Frontiers in Molecular Pharming: Volume 2

Table of Contents

Chapter 1: System Biology – In Silico Characterization Of Proteins And And Peptides Chapter 1 Tools For Prediction And Validation Of Epitopic Regions On Protein Targets For Vaccine

1. Immune System-An Overview

2. Identification Of Epitopes

3. Target Selection For Epitope Prediction

4. Tools For Prediction Of Linear B-Cell Epitopes

5. Tools For Prediction Of Conformational B-Cell Epitopes

6. Prediction Of T-Cell Epitopes
6.1. Tools For Prediction Of Mhc Class I Binding Peptides
6.2. Tools For Prediction Of Mhc Class Ii Binding Peptides

7. Further Considerations

8. Limitations Of Epitope Prediction Tools And The Way Forward

9. Validation Of B- And T-Cell Epitopes
9.1. Tools For Validation Of B-Cell Epitopes
9.1.1. Enzyme-Linked Immunosorbent Assay
9.1.2. Immunoblotting
9.1.3. Virus Neutralization Test
9.1.4. Lateral Flow Assay
9.2. Tools For Validation Of T-Cell Epitopes
9.2.1. Mass Spectrometry (Ms)
9.2.2. Enzyme-Linked Immune Absorbent Spot (Elispot)
9.2.3. Intracellular Cytokine Staining (Ics) Assay
9.2.4. Tetramer Staining

• Concluding Remarks
• Consent For Publication
• Conflict Of Interest
• Acknowledgements
• References

Chapter 2 Immunoinformatics And Its Role In Vaccine Development

• Iqra Mehmood, Amna Bari, Sajjad Ahmad, Anam Naz, Farah Shahid, Usman Ali, Ashfaq, Kishver Tusleem And Muhammad Tahir Ul Qamar

1. Introduction

2. Transformation Of Vaccinology From Conventional To Modern Era

3. Subtractive Genomics And Reverse Vaccinology
3.1. Epitope Based Vaccine Design
3.2. Multiple Epitope Sub-Unit Vaccines
3.3. Antigen Based Vaccine Design

4. Recent Advancements In Immunoinformatics
4.1. B And T Cell Epitope Prediction Tools And Databases
4.2. Allergens Informatics

5. Immunoinformatics Quest Against Sars-Cov-2

6. Limitations Of Immunoinformatics

7. Future Perspective And Conclusions

• Consent For Publication
• Conflict Of Interest
• Acknowledgments
• References

Chapter 3 Computational Toolbox For Analysis Of Protein Thermostability

• Syed Farhat Ali

1. Introduction

2. Basis Of Protein Thermostability
2.1. Electrostatic Interactions
2.2. Hydrogen Bonds
2.3. Hydrophobic Interaction
2.4. Disulfide Bonds
2.5. Protein Rigidity And Flexibility
2.6. Amino Acid Composition

3. Tools And Approaches For In Silico Analysis Of Protein Thermostability
3.1. Fireprot
3.2. Scoop
3.3. Kstable
3.4. Cupsat
3.5. Prots
3.6. Foldx
3.7. Rankprot
3.8. Istable2.0
3.9. Rosetta Design
3.10. Comparative Analysis Of Tools For Thermostability Prediction

4. Relevant Databases

5. Applications Of In Silico Approaches For Protein Thermostability Analysis And Improvement

• Conclusion
• Consent For Publication
• Conflict Of Interest
• Acknowledgments
• References

Chapter 4 Pan-Proteomics To Analyze The Functional Complexity Of Organisms

• Muhammad Tahir Ul Qamar, Barira Zahid, Fatima Khalid, Anam Naz, Jia-Ming -Song, Sajjad Ahmad, Xitong Zhu, Feng Xing, Muhammad Sarwar Khan And Ling, Ling Chen

1. Introduction

2. Concept Of Pan-Proteomics

3. Approaches And Software Used For Pan-Proteomics

4. Applications And Experimental Design Of Pan-Proteomics In Prokaryotes Research
4.1. Proteome Retrieval And Removal Of Duplicate Sequences
4.2. Searching Of Essential, Non-Homologous Proteins
4.3. Metabolic Pathway Analysis
4.4. Drug-Ability Analysis
4.5. Prediction Of Subcellular Localization

5. Application Of Pan-Proteomics In Eukaryotes Research
5.1. Utilization In Plant's Research
5.2. Utilization In Animals And Human Research
5.3. Utilization In Cancer Studies

• Conclusions And Future Perspectives
• Consent For Publication
• Conflict Of Interest
• Acknowledgments:
• References

Chapter 5 Functional Characterization Of Proteins And Peptides Using Computational Approaches

• Zeshan Haider And Adnan K. Niazi

1. Introduction

2. In-Silico Analysis Of Peptides
2.1. Classification And Databases Of Peptides
2.2. Algorithm For Prediction Of Peptides And Their Function
2.2.1. Search For Similar Fragments
2.2.2. Search For Evolutionary Conservation
2.2.3. Search For Statistical Patterns
2.3. Prediction Features For Prediction Of Peptides Model
2.3.1. Amino Acid Composition
2.3.2. Atomic Composition Of Amino Acids
2.3.3. Chemical Descriptors

