INVESTIGATING THE INHIBITION MECHANISM OF L,D-TRANSPEPTIDASE 5 FROM MYCOBACTERIUM TUBERCULOSIS USING COMPUTATIONAL METHODS BY: GIDEON FEMI TOLUFASHE 216076453 Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in Pharmaceutical Chemistry School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa. 2018 PREFACE The work described in this thesis was conducted at the Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa, under the supervision of Dr Bahareh Honarparvar, Prof. H.G. Kruger and Dr G.E.M. Maguire. This work has not been submitted in any form for any degree or diploma to any institution, where use has been made of the work of others, it is duly acknowledged in the text. Supervisors: Dr B. Honarparvar Date 30/10/2018 Prof. H. G. Kruger________________ Date ___________ Dr. G.E.M Maguire_______________ Date ___________ As candidate’s supervisor I agree to the submission of this thesis. i DECLARATION DECLARATION I- PLAGIARISM I, Gideon Femi Tolufashe declare that (i). The research reports in this thesis, except where otherwise indicated, is my original work. (ii). This thesis has not been submitted for any degree or examination at any other university. (iii). This thesis does not contain other person’s data, pictures, graphs or other information, unless specifically acknowledged as being sourced from other persons. (iv). This thesis does not contain other person’s writing, unless specifically acknowledged as being sourced from other researchers. Where other written sources have been quoted, then: a. Their words have been re-written, but the general information attributed to them has been referenced. b. Where their exact words have been used, then their writing has been placed in italics and inside quotation marks, and referenced. (v). This thesis does not contain text, graphics or tables copied and pasted from the internet, unless specifically acknowledged, and the source being detailed in the thesis and in the references sections. Signed ………………………… ii DECLARATION II-PUBLICATION List of publications included in this Thesis 1. Gideon F. Tolufashe, Victor T. Sabe, Colins U. Ibeji, Thandokuhle Ntombela, Thavendran Govender, Glenn E. M. Maguire, Hendrik G. Kruger, Gyanu Lamichhane, and Bahareh Honarparvarar. (2018). Structure and function of L,D- and D,D-transpeptidase family enzymes from Mycobacterium tuberculosis. Current Medicinal Chemistry. DOI: 10.2174/0929867326666181203150231 Contributions: Tolufashe, G.F: Main author- contributed to the project by performing all literature reviews, manuscript preparation and writing. Sabe, V.T, Ibeji, C.U, Ntombela, T., Govender, T., Lamichhane, G.: Helped with technical, experimental and financial supports. Honarparvar, B.: Supervisor Kruger, H. G. and Maguire, G. E.: co-supervisors with academic contribution 2. Gideon F. Tolufashe, Thavendran Govender, Amit K. Halder, Collins U. Ibeji1, Monsurat M. Lawal, Thandokuhle Ntombela, Glenn E. M. Maguire, Gyanu Lamichhane, Hendrik G. Kruger, and Bahareh Honarparvar. Inhibition of Mycobacterium tuberculosis L,D-transpeptidase 5 by carbapenems: MD and QM/MM Mechanistic Studies, ChemistrySelect 2018, 3, 1-11. DOI: 10.1002/slct.20180318 Contributions: Tolufashe, G.F: Main author- contributed to the project by performing all literature reviews, manuscript preparation and writing. Halder, A.K., Ibeji, C.U, Lawal, M.M., Ntombela, T., Govender, T., Lamichhane, G.: Provided assistance with technical, experimental and financial supports. Honarparvar, B.: Supervisor Kruger, H. G. and Maguire, G. E.: co-supervisors with academic contribution 3. Victor T. Sabe, Gideon F. Tolufashe , Collins U. Ibeji, Sibusiso B. Maseko, Thavendran Govender , Glenn E. M. Maguire, Gyanu Lamichhane, Bahareh Honarparvar and Hendrik G. Kruger. Identification of potent L,D-transpeptidase 5 inhibitors for Mycobacterium tuberculosis as potential anti-TB leads: Virtual Screening and Molecular Dynamics Simulations Manuscript Submitted to Journal of molecular modelling on 5 October 2018 iii Contributions: Victor T. Sabe: Principal investigator in the design of this project and first author responsible for writing and preparation of this manuscript. Gideon F. Tolufashe and Collins U. Ibeji: Provided technical assistance on the project. He did part of the calculations and writing of the manuscript. Sibusiso Maseko: Performed experimental work. Thavendran Govender and Gyanu Lamichhane: Provided technical and experimental assistance in the overall project. Bahareh Honarparvar: Supervisor. Hendrik G. Kruger and Glenn E. M. Maguire: Co-supervisors. 