1. Introduction and Definitions
Biotechnology is the use of living systems and organisms to develop or make products, or "any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use”.
Depending on the tools and applications, it often overlaps with the (related) fields of bioengineering, biomedical engineering, biomanufacturing, molecular engineering, etc.
For thousands of years, humankind has used biotechnology in agriculture, food production, and medicine.The term is largely believed to have been coined in 1919 by Hungarian engineer Károly Ereky. In the late 20th and early 21st centuries, biotechnology has expanded to include new and diverse sciences such as genomics, recombinant gene techniques, applied immunology, and development of pharmaceutical therapies and diagnostic tests.

2. Genomics is an area within genetics that concerns the sequencing and analysis of an organism’s genome.
The genome is the entire DNA content that is present within one cell of an organism. Experts in genomics strive to determine complete DNA sequences and perform genetic mapping to help understand disease.
Genomics also involves the study of intragenomic processes . Genomics does not involve single gene research unless the purpose is to understand a single gene’s effects in context of the entire genome.

3. The terms “proteome” and “proteomics” mirror the terms “genomics” and “genome”.
Since the first use of the term “proteome”, its meaning and scope have narrowed. Post-translational modifications, alternative splice products, and proteins intractable to classic separation techniques have presented a challenge towards the realization of the conventional definition of the word.
Proteomics include protein-protein interaction studies, protein function, protein modifications, and protein localization studies. The fundamental goal of proteomics is not only to pinpoint all the proteins in a cell, but also to generate a complete three-dimensional map of the cell indicating their exact location.
Proteomics runs parallel to genomics. The starting point for genomics is a gene in order to make inferences about its products (i.e. proteins), whereas proteomics begins with the functionally modified protein and works back to the gene responsible for its production.

4. Pharmaceutical biotechnology is a relatively new and growing field in which the principles of biotechnology are applied to the development of drugs.
A majority of therapeutic drugs in the current market are bioformulations, such as antibodies, nucleic acid products and vaccines.
Such bioformulations are developed through several stages that include: understanding the principles underlying health and disease; the fundamental molecular mechanisms governing the function of related biomolecules; synthesis and purification of the molecules; determining the product shelf life, stability, toxicity and immunogenicity; drug delivery systems; patenting; and clinical trials

5. What are biopharmaceuticals?
A biopharmaceutical is a protein or nucleic acid based biopharmaceutical product used for therapeutic or in vivo diagnostic purposes, which is produced by means other than direct extraction from a native (non engineered) biological source’’
Synonyms: biotechnology products, biotechnology medicines, products of pharmaceutical biotechnology
The definition includes: recombinant proteins, recombinant antibodies, gene therapy products, antisense oligonucleotides
Recombinant technology started in the seventies, today, there are 100 products approved around the world.

7. First generation biopharmaceuticals
Generally replacement proteins: proteins displaying an identical amino acid sequence to a native human protein and administered in order to replace or augment levels of that protein. e.g. recombinant forms of human insulin, growth hormone and blood factors.
Second generation biopharmaceuticals
Engineered proteins
Protein engineering (site directed mutagenesis): the controlled alteration of a gene’s nucleotide sequence, such that specific pre-determined alterations in the resultant polypeptide’s amino acid sequence are introduced.
Used to tailor the functional attributes of commercially important proteins. Objectives, (a) alteration of the protein’s mmunogenicity;
(b) alteration of biological half life;
(c) generation of faster/slower acting product; and
(d) the generation of novel hybrid/synthetic therapeutic proteins

8. Engineered Insulins
Engineered antibodies
Hybridoma, murine source: HAMA response
Humanized antibodies (chimaeric)
Post translational engineering
Covalent attachment of a chemical group
(PEG and increased half life)
Alteration in glycosylation pattern

10. Future trends
Alternative production systems: Escherichia Coli, Saccharomoycese cerevisae, animal cell lines (CHO)
Alternative delivery
Nucleic acid based therapeutics: gene therapy, antisesne oligonucleotides
Stem cell based therapy

11. Peptide and Protein Drugs Therapeutic applications, structure, stability

12. Proteins have the most dynamic and diverse role of any macromolecule in the body
Catalysing biochemical reactions,
Forming receptors and channels in membranes,
Providing intracellular and extracellular scaffolding support,
Transporting molecules within a cell or from one organ to another.
There are 25,000–40,000 different genes in the human genome, and with alternative splicing of genes and post-translational modification of proteins (for example, by cleavage, phosphorylation, acylation and glycosylation), the number of functionally distinct proteins is likely to be much higher
! Involved in disease conditions

