EnzyCore Bio: Pioneering Artificial Enzyme Design through Directed Evolution to Transform Industrial Catalysis

On October 3, 2018, American scientist Frances Arnold was awarded the 2018 Nobel Prize in Chemistry for her outstanding contributions to the “directed evolution of enzymes.” The Royal Swedish Academy of Sciences stated that the laureates of the 2018 Nobel Prize in Chemistry had “taken control” of evolution and harnessed it for the benefit of humanity.

Directed evolution of enzymes has become a widely used method in academic research as well as in the chemical and pharmaceutical industries. The Royal Swedish Academy of Sciences stated, “We are in the early stages of a directed evolution revolution that will benefit humanity in many different ways.”

Currently, scientists are studying enzymes as potential substitutes for chemical catalysts, and many research institutions in China have already launched studies in this area. One company, Enzymaster, began researching this technology as early as 2013 and has already achieved certain results. This hard-tech company is Enzymaster.

Enzymaster, established in late 2013, is a technology-driven biotechnology company that provides comprehensive solutions for protein engineering and enzymatic biocatalysis.

Dr. Huang Yongkai, founder of Enzymaster, studied at the National University of Singapore, where he earned a Bachelor’s degree in Pharmacy and a Ph.D. in Medicinal Chemistry. After graduation, Dr. Huang served as the Head of the Singapore R&D Center at Codexis, a biocatalyst development company, and later as Deputy Director at Merck & Co.’s Singapore laboratory. “With over a decade of industry experience, I have led my team in developing more than 100 enzymatic projects for pharmaceutical giants such as Merck and Novartis, and filed 14 international patents, accumulating extensive expertise in R&D and industrialization within the enzyme catalysis sector,” said Dr. Huang.

Dr. Huang Yongkai, Founder of Enzymaster

During his work, Huang Yongkai discovered that many chemical production methods in the catalyst market could be replaced by biological approaches, which are greener, more environmentally friendly, and safer. Huang Yongkai explained, “In 2012, environmental issues gradually garnered increasing public attention, and we firmly believed that these concerns would continue to grow in importance. Our team’s enzyme-based technology can help alleviate environmental pressures. On the other hand, we observed strong market demand for enzymes; however, naturally occurring wild-type enzymes have limited catalytic capacity and cannot keep pace with the demand for synthetically produced compounds. As our team’s directed evolution technology has matured, it can fundamentally address the issue of insufficient enzymatic catalytic efficiency. Based on these two factors, we decided to establish Enzymaster.”

Enzymaster’s founding team consists of six members, five of whom hold Ph.D. degrees, while the sixth is responsible for marketing and business development. The five Ph.D. holders all previously worked at Codexis’s Singapore R&D Center, where they first connected. Among them, Dr. Thomas Daussmann brings over two decades of experience in entrepreneurship, R&D, and sales related to enzymes; his previous startup was acquired by Codexis, marking a successful exit. The team also includes Dr. Chen Haibin, a molecular biologist; Dr. Barry Sun, who oversees analytical chemistry and automation; Dr. Song Shiwei, who leads high-throughput enzyme screening; and Mr. Lü Zhenlin, who handles marketing and business development with extensive experience in the production and sales of pharmaceutical intermediates. Huang Yongkai stated, “Directed enzyme evolution is a broad discipline that is difficult for any single individual to master. However, we are a complete, complementary team capable of tightly integrating every aspect of this project. The combination of our technical team and our business team’s experience in the domestic market enables our technology to be applied and developed within the Chinese context while expanding internationally.”

In early 2014, Enzymaster was still a startup. It was a time when the “Internet Plus” initiative was gaining tremendous momentum and the national campaign of “Mass Entrepreneurship and Innovation” was sweeping across China. While entrepreneurs flocked to the internet sector, Enzymaster, as a biotechnology company, remained committed to building its technological platform. Huang Yongkai stated, “Our mindset was somewhat out of step with the prevailing trend at that time. When everyone was focused on internet-based ventures, our founding team had to exercise patience, resist temptations, and quietly establish our platform.”

Through perseverance, Enzymaster successfully established its directed evolution platform, BioEngine, in 2015.^®。

To understand directed enzyme evolution, it is essential to first recognize the importance of enzymes. Enzymes are vital biological catalysts—organic substances produced by living cells that exhibit catalytic activity, with the majority being proteins. The advantages of enzymatic catalysis in terms of environmental friendliness and efficiency have led to its widespread application in fields such as pharmaceuticals, agriculture, food processing, chemical engineering, and environmental protection. However, enzymes also possess certain limitations, including instability, narrow substrate specificity, and stringent reaction conditions.

