A SEMINAR ON DESIGN OF LIGANDS FOR KNOWN

RECEPTORS

DEPARTMENT OF PHARMACEUTICAL CHEMISTRY MCOPS

SUBMITTED TO SUBMITTED BY Dr Suvarna G. kinni Shikha TyagiAsst. professor 100602017

CONTENTSINTRODUCTION

SITE IDENTIFICATION

SITE CHARACTERISATION• HYDROGEN BONDING AND OTHER GROUPS• ELECTROSTATIC AND HYDROPHOBIC FIELD

DESIGN OF LIGANDS• VISUALLY ASSISTED DESIGN• 3-D DATABASE• DE NOVO DESIGN

CALCULATION OF AFFINITY

A ligand (from the Latin ligandum, binding) is a substance that forms a

complex with a biomolecule to serve a biological purpose.

LIGAND

INTRODUCTION

A RECEPTOR IS A PROTEIN MOLECULE, EMBEDDED IN EITHER THE PLASMA MEMBRANE OR THE CYTOPLASM OF A CELL, TO WHICH ONE OR MORE SPECIFIC KINDS OF S IGNALING MOLECULES MAY ATTACH.

RECEPTOR:

Membrane receptor

Cytoplasmic receptor

PHARMACOPHORE:

THE IUPAC DEFINES A PHARMACOPHORE TO BE "AN ENSEMBLE OF STERIC AND ELECTRONIC FEATURES THAT

IS NECESSARY TO ENSURE THE OPTIMAL SUPRAMOLECULAR INTERACTIONS WITH A SPECIFIC

BIOLOGICAL TARGET AND TO TRIGGER (OR BLOCK) ITS BIOLOGICAL RESPONSE.

A PHARMACOPHORE IS AN ABSTRACT DESCRIPTION OF MOLECULAR FEATURES WHICH ARE NECESSARY FOR MOLECULAR RECOGNITION OF A LIGAND BY A

BIOLOGICAL MACROMOLECULE.

DESIGN OF LIGANDS TWO TYPES LIGAND BASED AND STRUCTURE BASED

STRUCTURE BASED LIGAND BASED

SITE IDENTIFICATION 3-D STRUCTURE BY NMR AND X –RAY CRYSTALLOGRAPHY

BUT IT DOES NOT GUARANTEE THE SITE OF ACTION BY LIGANDS SOMETIMES CONFORMATIONAL CHANGES OCCURES DURING THE BINDING WHICH ARE NOT REFLECTED IN 3-D STRUCTURE

FOR EXAMPLE : WHEN MVT-101 A ANTI HIV DRUG BINDS TO THE HIV PROTEASE ENZYME CONFORMATIONAL CHANGES OCCURS

the two β-strand flaps have been folded in, to complete the active site of HIV protease, the important interactions for recognition in this proteolytic system

NMR- NOE CAN HELP IN INDENTIFICATION OF SUCH CONFORMATIONAL CHANGES.

Figure 3.14. Ribbon diagram of HIV-1 protease in the absence of inhibitor (a) and when bound to theinhibitor MVT-10103). Diagrams based on crystal structures as reported by Miller et al.

Ribbon diagram of HIV-1 protease in the absence of inhibitor (a) and when bound to the inhibitor MVT-101.

DYNAMICS OF RECEPTORS

IT IS VERY IMPORTANT TO ANSWER SOME QUESTIONS

Q1 HOW STABLE IS THE ACTIVE SITE TO MODIFICATION IN THE LIGAND ????????:.

Q1 Is THERE ANY ALTERNATIVE BINDING SITE WHICH IS COMPETING WITH THE BINDING SITE OF LIGAND.????????

FOR EXAMPLE- DIFFICULTY IN INTERPRETATION OF BINDING SITE AS A RESULT OF LIGAND MODIFICATION OCCURS WHEN AN ANALOG DESIGN IS BIND TO THE SPECIFIC SITE ON HEMOGLOBIN .ACTUALLY THIS ANALOG FOUND A MORE APROPREIATE SITE WITHIN THE PACKED SIDE CHAIN OF THE PROTEIN MOLECULE .THIS EMPHASIZE THE DYNAMICS OF PROTEIN MOLECULE.

