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DOCTOR of PHILOSOPHY in BIOCHEMISTRY Biochemical Profiling of Medicinal Plants and Bioinformatics of Bacterial Polyketide Synthases in Drug Discovery Perspective by Ghulam Mustafa M.Phil. (UAF) A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in BIOCHEMISTRY DEPARTMENT OF BIOCHEMISTRY FACULTY OF SCIENCES UNIVERSITY OF AGRICULTURE, FAISALABAD PAKISTAN 2016 DECLARATION I hereby declare that the contents of the thesis, “Biochemical profiling of medicinal plants and bioinformatics of bacterial polyketide synthases in drug discovery perspective” are product of my own research and no part has been copied from any published source (except the references, standard mathematical or genetic models/equations/formulae/protocols etc). I further declare that this work has not been submitted for award of any diploma/degree. The University may take action if the information provided is found inaccurate at any stage. Ghulam Mustafa 2005-ag-247 The Controller of Examinations, University of Agriculture, Faisalabad. “We the Supervisory Committee, certify that the contents and form of thesis submitted by Ghulam Mustafa, Regd. No. 2005-ag-247, have been found satisfactory and recommend that it be processed for evaluation, by the External Examiner (s) for the award of degree”. SUPERVISORY COMMITTEE 1. CHAIRMAN (Prof. Amer Jamil) 2. MEMBER (Dr. Muhammad Shahid) 3. MEMBER (Dr. Nisar Ahmed) ACKNOWLEDGMENT Words are bound and knowledge is limited to praise Allah, the omnipotent, the beneficent and merciful. Peace and blessings be upon Holy Prophet Muhammad (SAW), the everlasting source of guidance and knowledge for humanity. With genuine humanity, I acknowledge your aid, God. Please bless this work with your acceptance. I have a pleasure to ensure my sincere gratitude and deepest thanks to Prof. Amer Jamil, whose stimulating supervision, guidance and support made this work possible. I heartily thank him very much for his valuable help and for his kindness. I express my gratitude to Dr. Paul R. Jensen, who guided me to the fascinating world of actinomycetes during my research work in University of California, San Diego, CA, USA. His support, encouragement, inspiring attitude and enthusiasm were impressive. The support, help and company of the whole group are appreciated, especially Dr. Sibtain Ahmed, Dr. Nadine Ziemert and Dr. Greg Rouse for their help in research work. I wish to thank Dr. Muhammad Shahid, Department of Biochemistry and Dr. Nisar Ahmad, Centre of Agricultural Biochemistry and Biotechnology (CABB) for their guidance, encouragement and help throughout my PhD studies. I am also thankful to my genius friends and fellows Zahid Mushtaq, Muhammad Naeem, Sumaira Sharif, Dr. Asia Atta, Dr. Mazhar Abbas and my MBL fellows for their love providing amenities and friendship. Many thanks are due to my dearest family for giving me so much joy and happiness outside lab. Special thanks to my brothers Ilyas Ali, Atif Sajjad and Waqar Ali for their prayers, guidance and best wishes at each and every fraction of my life. I owe immense feelings of love and thanks for my affectionate mother and father, as their prayers are always behind my each success and my loving sisters, bhabhies and nephews for their continuous encouragement, untiring efforts and their patience while I did this work. Ghulam Mustafa CONTENTS 1. Introduction 1.1. Natural products …………………………………………………………… 1 1.2. Role of plants in drug discovery …………………………………………… 2 1.3. Biochemical profiling and related techniques ……………………………. 5 1.4. Importance of microbial secondary metabolites …………………………... 7 1.5. Objectives of the study …………………………………………………... 8 2. Review of Literature 2.1. History of medicinal plants …………………………………………….… 9 2.1.1. Bioactive compounds from medicinal plants ………………….. 11 2.2. Herbal medicines today …………………………………………………... 12 2.3. Herbal medicine in Pakistan ……………………………………………… 13 2.4. Medicinal plants from Northern areas of Pakistan ………………………. 15 2.5. Medicinal plants from Cholistan desert of Pakistan……………………… 18 2.5.1. Soil and climate of Cholistan desert ……………………………. 19 2.5.2. Vegetation of Cholistan desert …………………………………… 20 2.5.3. Use of medicinal plants by local inhabitants …………………… 21 2.6. Secondary plant metabolites with medicinal properties …………………. 27 2.6.1. Carbohydrates and related compounds …………………………… 27 2.6.2. Alkaloids ………………………………………………………… 27 2.6.3. Phenolics ………………………………………………………… 28 2.6.4. Terpenoids ………………………………………………………. 29 2.6.5. Glycosides ………………………………………………………. 30 2.7. Bioactive compounds and defense mechanisms in plants ……………… 30 2.7.1. Antimicrobial peptides (AMPs) ………………………………... 32 2.7.2. Anticancerous compounds ……………………………………... 32 2.8. Natural products from bacteria …………………………………………… 33 2.8.1. Polyketides ……………………………………………………… 34 2.8.2. Biosynthesis of polyketides ………………………………….