A RESEARCH PROJECT ON

DOCKING STUDIES OF BRCA1 GENE AGAINST ANTHRACYCLINE DRUGS

Submitted to PUNJAB UNIVERSITY CHANDIGARH In partial fulfillment of the requirements For the degree of M.Sc. BIOTECHNOLOGY

Submitted by Iqbal Kaur

Department of Biotechnology Guru Nanak Girls College Model Town Ludhiana 2013

CONTENTS CERTIFICATE STUDENT DECLARATION ABSTRACT ACKNOWLEDGEMENT LIST OF FIGURES CHAPTER 1 1.1 1.2 1.3 1.4 1.5 1.6 INTRODUCTION General Breast Cancer Genes Responsible for Breast Cancer Targeting of Breast Cancer with Anthracycline Drugs Protein Structure Drug Designing CHAPTER 2 LITERATURE REVIEW Introduction Cloning Structure of Gene Mapping Pseudogene Gene Fuction Molecular Genetics Genotype/Phenotype Correlation Evolution Anthracycline Drugs Mitoxantrone and Ametantrone Pixantrone Page No. 1-29 2 2 3 11 16 20 30-55 31 31 32 33 33 34 43 44 44 45 45 51

2.1 2.1.1 2.1.2 2.1.3 2.1.4 2.1.5 2.1.6 2.1.7 2.1.8 2.2 2.2.1 2.2.2

CHAPTER 3 3.1 3.2 3.2.1 3.2.2 3.2.3 3.3 METHODOLOGY PDB Searching Docking Hex Dock Swiss Dock Patch Dock UCSF CHIMERA CHAPTER 4 RESULT and DISCUSSION 56-58 57 57 57 57 58 58 59-73

CONCLUSION BIBLIOGRAPHY

74-75 76-96

LIST OF FIGURE

Figure No. 1.1 1.2 1.3 1.4 1.5a 1.5b 1.5c 1.6 4.1 4.2a 4.2b 4.2c 4.3a 4.3b 4.3c 4.4a 4.4b 4.4c 4.5a 4.5b 4.5c 4.6a 4.6b 4.6c 4.7a 4.7b 4.7c 4.8a 4.8b 4.8c

Figure Caption Location of BRCA1 Gene on Chromosome 3D Structure of BRCA1 Gene Location of BRCA2 Gene on Chromosome 3D Structure of BRCA2 Gene Molecular Structure of Mitoxantrone Molecular Structure of Ametantrone Molecular Structure of Pixantrone Dihedral Angles of and 3D Structure of BRCA1 Gene Molecular Structure of Mitoxantrone Molecular Structure of Ametantrone Molecular Structure of Pixantrone Best Dock Pose of Ametantrone (Patch Dock) Best Dock Pose of Ametantrone with Chain A Hydrophilic Interactions of BRCA1 with Ametantrone Best Dock Pose of Mitoxantrone (Patch Dock) Best Dock Pose of Mitoxantrone with Chain A Hydrophilic Interactions of BRCA1 with Mitoxantrone Best Dock Pose of Pixantrone (Patch Dock) Best Dock Pose of Pixantrone with Chain A Hydrophilic Interactions of BRCA1 with Pixantrone Best Dock Pose of Ametantrone (Hex Dock) Best Dock Pose of Ametantrone with Chain A Hydrophilic Interactions of BRCA1 with Ametantrone Best Dock Pose of Mitoxantrone (Hex Dock) Best Dock Pose of Mitoxantrone with Chain A Hydrophilic Interactions of BRCA1 with Mitoxantrone Best Dock Pose of Pixantrone (Hex Dock) Best Dock Pose of Pixantrone with Chain B Hydrophilic Interactions of BRCA1 with Pixantrone

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CERTIFICATE
This is to certify that Iqbal Kaur of M.Sc. Biotechnology has worked sincerely on research project entitled, DOCKING STUDIES OF BRCA1 GENE AGAINST ANTHRACYCLINE DRUGS in partial fulfillment of the requirements for the degree of M.Sc. Biotechnology from Punjab University, Chandigarh.

HEAD OF DEPARTMENT and Supervisor (Dr. Manpreet Kaur) Assistant Professor Department of Biotechnology Guru Nanak Girls College, Ludhiana.

STUDENT DECLARATION
I hereby declare that the research project entitled, DOCKING STUDIES OF BRCA1 GENE AGAINST ANTHRACYCLINE DRUGS submitted for the degree of M.Sc. Biotechnology from Punjab University, Chandigarh, is my original research work and that no part of this thesis has been submitted for award of any other degree.

Place Ludhiana

Iqbal kaur

ABSTRACT
Breast cancer occurs when a malignant tumor originates in the breast. The BRCA1 and BRCA2 genes are well known genes causing breast cancer. As breast cancer tumors mature, they may metastasize (spread) to other parts of the body. The primary route of metastasis is the lymphatic system which, ironically enough, is also the body's primary system for producing and transporting white blood cells and other cancer-fighting immune system cells throughout the body. Metastasized cancer cells that aren't destroyed by the lymphatic system's white blood cells move through the lymphatic vessels and settle in remote body locations, forming new tumors and perpetuating the disease process. Anthracycline drugs have proven to be effective target against breast cancer. Anthracyclines (or anthracycline antibiotics) are a class of drugs (CCNS or cell-cycle

non-specific), used in cancer chemotherapy derived from streptomyces bacterium Streptomyces peucetius var. caesius. In the present study three well known drugs namely, mitoxantrone, ametantrone and pixantrone were docked against BRCA1 gene using PatchDock and HexDock docking algoritms which predicts the binding of the ligands or drugs conformation and orientations with in the targeted binding sites. These results are evaluated on the basis of the shape and electrostatics, complementary principles. This study aims at to get insight into the mechanism of drug action against BRCA1 genes. Best results have been obtained for ametantrone which does not posses the 1-oH and 4OH as in the mitoxantrone. Ametantrone showing the best binding with BRCA1 gene.

ACKNOWLWDGEMENT
I owe a great many thanks to a great many people who helped and supported me during the writing of this project report. I express my thanks to the Principle, Dr. (Mrs.) Charanjit Mahal of Guru Nanak Girls College, for extending her support. My deepest thanks to lecturer, Dr. (Mrs.) Manpreet Kaur, Supervisor of the Project for guiding and correcting various documents of mine with attention and care. She

has taken pain to go through the project and make necessary correction as and when needed. I would also thank my Institution and my faculty members Dr.(Mrs.) Archana Tiwari, Dr.(Mrs.) Ved Priya, Ms. Harleen Chawla, Mr. Vikas (Bioinformatics Department) and many other teachers without whom this project would have been a distant reality. My deep sense of gratitude to my loving parents, for their support and guidance. I also extend my heartfelt thanks to all my friends for giving me moral support and encouragement. At last, but not the least, I am extremely grateful to God for giving me strength to overcome difficulties for accomplishment of this Project report.