IN –SILICO DRUG IN –SILICO DRUG TARGET DESIGNING TARGET DESIGNING

FOR MIGRAINEFOR MIGRAINE

UNDER GUIDANCE OFUNDER GUIDANCE OF

Mr. ARVIND SINGH Mr. ARVIND SINGH FACULTY BII,NOIDA,INDIAFACULTY BII,NOIDA,INDIA

BY- BY- CHINMAYA MAHAPATRACHINMAYA MAHAPATRA

INTRODUCTIONINTRODUCTION

• In-silico Drug Design

• In silico drug designing is defined as the identification of the drug target molecule by employing computational tools

In silicoIn silico methods methods

• Identifying drug targets via bioinformatics tools.

• To analyze the target structures for possible binding/ active sites.

• Generating candidate molecules, checking for their drug likeness.

• Docking these molecules with the target• Ranking them according to their binding

affinites • Further lead optimization to improve binding

characteristics

Steps in Drug DesigningSteps in Drug Designing

MIGRAINEMIGRAINE• Migraine is a neurological disorder .A

migraine headache is a severe pain that is typically on one side of the head but sometimes on both sides.

• Migraines can occur at any time of the day and can last a few hours or up to one or two days.

• Migraine attacks can be very intense, forcing the sufferer to abandon normal daily activities.

• Migraine is commonly experienced between the ages of 15 and 55.

SYMPTOMS OF MIGRAINESYMPTOMS OF MIGRAINE

• Intense pulsating or throbbing headache• Moderate to intense pain affecting daily activities• Nausea, vomiting or diarrhea• Increased sensitivity to smells• Increased sensitivity to sounds• Increased sensitivity to light (photophobia)• Visual disturbances or ‘aura’

TYPES OF MIGRAINETYPES OF MIGRAINE

• Common Migraine (migraine without aura)

• Classical Migraine (migraine with aura)

• Opthalmoplegic migraine

• Hemiplegic migraine

• Basilar type migraine

• Abdominal migraine

• Acephalgic migraine

PATHOPHYSIOLOGYPATHOPHYSIOLOGY

• Depolarization Theory.

• Vascular theory

• Serotonin theory

DRUGS PREVIOUSLY PRESCRIBED DRUGS PREVIOUSLY PRESCRIBED TO CURE MIGRAINETO CURE MIGRAINE

• Paracetamol - It is used to cure normal headaches but not effective in acute cases.

• Aspirin - Help relieve symtoms of nausea and help prevent vomiting. But effective only if taken early.

• Sumatriptan- Best drug available • Naproxen-Taken with caffiene• Ibuprofen-Generally taken with aspirin to be

effective• Ergotamine-Quite effective but has the side-

effect that it itself is very nauseated• Feverfew-Herbal medicine

DESCRIPTION OF PROCESS WITH SOFTWARES DESCRIPTION OF PROCESS WITH SOFTWARES

USEDUSED • TAKING A PROTEIN SEQUENCE FROM NCBI FOR

PROTEIN S(WHOSE DEFICIENCY CAUSES MIGRAINE).

• PROTEIN TAKEN IS BAF85683[Unnamed protein]. THEN PERFORMING ITS BLASTP.

• BLASTP (Basic Local Alignment Search Tool For Protein)

• Uses the BLAST algorithm to compare an amino acid query sequence against a protein sequence database.

BLASTP RESULTSBLASTP RESULTS

• Then taking a known protein similar in nature i.e. P98118(for RABBIT). And performing the comparative modelling through using GENO-3D.

• GENO-3D

• GENO-3D i.e. Homology Modeling involves taking a known sequence with an unknown structure and mapping it against a known structure of one or

several similar (homologous) proteins. • GENO-3D RESULTS

• SINCE THE MODEL 2 IS HAVING THE MAXIMUM SEQUENCE IDENTITY OF 87%. ITS RAMACHANDRAN PLOT IS DRAWN TO PREDICT THE RESIDUES AND THE STEREOCHEMISTRY OF THE UNKNOWN PROTEIN.

• RAMACHANDRAN PLOTS[USING PROCHECK SOFTWARE]

• A Ramachandran plot is a way to visualize dihedral angles φ against ψ of amino acid residues in protein structure. It shows the possible conformations of φ and ψ angles for a polypeptide.