…. 35 2.8.3. Types of Polyketide synthases (PKSs) …………………………. 38 2.9. The Natural Product Domain Seeker (NaPDoS) ………………………... 44 2.9.1. NaPDoS working ……………………………………………..… 44 2.9.2. Domain classification 45 3. Materials and Methods Section A 3.1. Study areas ………………………………………………………………... 48 3.2. Collection and identification of plant species ………………………….… 48 3.3. Chemicals …………………………………………………………………. 49 3.4. Preparation of plant extracts ……………………………………………… 49 3.4.1. LC/MS analyses …………………………………………………. 49 3.4.2. Antibacterial activity ……………………………………………. 53 3.4.3. Cytotoxicity Bioassay …………………………………………… 53 i Section B 3.5. Comparison of phylogenetic softwares ………………………………...… 55 3.6. Working with bacterial type II PKS sequence data ……………………… 55 3.6.1. Retrieval/Collection of Type II PKS sequences (KSα) ………… 55 3.6.2. Creating alignment of KSα domains of type II PKS …………… 55 3.6.3. Editing the alignment ………………………………………….. 57 3.6.4. Model tests ……………………………………………………… 57 3.6.5. Generating a reference phylogenetic tree for NaPDoS …………… 57 3.6.5.1. Neighbor-Joining (NJ) ………………………………… 58 3.6.5.2. Maximum parsimony (MP) ………………………...… 58 3.6.5.3. Maximum likelihood (ML) …………………………… 58 3.6.5.4. Minimum evolution (ME) ……………………………. 58 3.7. Study of structural similarities …………………………………………… 59 3.8. Gene cluster analyses of type II PKS …………………………………….. 59 4. Results and Discussion Part A 4.1. Biochemical profiling of selected medicinal plants ……………………... 60 4.1.1. Flavonoids ………………………………………………………. 69 4.1.2. Sesquiterpene lactones …………………………………………. 69 4.1.3. Isoflavones ……………………………………………………… 70 4.1.4. Phenolics ………………………………………………………… 70 4.1.5. Non-alkaloids ……………………………………………………. 71 4.2. Antibacterial study of selected plants ……………………………………. 71 4.3. Cytotoxic study of selected medicinal plants ……………………………. 73 Part B 4.4. Comparison between PHYLIP and MEGA ……………………………… 77 4.4.1. Advantages of PHYLIP ………………………………………… 77 4.4.2. Disadvantages of PHYLIP ……………………………………… 77 4.5. Up-gradation of Natural Product Domain Seeker (NaPDoS) …………… 78 4.5.1. Retrieval/Collection of Type II PKS sequences (KSα) ………... 79 4.5.2. Creating and editing the alignment ……………………………. 81 4.6. Generation and analysis of NaPDoS reference PKS tree …………………… 83 4.6.1. Angucyline ……………………………………………………… 86 4.6.2. Naphthoquinone ……………………………………………….. 89 4.6.3. Anthracycline …………………………………………………... 91 4.6.4. Naphthacenequinone and tetracyclic quinone ………………… 93 4.6.5. Pentangular polyphenols and Aureolic acids ………………….. 95 4.6.6. Tetracyclines ……………………………………………………. 97 4.6.7. Resistomycin-like ………………………………………………. 99 4.6.8. Spore pigment …………………………………………………... 100 4.7. The Natural Product Domain Seeker (NaPDoS 2.0) …………………….. 101 Summary ……………………………………………..…………………. 106 Literature Cited ……………………………………….………………… 108 ii LIST OF TABLES Table No. Title Page No. 2.1 Medicinal plants which laid the foundation of drug discovery 10 2.2 Major organizations of Pakistan involved in medicinal plants 15 research 2.3 Some medicinal plants from Northern areas with their traditional 17 uses 2.4 Some medicinal plants from Cholistan desert with their traditional 23 uses 2.5 Ethnopharmacological applications of some medicinal plants 24 alongwith their phytochemicals 2.6 Some bacterial polyketides with their activities 36 2.7 Survey of PKSs types 38 3.1 Indigenous medicinal plants used in the study with their reported 50 medicinal uses 3.2 Methods with different models used to generate phylogenetic trees 58 4.1 List of compounds (by Library matching) present in each medicinal 67 plant with their medicinal use 4.2 Antibacterial and cytotoxic activities of indigenous medicinal 74 plants samples 4.3 Compounds with their classes selected to generate a reference 80 phylogenetic tree of KSα domain of type II PKS 4.4 Maximum Likelihood fits of substitution models 86 iii LIST OF FIGURES Figure No. Title Page No. 2.1 Floristic regions of Pakistan 14 2.2 Map of Northern areas of Pakistan (internet source) 16 2.3 Map of Cholistan desert of Pakistan 19 2.4 Structure of reserpine (an alkaloid) 28 2.5 Basic structure of flavonoids 29 2.6 Structure of bisabolol 29 2.7 Structure of aloesin (a glycoside) 30 2.8 Representative examples of some polyketide drugs 37 2.9 Fatty acids and polyketide biosyntheses 39 2.10 Biosynthesis of erythromycin A 40 2.11 Iterative PKS involved in the biosynthesis of lovastatin (fungal 41 iterative type I PKS) 2.12 Schematic view of actinorhodin KSα and KSβ enzyme (type II 42 PKS) 2.13 Biosynthesis of doxorubicin (bacterial type II PKS) 43 2.14 Biosynthesis of naringenin chalcone (plant type III PKS, chalcone 43 synthase) 2.15 NaPDoS bioinformatic pipeline 46 2.16 Phylogeny based KS domain classification 47 3.1 Selected medicinal
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