This document discusses key bioprocess parameters that influence the production of therapeutic proteins. It describes parameters in the upstream and downstream processes. In the upstream, parameters like temperature, pH, substrates, inoculum size, incubation time, agitation, aeration, moisture, and molecular factors influence protein expression and yield. In the downstream, extraction solvents and purification methods are important. The document emphasizes that bioprocess optimization is needed to improve protein production yields and lower costs of therapeutic proteins.

1. Bioprocess parameter of
Therapeutic protein production

2.  Introduction
 Bioprocess
 Therapeutic protein
 Bioprocess parameter
 upstream
 Physical
 Chemical
 Biological
 Molecular
 Mechanical
 Downstream
 Conclusion
 References

3. • Bioprocesses are a subset of manufacturing processes and also called assembly operations. In the
bioprocess industry, two main steps are followed i.e., fermentation and purification.
• There are mainly two aspects: mechanical aspects and biological aspects
• Biological aspects consists of level of expression, location and state of the protein produced using different
strain as expression system.
• Hosts like E. coli, yeast, insect and mammalian cells, used as expression hosts for the production of
different therapeutic proteins.
• Bioprocess technologies also consist of computational models and software designs and monitor for
observation of multiple cultivation parameters.
• Some parameter are easily controllable with well-established technologies i.e. temperature.
• Some parameters create difficult challenges to process development i.e., substrate and product
concentration.
• Generally engineered version of naturally occurring human protein are called as therapeutic protein is also
known as protein drug. Use to restore deficient protein in cancer, infectious disease, hemophilia, anemia,
hepatitis.

4. • Classification of therapeutic protein:
 Group 1: protein under enzymatic or regulatory activity,
 group 2: protein based special targeting activity,
 group 3: protein vaccine
 group 4: protein diagnostics
• A. Lupirudin- protein based direct thrombin inhibitor used to reverse and prevention of thrombus formation.
• B. Cetumixab- endothelial growth factor receptor binding fragment used to treat colorectal cancer.
• C. Dornase-α- synthetic form of human deoxyribo-nuclease, used to breakdown extracellular DNA in lungs,
a major factor of mucus viscosity in cystic fibrosis.
• D. Sermorelin- for the treatment of dwarfism, prevention of HIV induced weight loss.

6. Temperature
• Temperature is an important physiological parameter that influences microbial growth, mammalian cell
culture and their metabolism.
• Each culture has an optimum temperature at which it shows maximum growth and productivity.
• Inoculating and incubating the media flasks at various temperatures between 25° to 100°C at small scale.
• Low temperature causes suppressed substrate transport across the cells and higher temperature cause of the
thermal Denaturation of protein.
• There may be biphasic culture operation where cells are maximize their growth and biomass at 37°C and
maintain 28–33°C due to longer and more viable stationary phase.
• Mammalian cells need low tempt. cell viability and inhibiting growth rate causes arrest cell in G1-phase of
cell cycle which increase productivity.
pH
• Chemical parameter which is check before inoculation and in between bioprocess.
• Every culture has different optimum pH at which its maximum activity reached and their activity increases
or decreases according to change in pH.
• Initial pH of the culture medium can create strong influence on cell growth and division, cell membrane
transport processes, and protein synthesis.
• Production of protein and stabilize it conformation between pH 6 to 7.5, also the protein yield decreased
with increasing pH values.
• Saccharomyces cerevisiae stops growing at pH 8.0, due to high pH (usually 8.0) has changes of gene
expression and synthesis of several protein , 6.0 to 7.5 is the optimum pH.

7. Substrate
• Raw materials contain an appropriate amounts of nutrient required for the preparation of culture media and
are significant factors for bioprocess.
• Growth of microorganisms and cell culture for synthesis of protein is dependent on concentration of
nutrient.
• Carbon, nitrogen, P, S, trace minerals, and inducers are required in defined calculation according to time for
growth of microbes or cell culture to obtain high yields in a bioprocess.
• The concentrations of nitrogen sources for essential elements and carbon for energy and cofactor of
enzyme, in media.
Carbon sources
• Carbohydrates are major source of carbon, oxygen, hydrogen and metabolic energy for micro-organisms
and cell culture.
• Simple sugars like glucose, molasses, and sucrose or sugar polymers such as starch, dextrin, cellulose and
hemicelluloses can be used for media preparation.
• Biomass contain 50% carbon on a dry weight basis, that why carbohydrates consist as the main medium
components.
Nitrogen sources
• Ammonium or nitrates are sole source of nitrogen for microbe or cell culture. Some of recombinant strain
easily uses ammonium salts, ammonium sulphate which is low cost and most commonly used in media
preparation.
• Sodium nitrate and Ammonium nitrate are most common nitrogen sources avail for many algae and fungi
but less extensively use by bacteria and yeasts.
• Some of by-products of the food processing and agricultural industries are also use bioprocess industry
which may less expensive and often more effective than salts, and can also contain various growth factors
and vitamins.

