Duquesne University Duquesne Scholarship Collection Electronic Theses and Dissertations Fall 2014 Design, Synthesis and Evaluation of Diphenylamines as MEK5 Inhibitors Suravi Chakrabarty Follow this and additional works at: https://dsc.duq.edu/etd Recommended Citation Chakrabarty, S. (2014). Design, Synthesis and Evaluation of Diphenylamines as MEK5 Inhibitors (Master's thesis, Duquesne University). Retrieved from https://dsc.duq.edu/etd/388 This Immediate Access is brought to you for free and open access by Duquesne Scholarship Collection. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Duquesne Scholarship Collection. For more information, please contact [email protected]. DESIGN, SYNTHESIS AND EVALUATION OF DIPHENYLAMINES AS MEK5 INHIBITORS A Thesis Submitted to the Graduate School of Pharmaceutical Sciences Duquesne University In partial fulfillment of the requirements for the degree of Master of Science (Medicinal Chemistry) By Suravi Chakrabarty December 2014 Copyright by Suravi Chakrabarty 2014 DESIGN, SYNTHESIS AND EVALUATION OF DIPHENYLAMINES AS MEK5 INHIBITORS By Suravi Chakrabarty Approved August 7, 2014 ________________________________ ________________________________ Patrick Flaherty, Ph.D. Aleem Gangjee, Ph.D., Chair, Thesis Committee Professor of Medicinal Chemistry Associate Professor of Medicinal Mylan School of Pharmacy Chemistry Distinguished Professor Graduate School Pharmaceutical Sciences Graduate School Pharmaceutical Sciences Duquesne University Duquesne University Pittsburgh, PA Pittsburgh, PA ________________________________ ________________________________ David J. Lapinsky, Ph.D. Jane E. Cavanaugh, Ph.D. Associate Professor of Medicinal Assistant Professor of Pharmacology Chemistry Graduate School Pharmaceutical Sciences Graduate School Pharmaceutical Sciences Duquesne University Duquesne University Pittsburgh, PA Pittsburgh, PA ________________________________ ________________________________ David A. Johnson, Ph.D. Director of Graduate Studies Associate Professor of Pharmacology- Toxicology Graduate School Pharmaceutical Sciences Duquesne University Pittsburgh, PA iii ABSTRACT DESIGN, SYNTHESIS AND EVALUATION OF DIPHENYLAMINES AS MEK5 INHIBITORS By Suravi Chakrabarty December 2014 Dissertation supervised by Dr. Patrick T. Flaherty The mitogen-activated protein kinases (MAPK) are a family of interrelated signal transduction kinases mediating intracellular responses to extracellular events. They are involved in mediating complex cellular events including, cell differentiation, cell proliferation, and cell death. Extracellular mitogens or the binding of other ligands to cell-surface receptors begin a signaling cascade that activates MEK resulting in phosphorylation of its corresponding and specific and parallel ERK (Extracellular signal- Regulated Kinase) substrate. The MEK5/ERK5 pathway is involved in cell survival, anti-apoptotic signaling, angiogenesis, and cell motility. It is significantly up-regulated in specific tumor types including breast and prostate cancers. A novel series of compounds utilizing the diphenylamine scaffold was designed and synthesized based on a homology model of MEK5 using the X-ray crystal structure of MEK1 (PDB ID: 3EQC) iv as a template. The compounds were tested for their MEK12, and MEK5 inhibition in a cell based assay. v DEDICATION To my grandparents, Shri Dwijapada Chakrabarty and Smt. Shyamala Chakrabarty Shri Nripendra Mohan Chaudhuri and Smt. Arati Chaudhuri vi ACKNOWLEDGEMENT First and foremost, I would like to sincerely thank my advisor, Dr. Patrick T. Flaherty. I am so thankful to him for giving me the opportunity to work in his research group and his guidance throughout this process, which has helped me to become an inquisitive learner. His optimism, encouragement and support helped me tremendously in my journey as a researcher. Additionally, I would also like to thank Drs. Aleem Gangjee, David J. Lapinsky and Jane E. Cavanaugh for serving on my committee. I have learned a great deal, not only from the courses they taught, but more importantly, their valuable suggestions and encouragement in our many research meetings. Likewise, I thank Drs. Mark W. Harrold and Kevin J. Tidgewell for the knowledge they shared with me throughout my course work. I am especially grateful to Dr. Fraser F. Fleming for continually trying to bring out the best in me in my learning, and research. A great deal of appreciation is shared with Dr. James K. Drennen and the Graduate School of Pharmaceutical Sciences for their financial support. Mrs. Mary Caruso, Mrs. Jackie Farrer, Mrs. Nancy Hosni and Mrs. Deb Wilson have helped me personally and emotionally throughout my several years at Duquesne. Tom and Miss T. deserve special thanks for