3. In-Silico Analysis Of Proteins
3.1. Protein Databases For Sequence Retrieval
3.1.1. Organism-Specific And Protein Family Based-Databases
3.1.2. Protein Family-Based Databases
3.1.3. Organism Specified Protein Databases
3.2. Classification Of Protein Sequences
3.2.1. Methods For Classification Of Protein Sequences
3.2.2. Signatures Databases For Protein
3.2.3. Super Integrated Signatures Databases For Proteins

4. Molecular Docking-Based Peptide Prediction

• Conclusion
• Consent For Publication
• Conflict Of Interest
• Acknowledgements
• References
• Section Ii: Molecular Pharming For Human Beings Chapter 6 Molecular Pharming: Research, Developments And Future Perspective
• Muhammad Sarwar Khan, Ghulam Mustafa And Faiz Ahmad Joyia

1. Introduction

2. History Of The Biopharmaceutical Industry

3. Various Production Systems For Biopharmaceuticals
3.1. Using Microbes For Biopharming
3.2. Using Mammalian Cell Lines For Biopharming
3.3. Using Gm Animals For Biopharming
3.4. Using Gm Crops For Biopharming

4. Types Of Plant-Based Biopharmaceutical Products
4.1. Antibodies
4.2. Vaccines
4.3. Other Therapeutic Agents

5. Transgenic Plants In The Biopharmaceutical Market

6. Methodological Aspects Of Plant-Based Biopharmaceuticals
6.1. Upstream Processing
6.1.1. Plant Transformation
6.1.2. Media Hydration
6.1.3. Cell Culture (Bioreactor)
6.2. Harvesting
6.2.1. Harvesting From Plant Material (Centrifugation Or Filtration)
6.3. Downstream Processing Of The Proteins Of Pharmaceutical Value
6.3.1. Protein Extraction
6.3.2. Clarification
6.3.3. Flocculation
6.3.4. Protein Purification

7. Recent Advances In Biopharmaceutical Production
7.1. Cell And Tissue Culture
7.2. Virus-Infected Plants - A Valuable Therapeutic Protein Production Source
7.3. Expression Of Therapeutic Proteins In Plants Through Agro-Infection

8. Quality Assurance In Biopharmaceutical Production
8.1. Biopharmaceutical Production Validation

9. Applications Of Biopharmaceutical For Veterinary And Humans 147

10. Prospects

• Consent For Publication
• Conflicts Of Interest
• Acknowledgments
• References

Chapter 7 Green Factories: Plants As A Platform For Cost-Effective Production Of High-Value Targets

• Muhammad Omar Khan, Ayesha Siddiqui And Niaz Ahmad

1. Why Plant-Based Expression Systems?

2. Development Of Transgenic Plants

3. Summary And Outlook

• Consent For Publication
• Conflict Of Interest
• Acknowledgments
• References

Chapter 8 Analysis Of Cross-Reactivity, Specificity And The Use Of Optimised Elisa For Rapid Detection Of Fusarium Spp.

• Phetole Mangena And Phumzile Mkhize

1. Introduction

2. Fungal Diseases And Host Range Of Fusarium Spp. Infecting Plants And Animals

3. Detection Systems For Fusarium Pathogens
3.1. Traditional And Current Methods Of Fusarium Detection
3.2. Limitations In The Traditional And Current Fusarium Detection Systems

4. Antibody Reactivity And Specificity Involving Fusarium Spp.

5. Nature Of Antigen Variation And Distribution

6. Antibody Recognition
6.1. Epitope Structure And Functionality
6.2. Paratope Binding
6.3. Maturation Of Antibody Specificity
6.4. Contrast Binding Affinity And Specificity

7. Diversity Of Fusarium Antibodies And Their Specificity

8. Cross-Reactivity In Monoclonal And Polyclonal Antibodies Against Fusarium Antigens

9. Development Of Optimised Elisa For Rapid Detection Of Fusarium Species

• Final Considerations Or Conclusions
• Abbreviations
• Consent For Publication
• Conflict Of Interest
• Acknowledgements
• References

Chapter 9 Plant Molecular Pharming For Human Diseases

• Kiran Saba, Muhammad Suleman Malik, Sara Latif, Fatima Ijaz, Muhammad Sameeullah And Mohammad Tahir Waheed

1. Introduction

2. Millennium Development Goals (Mdgs)

3. Sustainable Development Goals (Sdgs)
3.1. Role Of Plant Molecular Pharming In Achieving Sustainable Development Goals

4. Current Status Of Molecular Pharming In The Last Decade For Emerging Infectious Diseases
4.1. Chikungunya
4.2. Crimean-Congo Hemorrhagic Fever
4.3. Ebola Virus Disease
4.5. Human Respiratory Syncytial Virus
4.6. Influenza
4.7. Marburg Virus Disease
4.8. Rift Valley Fever
4.9. Severe Acute Respiratory Syndrome
4.10. Nipah Virus Disease
4.11. Zika Virus Disease

• Concluding Remarks
• Consent For Publication
• Conflict Of Interest
• Acknowledgements
• References

Chapter 10 Plant Molecular Farming For Human Therapeutics: Recent Advances And Future Prospects

• Amna Ramzan, Zainab Y. Sandhu, Saba Altaf, Aisha Tarar, Iqra Arshad, Sumera Rashid, Huma Shakoor, Rabia Abbas And Bushra Rashid

1. Introduction

2. Significance Of Plant Molecular Farming (Pmf) Applications
2.1. Recombinant Antibodies

Author

• Muhammad Sarwar Khan