SOLUTION – 3-D STRUCTURE OF CAVITY AND POCKETS ASSIST THE BINDING INTERACTION AND DESIGN OF NOVEL LIGANDS

HOW IT IS DONE???????????????? DOCKING

IT EXPLORE THE STERIC COMPLEMENTORY BETWEEN LIGANDS AND RECEPTORS OF 3-D STRUCTURE USING THE MOLECULAR SURFACE OF RECEPTORS

USING THE MOLECULAR SURFACE OF RECEPTORS VOLUMETRIC APPOXIMATION OF SURFACE IS DONE.

IN THIS METHOD SET OF SPHERE OF VARIOUS SIZES PACKED MATHEMATICALLY WITHIN IN IT.

THE DISTANCE BETWEEN THE CENTERS SERVES AS THE A COMPACT REPRESENTATION OF SHAPE OF CAVITY

LIGANDS ALSO CHARACTERISED IN THE SAME WAY AND THE DISTANCE MATRIX OF LIGAND AND THE RECEPTOR IS COMPARED

AND THE POTENTIAL LIGAND IS SELECTED

CHARACTERISATION SITEONCE THE SITE IS IDENTIFIED IT IS CHARACTERISED FOR VARIOUS PARAMETERS AS DESCRIBED BELOW

1 HYDROGEN BONDING AND OTHER GROUPS

IN EVALUATING THE POTENTIAL LIGANDS IT IS NECESSORY TO HAVE THE KNOWLEDGE OF OPTIMAL POSITIONS OF THE FUNCTIONAL GROUPS

GRID- ALLOWS A PROBE ATOM OR GROUP TO EXPLORE RECEPTOR SITE CAVITY ON A LATTICE OR A GRID WHILE ESTIMATING THE ENTHALPY OF INTERACTION.

3-D CONTOUR MAP IS GENERATED FROM THE INTERACTION ENERGY WHICH GIVES THE GRAPHICAL REPRESENTATION OF POSITION OF FUNCTIOL GROUP AND HENCE THE HYDROGEN BONDING .

COMFA-COMPARATIVE MOLECULAR FIELD ANALYSIS

COMPUTE INTERACTION OF PROBE WITH MOLECULE AT EACH POINT

ACTIVITY IS DIRECTLY RELATED TO STRUCTURAL PROPERTIES OF SYSTEM

STEPS INVOLVED

HYPOTHESIZE MECHANISM FOR BINDING BY IDENTIFING STRUCTURE OF BINDING SITE

FIND EQUILIBRIUM GEOMETRY

CONSTRUCT LATTICE OR GRID OF POINTS

COMPUTE INTERACTION OF PROBE WITH MOLECULE AT EACH POINT

APPLY PLS

PREDICT

DYLOMS-

ELIMINATE THE PROBLEM OF RESOLUTION BY GRID .

IT ORIENT THE FUNCTIONAL GROUP FOR OPTIMAL INTERACTION WITH THE BINDING SITE AND GENERATE NOVEL STRUCTURE.

HOW???MULTIPLE COPIES OF LIGANDS IS DISTRIBUTED AT THE BINDING SITE BY SIMULATION AND THEIR RELATIVE DISTRIBUTION IS EXAMINED.

POPULATION OF LIGANDS IS CONCENTRATED ON OPTIMAL BINDING SITE .

LIGANDS ARE CONNECTED WITH THE MOST ENERGETICALLY FAVOURED BINDING SITE (I.e THE C-C OVERLAP OF THE LIGAND WITH THE FRAGMENT OF BINDING SITE)

NOVEL LIGANDS ARE DESIGNED

ELECTROSTATIC AND HYDROPHOBIC INTERACTIONS

SURFACE DISPLAYS THE PROPERTIES LIKE HYDROPHOBICITY AND ELECTROSTATIC FIELD

MOLECULAR SURFACES DISPLAYS MAY BE COLOR CODED TO DEPICT THE VARIOUS PROPERTIES.

