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Introduction to
Pharmaceutical
Biotechnology
Enzymes, proteins and bioinformatics
Ahmed Al-Harrasi
Saurabh Bhatia
Ajmal Khan
SECOND
EDITION
VOLUME
TWO
Introduction to Pharmaceutical
Biotechnology, Volume 2
(Second Edition)
Enzymes, proteins and bioinformatics
Online at: https://doi.org/10.1088/978-0-7503-5387-8
Introduction to Pharmaceutical
Biotechnology, Volume 2
(Second Edition)
Enzymes, proteins and bioinformatics
Ahmed Al-Harrasi
Natural & Medical Sciences Research Center, University of Nizwa
Saurabh Bhatia
Natural & Medical Sciences Research Center, University of Nizwa
and
School of Health Sciences, University of Petroleum and Energy Studies, Dehradun,
Uttarakhand, India
Ajmal Khan
Natural & Medical Sciences Research Center, University of Nizwa
IOP Publishing, Bristol, UK
ª IOP Publishing Ltd 2024. All rights, including for text and data mining (TDM), artificial
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This book is available under the terms of the IOP-Standard Books License
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Clearance Centre and other reproduction rights organizations.
Permission to make use of IOP Publishing content other than as set out above may be sought
at permissions@ioppublishing.org.
Ahmed Al-Harrasi, Saurabh Bhatia and Ajmal Khan have asserted their right to be identified as
the authors of this work in accordance with sections 77 and 78 of the Copyright, Designs and
Patents Act 1988.
ISBN 978-0-7503-5387-8 (ebook)
ISBN 978-0-7503-5385-4 (print)
ISBN 978-0-7503-5388-5 (myPrint)
ISBN 978-0-7503-5386-1 (mobi)
DOI 10.1088/978-0-7503-5387-8
Version: 20240901
IOP ebooks
British Library Cataloguing-in-Publication Data: A catalogue record for this book is available
from the British Library.
Published by IOP Publishing, wholly owned by The Institute of Physics, London
IOP Publishing, No.2 The Distillery, Glassfields, Avon Street, Bristol, BS2 0GR, UK
US Office: IOP Publishing, Inc., 190 North Independence Mall West, Suite 601, Philadelphia,
PA 19106, USA
Saurabh Bhatia has dedicated this book to his Mother (Mrs Vinod Bala Bhatia), his
Father (Mr Ram Lal Bhatia) and his Brother (Mr Sanjay Bhatia).
Contents
Preface xxii
Acknowledgements xxiii
Author biographies xxiv
1 Introduction to enzymes and their applications 1-1
1.1 Introduction 1-1
1.2 Properties of enzymes 1-3
1.3 Catalysis 1-5
1.4 The structure of enzymes 1-5
1.5 Structural features: primary and secondary structures 1-7
1.6 Nomenclature and classification 1-7
1.6.1 Class 1—oxidoreductase 1-8
1.6.2 Class 2—transferase 1-8
1.6.3 Class 3—hydrolases 1-9
1.6.4 Class 4—lyases 1-9
1.6.5 Class 5—isomerases 1-9
1.6.6 Class 6—ligases 1-10
1.7 The mechanism of action of enzymes 1-10
1.7.1 The fisher template model (lock and key model) 1-11
1.7.2 Induced fit model 1-11
1.7.3 Covalent catalysis 1-12
1.8 Catalysis via chymotrypsin 1-12
1.8.1 Intermediary stages of chymotrypsin 1-12
1.8.2 Kinetic behavior of α-chymotrypsin 1-13
1.8.3 Selective proteolysis in creation of the catalytic sites of enzymes 1-14
1.8.4 Kinetic models for enzymes 1-15
1.8.5 Enzyme mediated acid–base (general) catalysis 1-19
1.8.6 Metallozymes 1-19
1.9 Enzyme inhibition 1-20
1.10 Pharmaceutical applications 1-22
