Drug discovery

Biopharmaceutical Manufacturing and the Drug Development Process

Overview of the Drug Development Process

  • Topics covered in the drug development process include:

    • Drug Discovery

    • Genomics/Proteomics

    • Product Characterization

    • Patenting

    • Delivery of Biopharmaceuticals

    • Preclinical Studies

    • Clinical Trials

    • Role and remit of regulatory authorities

Genomics and Proteomics

Definition of Genomics

  • Genomics refers to the systematic study of the entire genome of an organism.

  • The core aim is to sequence the entire DNA complement of a cell and assign exact positions in the genome to the various genes and non-coding regions of DNA.

Importance of Sequencing Technology

  • Prior to the 1990s, sequencing and studying a single gene was a significant task.

  • Advances in sequencing technology and highly automated hardware systems have made DNA sequencing faster, cheaper, and more accurate.

  • Modern sequencing systems can sequence thousands of bases per hour.

  • By 2006, the entire human genome was sequenced.

Relationship Between Genomics and Drug Development

  • Genome data provides full sequence information of every protein an organism can make, potentially leading to the identification of new drug targets and biopharmaceuticals.

  • All drugs on the market generally target one or more of a maximum of 500 targets, which include proteins such as enzymes, ion channels, hormones, and nuclear receptors.

Drug-Protein Interaction Example

  • Existing drug interacts effectively with the protein.

  • If gene alteration occurs, the existing drug may not interact with the changed protein.

  • Information about the altered protein is utilized to develop a new drug that effectively interacts with it.

New Drug Targets in the Human Genome

  • Estimates suggest there are between 3K and 10K new protein-based targets hidden in the human genome sequence.

  • Sequence data from human pathogens may reveal thousands of target proteins for potential drug development.

  • Gene products of pathogens may be essential for their viability or infectivity.

Functional Genomics

  • The challenge of identifying genes is hindered by the unknown biological function of sequenced gene products.

  • Functional Genomics is the field focused on elucidating the biological function of genes and assessing the relationship between genotype and phenotype.

Comparison of Genetics and Genomics

Genetics

  • Genetics is the study of heredity and focuses on the function and composition of single genes.

  • Gene refers to a specific sequence of DNA that codes for a functional molecule.

Genomics

  • Genomics examines the complete set of genetic information of an organism, including both coding and non-coding DNA.

  • It involves a systemic analysis of all genes as a whole, which aids in identifying and characterizing the entire protein set of an organism.

Branches of Genomic Study

  • Genomics encompasses various branches of study:

    • Transcriptomics: Study of RNA species expressed within a cell.

    • Proteomics: Analysis of the proteins expressed in a cell.

    • Metabolomics: Study of metabolites within a biological system.

    • Methylomics: Insight into DNA methylation processes affecting gene expression.

Approaches to Assigning Function to Gene Products

Various Methods

  • Assignment of function to gene products can be pursued through:

    • Sequence Homology Studies

    • Phylogenetic Profiling

    • Rosetta Stone Method

    • Gene Neighbourhood Method

    • Knockout Animal Studies

    • DNA Array Technology (Gene Chips)

    • Proteomics Approach

    • Structural Genomic Approach

Sequence Homology Studies

  • Relies on computer-based studies in Bioinformatics to compare genes of unknown function with those that have assigned functions.

  • High homology suggests likely related functional attributes; can help assign function to 40-60% of new gene sequences.

Phylogenetic Profiling

  • Establishes a pattern of presence or absence of certain genes across various organisms.

  • Identical patterns indicate potential functional similarities, exemplified by the case of Trappin-2, a protease inhibitor with anti-inflammatory roles.

Rosetta Stone Method

  • Observes that two separate polypeptides in one organism can occur as a single fusion protein in another.

  • If a newly discovered gene A's function is unknown but corresponds to a known function in gene AB, the function of gene A can be inferred.

Gene Neighbourhood Method

  • Another computational method based on the assumption that genes likely serve linked functions if they are found adjacent to each other in multiple organisms.