SURFACE CAN BE DISPLAYED BY DOTS OR CONTOURS.

CAVITY DISPLAY-THE LOCI OF THE FILLER ATOMS PACKING THE CAVITY IS COMPUTED

OUTRMOST LAYER OF THE FILLER SOLID IS IDENTIFIED .

THIS SURFACE DISPLAYS THE INTERFACE BETWEEN BINDING SITE AND THE LIGAND ELCTROSTATIC INTERACTION.

AT EACH POINT ELECTROSTATIC POTENTIAL IS CALCULATED.VALUES ARE ASSIGNED BY COLOR AND DISPLAYED

REGIONS OF ELECTROSTATIC COMPLEMENTARITY AND DISPARITY ARE DOCKED

A ROUGH APPROXIMATION OF COMPLEMENTARITY IS COMPUTED BY MULTIPLYING THESE POTENTIAL TOGETHER

NEGATIVE PRODUCT FAVOURS BINDING AND THE POSITIVE UNFAVOURABLE FOR BINDING

NOVEL LIGAND IS DESIGNED IN THIS WAY.

DESIGN OF LIGANDS

VISUALLY ASSISTED DESIGN

BY DIRECTLY EXAMINE THE LIGAND WE CAN SELECT THE REGIONS WHERE MODIFICATIONS CAN BE MADE.

BUT THIS IS DIFFICULT FOR THE RECEPTOR –LIGAND GAP REGION THIS IS DONE BY THE CAVITY DISPLAY

INTHIS APPROACH THE NEAREST DISTANCE BETWEEN THE ATOMS IN THE GAP IS CALCULATED THAT IS THE SURFACE TO SURFACE DISTANCE.

COLOR CODING IS DONE TO DISPLAY THIS .

3-D DATABASES

CAMBRIDGE STRUCTURAL DATA BASES—90,000 STRUCTURE

BROOKHAVEN PROTEIN DATABANK –

CONTAINS THE CRYSTALS CO-ORDINATES OF PROTEINS AND THE OTHER BIOMOLECULE

THIS CONSIST OF LOW ENERGY CONFORMER THAT IS READILY ATTAINABLE IN SOLUTION OR THE RECEPTORS

3-D DATABASE IS SEARCHED BY USING A QUERY FOR FRAGMENT THAT CONTAIN THE PHARMACOPHORIC FUNCTIONAL GROUP.IN PROPER 3-D DIMENSIONAL ORIENTATION.

USING FRAGNMENTS AS THE BUILDING BLOCKS COMPLETE NOVEL STRUCTURE MAY BE GENERATED BY ASSEMBLY AND PRUNING

PHARMACOPHORE MATCHING ESTROGEN MOLECULE

CONCORD

CHEMICAL ABSTRACTS ARE GENERATED BY USING THIS

7,00,000 ENTERIES

THIS IS NONCRYSTALLOGRAPHIC DATABASE

IT IS USED WHEN THE CRYSTAL STRUCTURE OF LIGNAD – RECEPTOR COMPLEX IS KNOWN.AND ITS BINDING IS WELL UNDERSTOOD IN TERMS OF FUNCTIONAL GROUP.IN SUCH CASE LIGANDS CAN BE GENERATED BY USING THE SCAFFOLDS THAT POSITION THE PHARMACOPHORIC GROUP OR THEIR ISOSTERS IN THE CORRECT 3-D ARRANGEMENT

MOLPAT IS THE FIRST PROTOTYPE TO SEARCH FOR MOLECULE THAT MATCH 3-D PHARMACOPHORIC PATTERN.

IT PERFORMS ATOM BY ATOM SEARCH TO VERIFY COMPARABLE INTERATOMIC DISTANCES BETWEEN THE PATTERN AND THE CANDIDATE.

