Molecular characterization, detection & quantitation of biological products Purin Charoensuksai, PhD

Molecular characterization, detection & quantitation of biological products Purin Charoensuksai, PhD Department of Biopharmacy, Faculty of Pharmacy, Silpakorn University

Example of critical checkpoints influencing biological activity and safety of biological products Vector construction Expression Purification Storage until usage Coding sequence Modification of proteins PTMs Cleavages/truncation Aggregation Host cell proteins/ DNA Residual growth factors Adventitious agents Virus Micoplasma Stability of cell lines Location of insert Copy number of insert Ability to concentrate target species/clear up contaminants Leachables from columns Re-usage of columns Stability Storage conditions Picture in cover slide taken from: http://www.imapac.com/business_conference /biologics-world-taiwan-2016/the-concept/

Various laboratory techniques are routinely used for the characterization of biological products Nucleic acid AGE Hybridization Sequencing PCR, qpcr Microarray Protein Amino acid analysis Edman degradation Peptide mapping: HPLC, MS, MS-MS SDS-PAGE & protein staining IEF 2D-gel Immunological assays Precipitation/ agglutination Western blot ELISA Picture taken from: http://www.imapac.com/business_conference/biologicsworld-taiwan-2016/the-concept/

Molecular assays for biological products Our main focuses: Brief review of the principle of each assay Example of their usage in biological product registration Multiple levels: nucleic acids, protein, immunological assays Common types of assays: Qualitative: detect the presence of something Quantitative: determine the exact (?) amount of something Limit test (semi-quantitative): check if the level of something exceeds certain amount

Molecular analysis of nucleic acids DNA agarose gel electrophoresis Nucleic acid hybridization DNA sequencing PCR, qpcr Microarray

DNA agarose gel electrophoresis (AGE) Separate fragments of DNA based on size 6

Porous structure of molecular sieve used to resolve DNA/proteins Picture taken from: ocw.mit.edu/courses/biological-engineering/20-109-laboratory-fundamentals-in-biological-engineering-spring-2010/labs/module-1-day-2-purify-aptamer-encoding-dna/

DNA in agarose gels can be visualized by various staining methods Ethidium bromide Ethidium bromide Fluorescent DNA dye

Picture taken from http://users.rcn.com/jkimball.ma.ultranet/biologypages/b/basepairing.html Picture taken from: http://www.discoveryandinnovation.com/biol202/notes/lecture22.html

Hybridization of nucleic acids Southern blot & Northern blot Southern blot > DNA Northern blot > RNA 2 3 4 1 1. AGE 2. Transfer to solid support (blotting) 3. Hybridization with probe specific for sequence of interest 4. Detection Picture taken from: http://www.gene-quantification.de/mrna.html 10

Applications of nucleic acid hybridization DNA gel electrophoresis Southern Blotting TaqI & SmaI Ladder Uncut TaqI SmaI Ladder Uncut TaqI SmaI TaqI & SmaI Example: roughly map the location of DNA insert (infer genetic stability of cell line) Picture taken from: http://www.discoveringdna.com/

DNA sequencing: Sanger method https://www.youtube.com/watch?v=nudg0r9zl2m 12

Sanger sequencing is also known as a chain-termination method 13

DNA sequencing: Sanger method Chain-termination method 5 main components: DNA template Primer dntps fluorescent labelled ddntps DNA polymerase Sequence 1 fragment (read 500-1000 bps) at a time Example: check DNA sequence of insert (DNA or mrna) 14

Polymerase chain reaction (PCR) Amplification of target DNA 15

Quantitative Polymerase Chain Reaction (qpcr) Picture taken from: http://www.biosyn.com/tew/taqman-vs-sybr-green-chemistries.aspx

Quantitative Polymerase Chain Reaction (qpcr) A B Picture taken from: http://www.mypols.de/qpcr-probe-2x-master-mix/

