Protein Modeling And In-Silico Drug Designing Approach

IN –SILICO DRUG TARGET DESIGNING FOR MIGRAINE UNDER GUIDANCE OF Mr. ARVIND SINGH FACULTY BII,NOIDA,INDIA BY- CHINMAYA MAHAPATRA

INTRODUCTION

In-silico Drug Design

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

In silico 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 Designing

MIGRAINE

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 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 MIGRAINE

Common Migraine (migraine without aura)

Classical Migraine (migraine with aura)

Opthalmoplegic migraine

Hemiplegic migraine

Basilar type migraine

Abdominal migraine

Acephalgic migraine

PATHOPHYSIOLOGY

Depolarization Theory.

Vascular theory

Serotonin theory

DRUGS PREVIOUSLY PRESCRIBED TO 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 USED

TAKING A PROTEIN SEQUENCE FROM NCBI FOR PROTEIN S(WHOSE DEFICIENCY CAUSES MIGRAINE).

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

BLASTP ( B asic L ocal A lignment S earch T ool For Protein)

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

BLASTP 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.

BETA SHEET ALPHA LEFTHELIX ALPHA HELIX

RAMACHANDRAN PLOT OF MODEL-2

COLOUR KEY GREEN - ALPHA REGION BLUE - ADDITIONAL ALLOWED REGIONS RED- 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 PROTEIN 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 THAT 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 WITH THEIR PROPERTIES

FOR LIGAND DERIVATIVES

D

DOCKING

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 DOCKING

RESULT FOR DOCKING SHOWING SUMATRIPTAN DERIVATIVE GIVING THE MINIMUM BINDING ENERGY VALUE.

DRUGS,THEIR DERIVATIVES AND THEIR BINDING ENERGY VALUE[EVALUE] -174.74 SUMATRIPTAN DERIVATIVES -162.74 SUMATRIPTAN -120.22 PARACETAMOL DERIVATIVES -156.39 PARACETAMOL -161.20 NAPROXEN DERIVATIVES -156.39 NAPROXEN -155.34 IBUPROFEN DERIVATIVES -147.18 IBUPROFEN -128.96 ASPIRIN DERIVATIVES -136.47 ASPIRIN

RESULTS AND DISCUSSIONS

REFERENCES

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)