13. Advantages of Protein Therapeutics Over Small Mol Wt Drugs
1. Proteins serve a highly specific and complex set of functions that cannot be mimicked by simple chemical compounds. 2. There is often less potential for protein therapeutics to interfere with normal biological processes and cause adverse effects. 3. As the body naturally produces many of the proteins, these agents are often well tolerated with less immune responses. 4. Fourth, for diseases in which a gene is mutated or deleted, protein therapeutics can provide effective replacement treatment without the need for gene therapy 5. The clinical development and FDA approval time of protein therapeutics may be faster than that of small-molecule drugs. ! Patents

14. Classification of therapeutic proteins according to their pharmacological function
Group 1 : Enzymes and regulatory proteins Group Ia: to replace a particular activity in cases of protein deficiency or abnormal protein production. Examples; lactase in patients lacking this gastrointestinal enzyme, replacing vital blood-clotting factors such as factor VIII and factor IX in haemophiliacs. Insulin for the treatment of diabetes. Patients with cystic fibrosis are often treated with a combination of pancreatic enzymes such as lipases, amylases and proteases .Diseases caused by metabolic enzyme deficiencies, such as Gaucher’s disease, mucopolysaccharidosis, Fabry disease

15. Group 1b: enhance the magnitude or timing of a particular normal protein activity Examples: recombinant erythropoietin in cases of chemotherapy induced anaemia it is used to increase erythrocyte production, renal failure. Neutropaenic patients with granulocyte-colony stimulating factor (G-CSF) which stimulate an increase in the number of neutrophils. In IVF procedures, FSH, hCG Life saving effects on thrombosis and haemostasis. Alteplase (recombinant tissue plasminogen activator (tPA), is used in blood clots in conditions as coronary artery occlusion, acute ischaemic stroke and pulmonary embolism It cleaves plasminogen to plasmin, which then degrades fibrin and thereby lyses fibrin-based clots Supra-physiological levels of coagulation factor VIIa may catalyse thrombosis and stop life-threatening bleeding in patients with haemophilia A or B Immunomodulators

16. Group 1c: foreign proteins with novel functions and endogenous proteins that act at a novel time or place in the body Examples: Papain, a protease, to degrade proteinaceous debris in wounds. Collagenase. Recombinant human deoxyribonuclease I (DNASE1), neutrophils DNA and cystic fiborosis

17. Group II: targeted proteins: The exquisite binding specificity of monoclonal antibodies and immunoadhesins Group IIa use the antigen recognition sites of immunoglobulin (Ig) molecules or the receptor-binding domains of native protein ligands to guide the immune system to destroy specifically targeted molecules or cells. Mostly for inflammatory disease situations, tumour necrosis factor (TNF) receptor and the Fc region of the human antibody protein IgG1 (inflammatory arithritis, psoriasis) Anti-infectives, viral infections Oncology, rituximab is a human/mouse chimeric monoclonal antibody that binds to CD20, a transmembrane protein expressed on >90% of B‑cell non-Hodgkin’s lymphomas, and targets the cells for destruction by the body’s immune system

20. Group IIb: selective delivery of small-molecule drugs and proteins to the intended therapeutic target. Examples: gemtuzumab ozogamicin, links the binding region of a monoclonal antibody directed against CD33 with calicheamicin, ibritumomab tiuxetan, a monoclonal antibody that is directed against CD20 and linked to a radioactive yttrium isotope Delivery of proteins and other macromolecules to the CNS, which is challenging owing to the highly selective blood–brain barrier (BBB).

21. Group III : protein vaccines: prophylactic or therapeutic vaccines Group IIIa are used to generate protection against infectious diseases or toxins. A successful example is the hepatitis B vaccine Group IIIb: therapeutic anticancer vaccines: B‑cell non-Hodgkin’s lymphoma

22. Group IV : protein diagnostics Examples: purified protein derivative (PPD) test, which determines whether an individual has been exposed to antigens from Mycobacterium tuberculosis. Imaging agents: Caromab pendetide is an indium‑111-labelled anti-PSA (prostate specific antigen) antibody that can be used to detect prostate cancer