8. • Peptone, tryptone, soybean meal, cotton seed extracts and yeast extracts are also used as nitrogen sources in
fermentation media.
Inorganic components
• Inorganic nutrients are also equally important in culture medium.
• Some are required in high quantity some are in less quantity like phosphorus and sulphur are required in
large quantity and potassium, magnesium, sodium, calcium, iron, copper, manganese, molybdenum, cobalt,
zinc, and chloride are required in small quantity.
• Phosphorus uses mainly in the formation of sugar phosphates such as nucleotides which compose DNA,
RNA and ATP and sulphur are mostly present in the amino acids like cysteine and methionine.
• Iron is associated with the cytochromes, essential function of zinc in alcohol dehydrogenase; magnesium
uses for activation of many enzymes like hexokinase ,etc.

9. Inoculum Size
• The effect of inoculum size on protein synthesis can be defined by seeding fermentation media with varied
concentrations of inoculums ranging from 1.0% to 15.0% inoculum and incubating under standard
conditions.
• Protein production will be maximum at an optimum concentration of inoculum. Found 105 –106 spores/mL
of inoculum was efficient for maximum protein synthesis.
• Due to low inoculum size, it controls and increases the initial lag phase.
• Larger inoculum size increase moisture content and high sugar , O2 uptake and Formation of product causes
the clumping of cells, and also due to autolysis of cells because of fast nutritional uptake causes nutritional
imbalance by tremendous growth.
Incubation Time
• Generally stationary phase is known for protein synthesis and count of Incubation time for protein
production is important parameter of bioprocess in large scale.
• Products are directly proportional to the incubation period up to a certain extent in any bioprocess
technique.
• Optimum incubation time can be studied by incubating the fermentation media flasks inoculated with
cultures and measuring the rate of protein production after every 1 day interval for 1 to 10 days.
• Incubation time increases productivity, and the optimum protein recovery period was found to be from 4 to
7 days studied on small scale shown on Yeast expression system, in which protein will be detected and
compared using SDS-PAGE protocol.
• Recombinant clones are incubated in medium for 0 h, 24 h, 48 h and 72 h for expression of therapeutic
proteins. Proteins mostly expressed after 72 hours of incubation time.

10. Agitation
• Impellers are the most important component which is used to convert mechanical energy to hydrodynamic
motion and due to required turbulence can created to maintain the cells in suspension and also for sufficient
mass transfer.
• The energy generated by the impeller blades must be controlled otherwise some cell lines can be in danger
by the elevated shear force.
• Proper mixing and minimize cell damage from high shear force can be done by selecting the proper
impeller shape, impeller tip speed and ratio of impeller to vessel diameter.
• Impeller diameter should be one third to one half of the tank diameter.
– Smaller impeller produces radial flow pattern cause gas dispersion.
– Larger impeller produces axial flow to eliminate “zones of mixing”.
• The influence of agitation rate on protein production can be determined by different agitation speed in small
scale on shaker incubator from 0 to 400 rpm at selected intervals.
• The optimum agitation speed for protein production at 300 to 400 rpm.
Aeration
• It is an important parameter for cell culture and for aerobic microorganisms in a fermentation process.
• According to oxygen demand aeration will increase or decrease as the biomass increases and thus the
biomass required continuous supply of oxygen in bioreactor.
• Due to lesser solubility of oxygen in medium and increasing metabolic consumption, required continuously
supply of oxygen to the culture.
• Design of bioreactor in which stirrer geometry and aeration sparger option, and running parameters such as
gas flow rate or power input, are altered to achieve a similar kLa, providing a similar cell density.
KLa = kL * a
Note: where kLa is the mass transfer coefficient from gas to liquid phase given in s–1, kL is the liquid side mass transfer coefficient (resistance in
gas side film can be neglected), and a is the bubble surface (available for diffusion).