working so diligently to keep our lab safe, clean, and healthy. Their daily hard work, often unrecognized, is very much appreciated. I am very grateful and give many thanks to Darlene Monlish and Sneha Potdar, from Dr. Cavanaugh’s lab and Dr. Matthew Burow from Tulane University, New Orleans, for the fruitful collaboration and for performing the biological evaluation of my vii compounds. Likewise, the company of my lab mates Prashi Jain, Dhruv Shah, Mohit Gupta and Si Qin provided not only serious reflection on the work we were conducting, but countless hours of joy and laughter. Similarly, the support of Sudhir Raghavan, Ravi Devambatla and Shaili Aggarwal throughout this process has been extremely helpful, and I thank them for assisting me through many scientific and personal concerns. Again, I thank all of them for their support and encouragement; it was a pleasure working with you all. I would also like to acknowledge and thank Diane Rhodes for her help as an instructor during my many TA sessions. Furthermore, I am thankful to Erin Rentschler and Michael McGravey for encouraging me to become a better teacher. I truly believe that life is incomplete without friends, and I am so lucky to have such great life companions. Many thanks are shared with Isha Makan, Upasana Banerjee, Shruti Choudhary, Manasa Ravindra, Khushbu Shah, Rishabh Mohan and Arpit Doshi. Each of you have unconditionally, and in your own ways, added to my life three most important ingredients of happiness: love, laughter and friendship. I will forever cherish the time spent with you all throughout my life. I would like to thank Abhishek Singh for his affection, patience and endurance in every step I have taken in my academic pursuits. Finally, and most importantly, I would like to express my gratitude for my mother and father for their never-ending love, patience and understanding. I am so fortunate to have parents who have always let me live my dream. Last, but not least, I would like to thank my younger brother, Debopam, for being my biggest strength, always and forever. viii TABLE OF CONTENTS Page Abstract .............................................................................................................................. iv Dedication .......................................................................................................................... vi Acknowledgement ............................................................................................................ vii List of Tables .......................................................................................................................x List of Figures .................................................................................................................... xi List of Schemes ................................................................................................................ xiv List of Abbreviations ....................................................................................................... xvi Biological Literature Review ...............................................................................................1 Chemical Literature Review ..............................................................................................45 Statement of the Problem ...................................................................................................56 Chemical Discussion ..........................................................................................................70 Biological Discussion ........................................................................................................91 Experimental ......................................................................................................................99 Summary ..........................................................................................................................114 Bibliography ....................................................................................................................122 Appendix ..........................................................................................................................134 ix LIST OF TABLES Page Table 1. Factors associated with increased risk of breast cancer ........................................3 Table 2. Characteristics of the basic molecular/intrinsic breast cancer subtypes .............10 Table 3. Kinase inhibitors approved by FDA in 2013 ......................................................15 Table 4. Optimization of the Carboxamide Side Chain ....................................................39 Table 5. Substitution on the Pyridone Nitrogen ................................................................40