BETASHEET

ALPHALEFTHELIX

ALPHAHELIX

• RAMACHANDRAN PLOT OF MODEL-2

COLOUR KEYGREEN-ALPHA REGIONBLUE-ADDITIONAL ALLOWED REGIONSRED-GENEROUSLY ALLOWED REGIONS

• SINCE FURTHER INFORMATION ABOUT THE UNNAMED PROTEIN IS NOT AVAILABLE .THE SECOND APPROACH IS TAKEN BY CHOOSING A KNOWN PROTEIN INVOLVED IN MIGRAINE IN THE PDB(PROTEIN DATA BANK). The protein is 2YX8(Crystal structure of the extracellular domain of human RAMP1 ).

• DS VISUALISER• The structure of the protein is visualised through the DS VISUALIZER

• SEQUENCE AS IN DS VISUALISER

DESINING OF INHIBITOR(LIGAND) FOR THE DESINING OF INHIBITOR(LIGAND) FOR THE PROTEIN MOLECULEPROTEIN MOLECULE

• WHAT IS LIGAND?• Ligand is either an atom, ion, or molecule that bonds to a central metal,

generally involving formal donation of one or more of its electrons.

• DESINING OF LIGAND MOLECULE IN CHEMSKETCH

• CHEMSKETCH :-ACD/ChemSketch is an advanced chemical drawing tool for drawing different chemical structures.

• Five different drugs previously available were drawn along with their derivatives. The drugs are,

-Aspirin

-Ibuprofen

-Naproxen

-Paracetamol

-sumatriptan

PROPERTIES OF THE DRUGS PROPERTIES OF THE DRUGS THAT WERE CACULATEDTHAT WERE CACULATED

• C log p:- partition (P) or distribution coefficient (D) is the ratio of concentrations of a compound in the two phases of a mixture of two immiscible solvents at equilibrium. Here ratio of (C octanol/C water) is taken.

• MOLECULAR WEIGHT• HYDROGEN BOND DONOR AND ACCEPTORS.• CHECKING FOR CALCULATING THE LIPINSKI 5’

RULES.• LIPINSKI 5’ RULES ARE –• Not more than 5 hydrogen bond donors• Not more than 10 hydrogen bond acceptors • A molecular weight under 500 g/mol • A partition coefficient log P less than 5

TABLE CONTAINING LIGAND TABLE CONTAINING LIGAND WITH THEIR PROPERTIESWITH THEIR PROPERTIES

CH3

O

NH

OH

Molecular Form ula = C 8H 9NO 2

Form ula W eight = 151.16256Com position = C(63.56%) H(6.00%) N(9.27%) O(21.17%)Molar Refractiv ity = 42.40 ± 0.3 cm 3

Molar Volum e = 120.9 ± 3.0 cm 3

FOR LIGAND DERIVATIVESFOR LIGAND DERIVATIVES

• D

DOCKINGDOCKING

• Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules

RESULTS OF DOCKINGRESULTS OF DOCKING• RESULT FOR DOCKING SHOWING SUMATRIPTAN DERIVATIVE GIVING

THE MINIMUM BINDING ENERGY VALUE.

DRUGS,THEIR DERIVATIVES AND THEIR DRUGS,THEIR DERIVATIVES AND THEIR BINDING ENERGY VALUE[EVALUE]BINDING ENERGY VALUE[EVALUE]

ASPIRIN -136.47

ASPIRIN DERIVATIVES -128.96

IBUPROFEN -147.18

IBUPROFEN DERIVATIVES -155.34

NAPROXEN -156.39

NAPROXEN DERIVATIVES -161.20

PARACETAMOL -156.39

PARACETAMOL DERIVATIVES

-120.22

SUMATRIPTAN -162.74

SUMATRIPTAN DERIVATIVES -174.74

RESULTS AND DISCUSSIONSRESULTS AND DISCUSSIONS

REFERENCESREFERENCES• CLINICAL APPROACH TO HEADACHE IN CHILDREN AND PREVENTIVE

THERAPY OF MIGRAINE-KK SINHA(JIACM 2005;6(1):64-2).

• Migrainous Stroke in a Young Patient Associated with Protein S Deficiency- Sachin Kumar, Naresh Gupta, NP Singh, Sandeep Garg, Sameer Gulati(JIACM 2006;7(2):156-8)

• Recent advances in the diagnosis and management of migraine-Peter J Goadsby(Journal of medical biology 13May 2008).

• The Tight-Fit Brain - Study Reveals Brain Swelling As Cause of Migraine Headaches (New Research Unveiled at Physiological meeting at UCL-June 2006).

• Gene influencing migraine-ScienceDaily (Apr. 21, 2008) (American Journal of Human Genetics) .

• Protein may promote migraines-Andrew Russo-spring conference,2007 at the UI Carver College of Medicine,U.S.A