IPRDC for low-cost yet high-quality protein production

The Integrated Protein Research & Development Center (IPRDC) program was established to contribute to a sustainable national biotechnological scene. The Center is housed in the Ateneo Research Institute of Science and Engineering (ARISE) and supported by the Department of Science and Technology - Science for Change Program (DOST-S4CP).

Through genetic engineering, the IPRDC and its four Filipino-made projects aim to manipulate the cellular genetics of bacteria to produce recombinant proteins, analyze cell growth patterns, devise necessary machinery for their processing, and create nanomaterials to purify these proteins.

The IPRDC is funded by DOST’s Niche Center in the Regions for R&D (NICER) Program and is monitored by the Philippine Council for Health Research and Development (DOST-PCHRD).This program is helmed by Dr. rer. nat. Crisanto M. Lopez of the Department of Biology.

Power beneath small-scale proteins

Proteins are large molecules composed of one or more long chains of amino acids–compounds made up of elements like carbon, hydrogen, nitrogen, oxygen or sulfur. Proteins within all living organisms have a multitude of diverse functions. Modern biomedical healthcare works through our understanding of these large molecules. In fact, proteins in their many forms are the targes of almost all therapeutic drugs and are used in diagnostics.

To be able to create proteins, researchers use host cells like a tiny factory by training them to produce proteins that they need. This is called recombinant protein production. Cells like animal cells, yeasts, and bacteria are employed to grow these. For IPRDC, their micro factory of choice is Escherichia coli (more commonly called E. coli) and the proteins they are making are enzymes for diagnostic purposes.

The first IPRDC Project’s goal is to expand the small scale production life of proteins that are considered vital in point-of-care diagnostics, such as enzymes and antibodies. “Enzyme Production: Cloning, Fermentation, Expression, and Characterization at Small-Scale” is a continued project design from a recombinant protein pilot project that Dr. Keith Moore of the Biology department led. IPRDC: Synthetic Biology is led by Dr. Lopez and Dr. Edjohn Aaron Macauyag. The project aims to demonstrate small-scale production and quality assurance for the five most critical proteins required for SARS-CoV2 molecular diagnostics. These enzymes make up the bulk of raw material costs for COVID-19 test kits.

Protein production, to what extent?

The IPRDC is designed to break away from research that just stays in the laboratory. It aims to become commercially viable manufacturers of proteins for the growth of the Philippine biotechnology sector. To do this, the IPRDC employs an interdisciplinary approach, with research projects that are interconnected to support one another’s objectives. Following the first project’s efforts in recombinant protein production, the second project leads the program in developing scale-up solutions.

The team working on the second project of the IPRDC, “Scaling Up and Optimization of Protein Production”, led by Dr. Rhea Abisado-Duque, will characterize the microenvironment that prompts the recombinant microbes to produce target proteins. Cultures of E. coli are used as agents to produce IPRDC’s target proteins, akin to farming animals for their meat. This project specifically determines the operational conditions (i.e. pH, dissolved oxygen, temperature, aeration and agitation rates, and the concentrations of growth media components) for maximum protein yields in various container sizes ranging from small fermentors to large bioreactors.

In identifying optimal cultivation conditions, IPRDC: Scaling Up employs Quality by Design methods, such as the Design of Experiments (DOE), which can maximize yield and minimize costs.

Advancing equipment for the next generation

One of the most expensive aspects of developing a center such as the IPRDC is instrumentation. To support the program’s efforts on sustainable protein production, the third project “Building Open-Source Instrumentation for Fermentation and Protein Purification,” led by Dr. Armando Guidote and Ms. Danielle B. Lapinig, focuses on designing and building opensource versions of bioreactors and a fast protein liquid chromatography (FPLC) system. Notably, these two types of equipment are relevant in increasing protein quantity among bacterial systems and the subsequent collection and purification of target products.

IPRDC: Instrumentation builds instruments that are more cost-efficient without sacrificing scientific output. Furthermore, the project envisions accessible hardware through its open-source designs, the education of more instrument specialists, and the establishment of stable revenue for the center through lowering operational expenses.

At present, the project has a laboratory equipped with tools for designing and prototyping work and have technical staff and interns trained in biotechnology and 3D printing. Furthermore, as the Program’s Science Communication arm, the project team has been actively seeking partners, collaborators, and potential clients and outside the University.

Bringing protein purification to different heights

Aside from reagents and instruments, purification consumables cost a lot. To further support IPRDC’s goals of sustainability and profitability, IPRDC’s fourth component project named “Development of Chemical Tools and Materials for Protein Purification” seeks to utilize nanoparticles in protein purification.

Spearheaded by Dr. Jose Mario Diaz with Balik Scientist Consultant Dr. Ricardo Jose Guerrero, magnetic iron oxide nanoparticles are being produced for more efficient binding capabilities of resins to proteins— which will be tested through size exclusion and affinity chromatography. In essence, IPRDC: Materials seeks to develop new methods and techniques with mentioned materials for batch emulsion and microfluidics for on-chip generation. From these developed methods and techniques, the products will also be used by other IPRDC projects in their conducted studies and experiments.

For instance, the usage of the products alongside the open-source FPLC from the Center’s Instrumentation arm will allow the IPRDC to conduct protein purification using in-house resins. This eventually allows further research without the need for high costs and long waiting times from other distributors and foreign suppliers.

Filipino-made breakthroughs for the Filipinos

Ultimately, the project seeks to scale up the local production of affordable and accessible recombinant proteins. These will be beneficial to research laboratories, biotechnology companies, and educational institutions that need to be equipped with advanced levels of biotechnology.

IPRDC is empowering local biotechnology by addressing supply chain and logistics issues. In turn, it is also in service of training the next generation of scientists through accessible reagents, equipment, and materials.

-

Text: Anna Pineda, Danielle Lapinig, and Christiane Oriana

Photo: IPRDC