CAVEAT

TO IDENTIFY THE CYCLIC STRUCTURES

ALLADIN,3-D SEARCH,MACCS-3-D

FOR MOLECULAR PROPERTIES LIKE ATOM TYPE ,BOND ANGLE,TORSIONAL ANGLE,LIGAND RECEPTOR COMPLEMENTORY.

CHEM-X

CONFORMATIONAL SEARCH

MDS

FOR THE CONFORMATIONAL SEARCH ,BINDING ENERGY ,FORCE FIELDS, 3 –D STRUCTURES.VARIOUS MODELS LIKE BALL –STICK MODEL SPACE MODEL

Sheridan et al screened candidate compounds to select those whose volumes would fit within the combined volumes of known active compounds.

SHAPE MATCHING ALGORITHM

BROMOPERIDOL

JG-365

FOUNDATION-3-D DATABASE OF CHEMICAL STRUCTURE FOR A USER DEFINED QUERY CONSISTING OF THE CO-ORDINATES OF ATOMS AND BOND

ALL POSSIBLE STRUCTURES THAT CONTAINS ANY COMBINATION OF A USER DEFINED MINIMUM NUMBER OF MATCHING ATOM AND BONDS ARE RETERIVED..

SPLICE- TRIMS THE MOLECULE FOUND FROM THE DATABASE TO FIT WITHIN THE ACTIVE SITE AND LOGICALLLY COMBINE THEM BY OVERLAPPING BONDS TO MAXIMIZE INTERACTION WITH THE SITE.

DE NOVO DESIGN

BRIDGE is based on geometric generation of possible cyclic compounds as scaffolds,given constraints derived from the types of chemistry the chemist is willing to consider.

LUDI to construct ligands for active sites with an empirical scoring functionto evaluate their construction.

Drug discovery and development is a complex, lengthy process, and failure of a candidate molecule can occur as a result of a combination of reasons, such as poor pharmacokinetics, lack of efficacy, or toxicity. De novo drug design involves searching an immense space of feasible, druglike molecules to select those with the highest chances of becoming drugs using computational technology. Traditionally, de novo design has focused on designing molecules satisfying a single objective, such as similarity to a known ligand or an interaction score, and ignored the presence of the multiple objectives required for druglike behavior. Recently, methods have appeared in the literature that attempt to design molecules satisfying multiple predefined objectives and thereby produce candidate solutions with a higher chance of serving as viable drug leads

BRIDGE is based on geometric generation of possible cyclic compounds as scaffolds,given constraints derived

CALCULATION OF AFFINITYCALCULATION OF BINDING AFFINITY BASED ON THE 3- D STRUCTURE

WILLIAM USED VANCOMYCIN-PEPTIDE COMPLEX TO CALCULATE BINDING AFFINITY IN TERMS OF GIBBS FREE ENERGY

∆G(Trans + rot) - free energy associated with translational and rotational freedomof the ligand. This has an adverse effect on binding of 50-70 kJ/mol (12-17 kcallmol)at room temperature for ligands of 100-300 Dalton, assuming complete loss of relative translational and rotational freedom

∆Grotors -free energy associated with the number of rotational degrees of freedom frozen. This is 5-6 kJ/mol (1.2-1.6 kcal/mol) per rotatable bond, assuming complete loss of rotational freedom.

∆H c o n f o m- is the strain energy introduced by complex formation (deformation in bond lengths, bond angles, torsional angles, etc.∑∆ Gi is the sum of interaction free energies between polar groups

∆Gvdw-ENERGY DERIVED FROM THE ENHANCED VANDERWAALS INTERACTIONS

∆GH- FREE ENERGY ATTRIBUTED TO HYDROPHOBIC INTERACTION

REFERENCESBURGER'S “MEDICINAL CHEMISTRY AND DRUG DISCOVERY”, 5th

Edition,Vol-I,Page no-599-612

http://pubs.acs.org/doi/abs/10.1021/ci800308h

http://en.wikipedia.org/wiki/File:biocomputing and drug design.

THANkU