Some examples of PCR/qPCR applications for the characterization of biological products PCR Amplify desired gene from suitable host for expression Detection of adventitious agents e.g. virus or micoplasma Detection of host cell DNA qpcr Determine the copy number of insert in master cell, working cell or cell at the end of production

DNA microarray By Squidonius https://commons.wikimedia.org/w/index.php?curid=39422948 Based on hybridization between probes & DNA of interest A Large number of probes are fixed on a solid support (CHIP) enabling the interrogation of multiple targets simultaneously

Picture taken from: http://bitesizebio.com/7206/introduction-to-dna-microarrays/ DNA microarray

Molecular analysis of proteins Polyacrylamide gel electrophoresis Edman degradation: N-terminal sequencing Peptide mapping: analysis of proteolytic cleavage pattern Mass-spectrometry: MS or MS-MS

Polyacrylamide gel electrophoresis (PAGE) Separate proteins based on size Usually performed in a denaturing condition (SDS-PAGE) Can be adapted to resolve proteins in their native conformation (native gel) 22

Proteins in polyacrylamide gels can be visualized by various staining methods Coomassie brilliant blue Silver stain Fluorescent stain e.g. Sypro Ruby http://www.komabiotech.com/product/product_detail.php?item=k14010

Edman degradation Phenyl isothiocyanate Phenylthiohydantoin (PTH)- amino acid derivatives are identified through chromatography N-terminal sequencing, up to 30 amino acids Will not work if N-terminal amino group is modified or buried within protein

Peptide mapping 1. Fragmentation of protein e.g. proteolytic cleavage by enzymes which cleave specific bond 2. Resolve peptides with appropriate methods e.g. SDS-PAGE, HPLC, MS, etc. www.promega.com

Peptide mapping Lys-C = K / X Arg-C = R /X

Some examples of peptide mapping applications in the registration of biological products Peptide mapping/finger printing reflects the identity of the parent protein Usage: Identity of drug substance Purity: detect modified forms of drug substance e.g. some PTMs

Protein mass-spectrometry (MS) analysis https://pharmchem.ucsf.edu/research/physbio/proteomics

2 types of protein mass-spectrometry (MS) analysis: Top-down and Bottom-up http://circgenetics.ahajournals.org/content/4/6/711/f1.expansion.html

Applications of protein MS analysis Mass fingerprint: MS Protein quantitation: quantitative MS Protein sequencing: MS-MS Post-tranlational modification characterization: MS-MS Example of MS application for the registration of biological products: analysis of amino acid variants e.g. deamidation, oxidation, glycation or glycosylation profile of drug substance

Immunological assays Exploit antigen-antibody interaction Examples: Precipitation/agglutination reactions Western blot ELISA

https://www.youtube.com/watch?v=av8npsiph_4 Precipitation/Agglutination

Precipitation/Agglutination Antibody/antigen interaction Similarity: antibody crosslink antigen and form precipitate Difference: nature of antigen Precipitation = soluble antigen Agglutination = insoluble antigen e.g. RBC, bacteria, antigen fixed on beads (HCG, bacterial toxins, etc.) Picture taken from: https://www.studyblue.com/notes/note/n/final-exam/deck/2914433

Example of precipitation/agglutination reaction Hemaglutination assay http://www.cdc.gov/flu/professionals/laboratory/antigenic.htm

Western blot Resolve proteins by SDS-PAGE 35

Western blot 1. Transfer proteins in gel onto other solid membrane Nitrocellulose PVDF (Polyvinylidene difluoride) 2. Stain with antibody specific to the protein of interest 3. Detect with appropriate methods Colorimetric Chemiluminescent Fluorescent, IR etc. 36

Diversity of amino acid

Isoelectric focusing

2D-SDS-PAGE

ELISA Enzyme-Linked ImmunoSorbent Assay Comparison of test samples with standard antigen with known concentration yield semi-quantitative/quantitative measurement of antigen in test sample

Example of ELISA application for the registration of biological products Host cell protein Leachable protein A Antibiotics Insulin Some small molecules: HEPES, resin components, etc.

Thank you!