Knockout Animal Studies

  • This method relies on phenotype observations rather than genotype.

  • It involves creating and analyzing mice where a specific gene has been deleted, yielding insights into the function of that gene.

DNA Array Technology

  • Allows profiling of genes present in a genome but does not indicate which genes are actively expressed.

  • Gene transcription results in mRNA production, leading to protein formation; this includes mRNA, tRNA, and rRNA.

Microarray Technology

  • Short oligonucleotides are affixed to surfaces; probe sequences from normal and cancer cells facilitate comparison.

  • The principle is based on DNA hybridization between complementary strands, with differing binding strengths based on sequence complementarity.

Proteomics Approach

  • Highlights that while drug targets are protein-based, the correlation between mRNA levels and protein concentrations can be misleading due to variations in differential splicing and post-translational modifications (PTMs).

  • Examples of PTMs include glycosylation, methylation, acetylation, and phosphorylation.

Differences Between Genome and Proteome

Genome

  • Essentially stable over time, providing a non-location-specific view of genetic information.

  • The human genome consists of approximately 20,000 genes and has been mapped (initially in 2000).

  • PCR technology is available to amplify DNA.

Proteome

  • Dynamic and location-specific, representing the entire set of proteins expressed in a particular cell or environment at a specific time.

  • The human proteome is not fully mapped, and there is no equivalent PCR method for proteins.

  • The proteome is often estimated to include over 1,000,000 distinct proteins due to factors such as alternative splicing and PTMs.

Complexity of the Proteome

  • The study of the proteome reveals significant complexity, arising from factors like alternative promoters, splicing, editing, and post-translational modifications, leading to a variety of protein forms.

Importance of Proteomics

  • Proteomics provides insights into gene function, aiding in the identification of proteins involved in both normal and diseased states.

  • Critical for uncovering pathogenic mechanisms and holds promise for discovering novel drugs by analyzing the proteomes of disease-affected tissues.

  • It also plays a role in studying drug resistance by examining changes in protein expression profiles.

Structural Genomics

  • A sub-discipline of proteomics focusing on cloning and analysis of cellular proteins through 3D structural analysis.

  • X-ray crystallography and NMR are two techniques utilized for this purpose.

  • Advancements in NMR have enabled the determination of larger and more complex protein structures.

  • Structural genomics aims to link specific functions to the known structures of proteins, facilitating functional predictions based on structure and vice versa.

Pharmacogenetics

Definition and Importance

  • Pharmacogenetics is the study of how specific DNA sequence variations correlate with drug responses.

  • It enables healthcare providers to tailor drug prescriptions to individual genetic profiles, improving treatment efficacy and minimizing adverse drug reactions (ADRs).

Genetic Variation in Drug Responses

  • Although responses to drugs can sometimes depend on non-genetic factors (e.g., health status), genetic variation, particularly Single Nucleotide Polymorphisms (SNPs), accounts for significant differences in drug responses.

  • The human genome houses around 3 million SNPs, with 1 in every 1000 nucleotide base showing variability.

Clinical Implications of SNPs

  • SNPs contribute to common human variations in traits like height and hair color, and their presence in relevant genes can influence drug effects.

  • Over 1.5 million SNPs have been identified and mapped, allowing correlations to be drawn between specific SNP patterns in drug-responsive and non-responsive populations.

Future of Drug Therapy

  • Pharmacogenetics may usher in a new era of precision medicine in drug therapy by personalizing treatment based on individual SNP profiles.

  • This could involve the development of drugs that are most effective for subsets of patients defined by their genetic variations.

  • Future concepts include microchips encoded with patients' SNP details to assist healthcare providers in optimal drug selection.

Considerations and Limitations

  • Assessing genetic determinants of diseases is complex, as treatment outcomes are influenced by multiple environmental factors alongside genetics.

  • The term Pharmacogenomics also exists, though it refers to the broader study of gene expression patterns involved in drug response, whereas pharmacogenetics focuses on specific SNPs and their implications.