4. Gideon F. Tolufashe, Victor T. Sabe, Collins U. Ibeji, Monsurat M. Lawal, Thavendran Govender, Glenn E. M. Maguire, Gyanu Lamichhane, Hendrik G. Kruger and Bahareh Honarparvar. (2018) Inhibition Mechanism of L,D-transpeptidase 5 in presence of the β-lactams using ONIOM Method. Journal of molecular graphics and modelling, 87, 204-210. DOI: 10.1016/j.jmgm.2018.11.009 Contributions: Victor T. Sabe: Principal investigator in the contextualisation and design of the project. Gideon F. Tolufashe: Responsible for the calculations, writing and preparation of the manuscript. Collins U. Ibeji and Monsurat M. Lawal: Provided technical assistance to the project. Bahareh Honarparvar: Supervisor. Hendrik G. Kruger and Glenn E. M. Maguire: Co-supervisors. Publication not included in this Thesis Ibeji, Collins U., Gideon F. Tolufashe, Thandokuhle Ntombela, Thavendran Govender, Glenn EM Maguire, Gyanu Lamichhane, Hendrik G. Kruger, and Bahareh Honarparvar. "The catalytic role of water in the binding site of L, D-Transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modeling." Tuberculosis (2018). iv RESEARCH OUTPUTS CONFERENCE PRESENTATIONS 1. Poster presentation “Binding free energy calculations of carbapenem inhibitors against L,D- transpeptidase 5 using molecular dynamics(MD) simulation”, CHPC National Meeting & Conference, East London, 4-9 December 2016. 2. Oral presentation “Inhibition mechanism of L,D-Transpeptidase 5 from Mycobacterium Tuberculosis in presence of Carbapenems: Molecular Dynamics study”, College of Health Sciences Annual Research Symposium, Nelson Mandela Medical School, K-RITH Building, 5-6 October 2017. v DEDICATION This thesis is dedicated to God Almighty, my ever-supporting father, loving wife and daughter. vi ACKNOWLEDGEMENTS To God be the Glory in the highest for His help and making this degree a successful one, I am very grateful. I would like to express my earnest gratitude and appreciation to: • My supervisors, Dr Bahareh Honarparvar, Prof. Gert Kruger and Dr Glenn Maguire for accepting to supervise, guide, motivate and impart on me out of what they have academically and morally during this program. These virtues inculcated in me are well appreciated. • Dr Adebayo Kutu and Dr Adeola Shobo for paving the way into UKZN and CPRU respectively. The opportunity is highly esteemed. • My deepest gratitude to my family (Mr & Mrs Michael Tolufashe, Ifeoluwa and Excellence), for the continuous support in terms of prayers, finances and unconditional love all through this program. These are things that kept me going. • The entire computational chemistry group for the assistance and readiness to work as a team; Dr Amit Halder, Dr Collins Ibeji, Dr Zaynab Fakhar, Monsurat Lawal, Zainab Sanusi, Thandokuhle Ntombela, Siyabonga Maphumulo, Victor Sabe, Chairmane Kahiya and Llyod. The entire Catalysis Peptide Research Unit (CPRU), most especially Prof Thavendran Govender and Dr Tricia Naicker. • The pastorate of Redeemed Christian Church of God, Durban (RCCG) for the spiritual oversight and teaching is well helpful and more appreciated. The love I received from my friends are immeasurable. • Dr Krishna Govender of Centre of High Performance Computing (CHPC) for the assistance in using the computational facilities when I encountered errors. The University of KwaZulu-Natal (College of Health Sciences), National Research Foundation (NRF, SA) for the financial support and CHPC for the resources. vii TABLE OF CONTENTS PREFACE ................................................................................................................................................. i DECLARATION..................................................................................................................................... ii RESEARCH OUTPUTS ........................................................................................................................ v DEDICATION........................................................................................................................................ vi ACKNOWLEDGEMENTS ................................................................................................................. vii LIST OF FIGURES .............................................................................................................................. xii LIST OF TABLES ................................................................................................................................ xiv ABBREVIATIONS ............................................................................................................................... xvi ABSTRACT ......................................................................................................................................... xviii CHAPTER ONE ....................................................................................................................................