Directed evolution is an in vitro enzyme engineering technique that has been successfully employed to enhance enzymatic activity, thermal stability, substrate specificity, and enantioselectivity. Enzymes generated through directed evolution can be utilized to manufacture a wide range of products, from biofuels to pharmaceuticals. One class of evolved enzymes serves as efficient and more environmentally friendly catalysts, capable of replacing metal and organic catalysts in the chemical and biotechnological industries. As directed evolution technology continues to advance, it is becoming a critical tool in new drug development and the optimization of pharmaceutical manufacturing processes. For instance, enzymatic catalysis can convert precursor substances into compound building blocks or generate optically active enantiomeric compounds with specific pharmacological effects. Furthermore, combining directed evolution with chemical synthesis methods enables the production of pharmaceutical intermediates via enzymes, which can then be further synthesized into active pharmaceutical ingredients (APIs).

Since the latter half of the 20th century, the fine chemical and materials industries have developed rapidly, with a continuous emergence of new synthetic compounds such as novel molecular materials, pharmaceuticals, and pesticides. While there has been a dramatic increase in substrates with artificial structures, nature lacks the enzymes to catalyze their synthesis, making artificial enzymes an inevitable choice. Huang Yongkai stated, “Many industrial processes require catalysts, which are currently mostly non-biological, such as metals like copper, nickel, molybdenum, and chromium, along with their compounds. This causes serious environmental pollution and can even lead to poisoning. Furthermore, enzymes offer advantages over non-biological catalysts in terms of reaction conditions, reaction rates, and selectivity. However, the major challenge plaguing the industry is the acquisition of enzymes. This ‘difficulty in acquisition’ does not refer to difficulties in the enzyme production process itself, but rather to the challenge of obtaining enzymes suitable for industrial-scale application, leaving market demand unmet.”

The market demand for artificial enzymes is substantial, and directed evolution platforms represent one of the key approaches to addressing enzyme limitations. Huang Yongkai stated, “Directed evolution can fundamentally resolve enzyme deficiencies. The BioEngine® platform mimics the process of natural selection, enabling proteins to evolve in ways desired by humans. Directed evolution can enhance enzyme stability and activity, alter enzyme specificity, and reduce the costs of enzymatic catalysis, making it currently the most promising approach for improving protein performance.”

Enzymaster’s independently developed directed evolution platform, BioEngine®, reduces the development cycle by more than 50% compared to traditional protein engineering methods, with a success rate exceeding 90%. When discussing the company’s competitiveness, Huang Yongkai remained modest: “Our partners in Europe and the United States have evaluated our technology platform as being on par with international standards.”

Enzymaster boasts a diverse enzyme library, including ketoreductase, transaminase, hydrolase, and oxidase libraries. By optimizing analytical methods, Enzymaster screens for suitable initial enzymes to determine their activity and selectivity. Based on the screening results, Enzymaster evaluates the feasibility of industrialization and the subsequent R&D investment required.

Enzymaster has not only developed a directed evolution platform but also established an industrialized enzymatic platform, achieving large-scale enzyme production and the industrialization of enzymatic catalysis processes. Currently, Enzymaster manages multiple collaborative product pipelines spanning various stages, including product evaluation, preliminary experiments, R&D, pilot-scale trials, manufacturing, and optimization. The production capacity of its partner factory network ranges from ten-ton to thousand-ton scales.

In 2018, Enzymaster produced and sold more than 300 tons of products. Huang Yongkai revealed, “One of our products holds a market share exceeding 50%. We plan to continue investing in the pharmaceutical sector, aiming for Enzymaster to gain significant influence in this market as newly launched collaborative products are introduced and the market matures.”

Regarding profitability, Enzymaster primarily relies on R&D services and product operations. The significance of R&D services lies in validating the platform’s technical capabilities and serving a cohort of major domestic and international clients. Revenue from product operations is growing rapidly and represents the key driver for future revenue and profit growth. Enzymaster incurred substantial costs in the early stages to build its technology platform; these advantages will become evident during the later industrialization phase, with greater economies of scale leading to more pronounced competitive benefits.

Regarding future plans, Huang Yongkai stated, “We will remain true to our original entrepreneurial mission, which is to bring greener and more efficient biocatalytic methods to the market through our technology. In the future, we will engage in deeper collaborations with more enterprises to industrialize our technology. Currently, our primary partnerships are with manufacturing facilities, but we do not rule out strengthening cooperation with companies through joint ventures in the future.” Additionally, Enzymaster is building intelligent software capabilities and enhancing automated hardware capabilities in R&D. On the business front, Enzymaster aims to diversify its sources of fine chemical products and expand into new fields such as materials chemistry.

According to the VCBeat database, Enzymaster received Series A investment from Fortune Capital and Oriental Fuhai in late 2017. Additionally, Enzymaster was granted approximately RMB 11 million in funding under the “Ningbo 3315 Plan” in 2014.

Codexis, a U.S. company, is regarded as a leader in the field of directed enzyme evolution. Leveraging its CodeEvolver technology platform, the company rapidly develops and produces highly optimized proteins to meet the needs of industries such as food, biopharmaceuticals, and fine chemicals. Currently, Codexis has established deep collaborative partnerships with renowned pharmaceutical companies including Novartis, GSK, and Merck & Co. The company was listed on the NASDAQ in 2010, and as of early August 2019, its market capitalization was approximately $1.02 billion.

It is worth studying whether China will see the emergence of similar hard-tech companies amid industrial upgrading.