRYSTALLOGRAPHY : 

45 CRYSTALLOGRAPHY X-ray crystallography is a method of determining the arrangement of atoms within a crystal. A beam of X-rays strikes a crystal and diffracts into many specific directions. From the angles and intensities of diffracted beams, a three-dimensional picture of the density of electrons within the crystal can be produced. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, and various other information.

CRYSTALLOGRAPHY : 

46 CRYSTALLOGRAPHY X-ray diffraction data can be collected by passing powerful X-rays through the crystals and measuring the intensity of the diffracted beams with extremely sensitive computer-controlled detectors. The diffraction data are related to the 3- dimensional arrangement of atom. The electron cloud surrounding each atom contributes to each point in the pattern.

CRYSTALLOGRAPHY : 

47 CRYSTALLOGRAPHY The structure of the crystal can be solved by: Multiple isomorphous replacement (MIR) method, which exploits the binding of heavy atoms to proteins. Molecular replacement – if a related structure is known, it can be used to determine the orientation and position of the molecules within the unit cell. This way can be used to generate electron density maps. On the basis of known structure, the atomic positions of the unknown structure within the crystal can be determined.

CRYSTALLOGRAPHY : 

48 CRYSTALLOGRAPHY Model building and phase refinement A protein crystal structure at 2.7 Å resolution. The mesh encloses the region in which the electron density exceeds a given threshold. The straight segments represent chemical bonds between the non-hydrogen atoms of an arginine (upper left), a tyrosine (lower left), a disulfide bond (upper right, in yellow), and some peptide groups (running left-right in the middle). The two curved green tubes represent spline fits to the polypeptide backbone.

CRYSTALLOGRAPHY : 

49 CRYSTALLOGRAPHY Having obtained initial phases, an initial model can be built. This model can be used to refine the phases, leading to an improved model, and so on. Given a model of some atomic positions, these positions can be refined to fit the observed diffraction data, ideally yielding a better set of phases. A new model can then be fit to the new electron density map and a further round of refinement is carried out. This continues until the correlation between the diffraction data and the model is maximized.

2D & 3D NMR : 

50 2D & 3D NMR Nuclear magnet resonance obtains the same high resolution using a very different strategy. NMR measures the distances between atomic nuclei, rather than the electron density in a molecule. In NMR, a strong, high frequency magnetic field stimulates atomic nuclei . The nuclei orients itself with respect to the applied magnetic field.

2D & 3D NMR : 

51 2D & 3D NMR The sample is then exposed to radio waves of varying frequencies, depending on the nucleus. Some of the radio photons have the right energy to cause a nucleus to jump from one energy level to the next. When the nucleus drops back to the lower energy level, the photon is emitted and recorded as an NMR spectrum.

2D & 3D NMR : 

52 2D & 3D NMR The distance and type of neighboring nuclei determines the resonance frequency of the stimulated atomic nuclei. This dependence on next neighbors known as chemical shift and reflects the local electronic environment. NMR is also used to identify receptor –ligand interactions.

NMR : 

53 NMR Structure determination by NMR progresses by the following steps: Preparing the sample Spectra data collection Assignment of chemical shifts Analysis of nuclear Overhauser effect measurements

NMR : 

54 NMR Nuclear Overhauser effects originates from dipole-dipole interactions between protons that are closer than 5 Å. Provide a mechanism for magnetization transfer between the signals corresponding to such protons in the 1H NMR spectrum. The success of structure solution by NMR depends on obtaining a large number of NOE measurements.

Slide 55: 

55 The local field at one nucleus is affected by the presence of another nucleus. The result is a mutual modulation of resonance frequencies. Nuclear Overhauser Effect

2D & 3D NMR : 

56 2D & 3D NMR Assignment of secondary structural elements Initial structural calculation , and Refinement of the structures.

Slide 57: 

57 THANK YOU