1.10.1 Diagnostic applications of enzymes 1-22
1.10.2 Enzymes in therapeutics 1-24
1.11 Plants and algae enzyme systems 1-29
1.12 Enzyme safety 1-30
1.13 Enzyme structure determination 1-31
vii
Introduction to Pharmaceutical Biotechnology, Volume 2 (Second Edition)
1.13.1 X-ray crystallography 1-31
1.13.2 NMR spectroscopy 1-31
1.13.3 Cryo-electron microscopy 1-32
1.14 Enzyme engineering and design 1-32
1.14.1 Directed evolution of enzymes 1-32
1.14.2 Rational design of enzymes 1-33
1.14.3 Applications of engineered enzymes 1-33
1.15 Enzymes in medicine and healthcare 1-33
1.15.1 Enzyme-targeted drug delivery 1-34
1.15.2 Enzymes as drug targets 1-34
1.15.3 Challenges and opportunities in enzyme drug discovery 1-35
1.15.4 Enzymes in gene therapy 1-35
1.15.5 Enzymes in personalized medicine 1-35
1.15.6 Enzyme biomarkers in disease diagnosis 1-36
1.15.7 Pharmacogenomics and enzyme variability 1-36
1.15.8 Enzyme-based therapies for personalized treatment 1-36
1.16 Enzymes in bioremediation 1-36
1.17 Enzymes in agriculture and crop production 1-37
1.18 Enzymes in waste management 1-38
References 1-38
2 Technologies and procedures involved in enzyme production 2-1
2.1 Introduction 2-1
2.1.1 Sources of enzymes 2-2
2.2 Enzyme production technology 2-6
2.2.1 Selection of microorganisms 2-6
2.2.2 Medium selection 2-8
2.2.3 Production process 2-9
2.2.4 Recovery and purification of enzymes 2-10
2.2.5 Cell debris removal 2-10
2.2.6 Nucleic acid removal 2-11
2.2.7 Precipitation of enzymes 2-11
2.2.8 Liquid–liquid partition 2-11
2.2.9 Chromatographic separation 2-12
2.2.10 Drying and packing 2-12
2.2.11 Regulation of microbial enzyme production 2-13
2.2.12 Induction 2-13
viii
Introduction to Pharmaceutical Biotechnology, Volume 2 (Second Edition)
2.2.13 Feedback repression 2-14
2.2.14 Nutrient repression 2-14
2.3 Procedures involved in enzyme production 2-15
2.3.1 Source and location of enzymes 2-15
2.3.2 The variety of microorganisms 2-16
2.3.3 Media for fermentation 2-17
2.3.4 Fermentation 2-17
2.3.5 Enzyme extraction 2-19
2.3.6 Purification of enzymes 2-24
2.3.7 Finishing operations 2-33
2.4 Recombinant proteins from algae 2-35
2.5 Enzyme immobilization techniques 2-36
2.5.1 Advantages and applications of enzyme immobilization 2-36
2.5.2 Methods of enzyme immobilization 2-38
2.6 Enzyme engineering for enhanced stability and activity 2-41
2.6.1 Protein engineering strategies 2-42
2.6.2 Improving enzyme thermostability 2-45
2.6.3 Enhancing enzyme substrate specificity 2-46
2.7 Upstream process intensification 2-46
2.7.1 High cell density fermentation 2-47
2.7.2 Solid-state fermentation 2-48
2.7.3 Continuous fermentation 2-48
2.7.4 Microbial consortia for enzyme production 2-49
2.7.5 In situ product removal strategies 2-50
2.8 Enzyme production from extreme environments 2-50
2.8.1 Psychrophiles (cold-loving) 2-50
2.8.2 Thermophiles (heat-loving) 2-52
2.8.3 Acidophiles (acid-loving) 2-52
2.8.4 Alkaliphiles (alkaline-loving) 2-53
2.8.5 Halophiles (salt-loving) 2-53
2.8.6 Applications of extremozymes in biotechnology 2-54
2.9 Downstream process intensification 2-54
2.9.1 Continuous chromatography 2-55
2.9.2 Process integration and optimization 2-55
2.9.3 Advanced filtration techniques 2-56
2.9.4 Automation and robotics in downstream processing 2-57
References 2-57
ix