11. Moisture
• Moisture contain water molecule which is a source of hydrogen and oxygen elements, which are essential for
the synthesis of various biomolecules in the cell.
• It is essential for the metabolism of organisms such as enzymatic hydrolysis processes and membrane
transport processes of nutrients and metabolites and an increase in moisture content increases protein
synthesis.
• if moisture is Lesser, then solubility reduces and diffusion of nutrients decreases, causing an insufficient
supply of nutrients for microbe and cell, leading to lower protein production and also causing high water
stress.
• Moisture increases higher than the optimum level can also decreased protein production because of reduced
porosity and gas volume, lower oxygen transfer, and increased contamination.
• An optimum moisture of 70% is required by E.coli in SSF to obtain a higher increase in protein production
when compared to SmF.
Extraction Solvent
• It is more advantageous technique than other technique because of its ease of operation and low processing
cost.
• The promising method for extraction proteins in inactive state by using organic solvents then C4 and C5
alcohols (butanol, pentanol) are most probably used due to their differentiating action.
• In case of therapeutic protein extraction use different organic solvent because such peptides found with highly
abundant proteins such as albumin and their depletion under native conditions can cause the loss of potential
biomarkers.
• Solvent like acetonitrile containing 0.1% of trifluoroacetic acid are used for separation of abundant proteins
i.e., albumin simultaneously smaller proteins and peptides stay in solution and compared by MALDI-TOF
MS.

12. Molecular parameter
Recombinant DNA technology
• Some factors influence the expression of cloned gene product in recombinant which is most frequently used
prokaryotic expression system for the production of heterologous proteins.
• At the molecular level, strength of transcriptional promoters, plasmid stability, copy number, status and the
stability of the expressed foreign protein in the host influences the expression levels.
• The factors which influence the efficiency of the overall protein production process act in a very complex and
interactive way at different stages.
 The first cell and molecular biology considerations,
 the second process engineering considerations.
• Cell and molecular biology considerations deal mainly with the level of expression, location and state of the
protein produced using micro-organism as expression system.
 Factors that influence these things in an expression system are host, vector/promoter system and the origin and the nature
of the protein of interest.
• Process engineering considerations deal with the large-scale culture of the recombinant organism and the
recovery of the expressed protein.
 It aims at high volumetric yield and high throughput recovery of the expressed protein in bioactive form.

13. Strains and Plasmids: Backbones of Recombinant Expression
• Plasmids for expression of heterologous genes were developed, from which one plasmid has been
commercialized in an expression kit.
• Episomal plasmids do not yield higher protein in the bioreactor since they require the maintenance of a
selection pressure in large-scale, and are less stable in any case.
• The established integration methods zeta integration (the integration locus of the expression cassette) or site-
directed integration using the pBR322 or zeta docking platform.
• CRISPR-Cas9 system for markerless integration, and targeted integration in intergenic sites with high gene
expression levels.
Copy Number
• Copy number of recombinant genes integrated in the genome, mono-copy expression stays predominant in
the reported reactor-scale productions.
• Multi-copy may be hampered by genetic stability issues, globally increasing with the number of copies
integrated in the genome, and is further influenced by the culture conditions, recipient strain, integration
locus, and individual cell behavior.
• The volumetric and specific glucose utilization rates increased with the copy number increase.
• Compared to mono-copy integration, multi-copy strategy resulted in a 3.5-fold and 4.5-fold increased
enzyme yield for manA and manB, respectively. By contrast, biomass yield was reduced by 2.2- and 1.9-
fold, respectively.

14. Promoters: an Inducible Advantage
• Expression pattern and efficiency rely on the selected promoter. The promoter of the AEP gene encoding
alkaline extracellular protease, namely pXPR2, was developed and exploited in the first attempts to control
recombinant expression in Y. lipolytica and has been patented by Pfizer Inc. in 1993.
• pXPR2 is a strong promoter, induced by high peptone concentrations. These specific conditions for induction
led to the design of pioneer fed-batch strategies.
• The development of more polyvalent promoters whose applications were not limited to rich, peptone-
containing media. One of them, named hp4d, is a synthetic promoter combining four copies of the upstream
activating sequences.
Downstream processing:
• It is impossible to have one purification process to fit a vast scope of different recombinant therapeutic
protein.
• Common purification platform has been developed using Protein A affinity resin as the capture step and the
key advantages of a platform purification process include:
 (1) Shortening of process development timelines using minimal resources;
 (2) Ease of process scale-up, validation, and technology transfer;
 (3) Reduced capital expense when bringing in a new product to the manufacturing facility;
 (4) Reduction of raw material inventory through the use of common components;
 (5) Streamlined documentation through the use of templates.

15. • The introduction of Capto L, the first industrial platform for the purification of antibody fragments is now
available .
• Antibody fragments (e.g., Fab, scFv, dAb, minibody, diabody, etc.) are becoming the next important class of
protein-based biotherapeutics after mAbs
M.M. Zhu & et.al 2017: Industrial Production of Therapeutic Proteins

16. • Therapeutic proteins are the most significant among all the industrially produced proteins.
• it is uses for cure of different incurable disease.
• The high price of the therapeutic proteins is still one of the major limiting factors for developing nation.
• More research in this field to ease in production of therapeutic protein and develop easy parameter help in
cost cutting.
• Identification of cheaper substrates, developing appropriate media, and standardizing bioprocess parameters
for microbial growth and cell culture production remain a great challenge for future microbiologists.

17. References
• Ana Rita Costa, Maria Elisa Rodrigues & et.al 2013: Glycosylation; impact, control and improvement
during therapeutic protein production IBB – Institute for Biotechnology and Bioengineering, Centre of
Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal.
• Sreedevi Sarsan, Ramchander Merugu 2018: Role of Bioprocess Parameters to Improve Cellulase
Production: Part II; Department of Microbiology, St. Pious X Degree & P.G. College, Hyderabad, India †
Department of Biochemistry, Mahatma Gandhi University, Nalgonda, India.
• Maurice Ekpenyong & et.al 2021: Bioprocess Optimization of Nutritional Parameters for Enhanced
Anti-leukemic L-Asparaginase Production by Aspergillus candidus UCCM 00117: A Sequential Statistical
Approach; Environmental Microbiology and Biotechnology Unit, Department of Microbiology, University
of Calabar, Calabar, Nigeria, Department of Pharmaceutical Microbiology and Biotechnology.
• Andrea Castellanos-Mendoza & et.al 2014: Influence of pH control in the formation of inclusion bodies
during production of recombinant sphingomyelinase-D in Escherichia coli. Departamento de Biología
Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de
México, AP. 70228, México, Mexico D.F, CP. 04510, México
• Oleg Chertov & et.al 2003: Organic solvent extraction of proteins and peptides from serum as an effective
sample preparation for detection and identification of biomarkers by mass spectrometry. Protein Chemistry
Laboratory, SAIC-Frederick, Experimental Transplantation and Immunology Branch, Center for Cancer
Research, NCI-Frederick, Mass Spectrometry Center, SAIC-Frederick, Frederick, MD, USA
• Mohammed Gagaoua & et.al 2016: Data in support of three phase partitioning of zingibain, a milk-
clotting enzyme from Zingiber officinale Roscoe rhizomes. Equipe Maquav, INATAA, Université Frères
Mentouri Constantine, Route de Ain El-Bey, 25000 Constantine, Algeria.
• Marie Vandermies and Patrick Fickers 2019: Bioreactor-Scale Strategies for the Production of
Recombinant Protein in the Yeast Yarrowia lipolytica. TERRA Teaching and Research Centre, Microbial
Processes and Interactions, University of Liège–Gembloux AgroBio Tech, 5030 Gembloux, Belgium.
• James A. Kent & et.al 2017: Industrial Production of Therapeutic Proteins: Cell Lines, Cell Culture, and
Purification. Jupiter Florida USA, Grand Island New York USA, Kingsport, Tennessee USA.

18. • Antonio Pena & et.al 2015: Effects of high medium pH on growth, metabolism and transport
in Saccharomyces cerevisiae. Departamento de Genética Molecular, Instituto de Fisiología Celular,
Universidad Nacional Autónoma de México.
• Donald F. Gerson & et.al 1988: Substrate Concentration Control in Bioreactors. Connaught Laboratories
Limited, 1755 Stecles Avenue. West.
• M.M. Zhu & et.al 2017: Industrial Production of Therapeutic Proteins: Cell Lines, Cell Culture, and
Purification. Agensys Inc., an Affiliate of Astellas Pharma Inc, 1800 Stewart Street, Santa Monica 90404,
CA