Overview
In 2025, the YNNU-China team has adhered to the principle of “driving scientific innovation through societal needs,” insights from social research and expert interviews as the core driving force of our iGEM project. We conducted 27 rounds of social practice activities, focusing on the challenges and potential solutions for the heterologous biosynthesis of high-value plant natural products that promote human health. goal is to enhance the accessibility of natural product–based medicines and nutraceuticals, helping underprivileged populations gain access to effective treatments.
Fig. 1 Overview of the YNNU-China team's 2025 comprehensive human practice.
We reviewed disease reports, biomanufacturing policies, and company annual reports (Fig. 1 I). We then conducted expert interviews and questionnaires (Fig. 1 II) to identify health risks, industry pain points, and needs for protein design. We summarized the limits of existing tools and proposed a solution for adapting plant enzymes to microbial hosts. Based on expert input (Fig. 1 III),we developed REvoDesign (Rational Evolutionary-Involved Enzyme Redesign) as our tool (Fig. 1 IV).
Based on expert advice, we designed the first version of REvoDesign and analyzed potential test cases. Discussions with doctors, industry leaders, and professors helped define the tool’s application goals (Fig. 1 V–VI). We focused on two cases: (1) Engineering the bifunctional phytoene synthase/lycopene cyclase CarRP enzyme for efficient lycopene production in yeast, and (2) redesigning the paclitaxel pathway enzyme Taxadiene-5α-hydroxylase T5αH to boost catalytic activity in yeast. Both cases hold strong scientific and industrial value (Fig. 1 VII).
We analyzed case study results, invited experts and companies for evaluation, and gathered feedback for future improvements. Both scholars and industry praised the tool’s practicality and commercial potential. Using REvoDesign, we partnered with multiple research teams and, through the lycopene synthesis case, signed a strategic cooperation agreement with Hubei Meiqi Health Technology Co., Ltd., moving REvoDesign from lab research to industrial application (Fig. 1 VIII). This feedback will guide further refinement of the tool.
Inspiration
Global health faces major challenges. The UN Sustainable Development Goals call for reducing infectious diseases, lowering non-communicable disease mortality, and improving access to medicines and vaccines. Chemically synthesized drugs ensure stable production but depend on petrochemicals, create pollution, and burden the environment. Plant natural products are key sources of drugs and supplements, yet their complex synthesis, high costs, and long cycles keep prices high and limit access to healthcare.
Synthetic biology offers a green, sustainable way to produce natural products through microbial “cell factories.” This enables efficient, scalable, and low-impact production. Yet plant enzymes often show poor stability and low activity in heterologous systems, creating a major bottleneck. To overcome this, new tools are needed for rational design and adaptive modification, improving enzyme stability and activity to drive industrialization and support the UN Sustainable Development Goals.
Project background research
Health Organization Disease Reports
We analyzed major global health challenges to highlight the need for heterologous biosynthesis of plant natural products.
| Disease category | Global data | Research implications |
|---|---|---|
| Malaria（WHO《World Malaria Report 2024》） | With 263 million cases globally in 2023, malaria remains a major infectious disease burden worldwide | Artemisinin and its derivatives are potent drugs that can rapidly reduce the number of malaria parasites in the blood of infected patients. |
| Cardiovascular Disease (CVD)（WHF、NCCD、World Heart Report 2023） | In 2021, cardiovascular diseases caused 20.5 million deaths worldwide, making them the leading cause of mortality globally. Currently, there are 330 million patients with cardiovascular diseases in China. | Develop functional foods and medicines that can lower blood pressure and blood lipids from natural products, such as flavonoids, isoginkgetin, lycopene, etc. |
| Cancer（IARC《Global Cancer Statistics Report 2022》） | According to Global Cancer Statistics 2022, there were nearly 20 million new cancer cases and approximately 9.7 million cancer-related deaths worldwide. | Plant natural products represent a vital source of lead compounds for anticancer drug development, with paclitaxel and camptothecin being prominent examples. |
| Hepatitis （《Global Hepatitis Report 2024》） | An estimated 254 million people were living with hepatitis B globally in 2022, resulting in approximately 1.3 million deaths annually due to the virus. | Hepatitis B vaccine and drugs such as entecavir and tenofovir, as well as plant-derived alkaloids and phyllanthin. |
Tab. 1 Major infectious and non-infectious diseases that endanger human health and their treatment methods.
By reviewing global disease reports, we confirmed the key role of plant natural products in treating major diseases. Yet, their long production cycles, low yields, and high costs limit accessibility and universal healthcare. Many countries now promote synthetic biology in medicine, food, and agriculture, so we analyzed biomanufacturing policies to guide our project(Tab. 1).
Government biomanufacturing policy
- In 2022, China released its "14th Five-Year Plan for Bioeconomy Development" strategic report.
- In 2023, the United States released its "Bold Goals for U.S. Biotechnology and Biomanufacturing" strategic report.
- In 2024, the European Union released its "Building the Future with Nature: Boosting Biotechnology and Biomanufacturing in the EU" strategic report.
- In 2024, Yunnan Province, China released its "Fully Promoting the High-Quality Development of the Biomanufacturing Industry" strategic report.
Impact on us
Many countries, including Yunnan Province where our team is based, have issued policies supporting biomanufacturing. These policies provide context and application scenarios, prompting us to align our research with regional industry needs. We then focused on leading biomanufacturing companies to analyze their technical challenges and future strategies.
Corporate Annual Report Survey
To accurately identify industry pain points, we systematically analyzed the annual reports of Angel Yeast Co., Ltd. (stock code: 600298), Shanghai Pharmaceuticals Holding Co., Ltd. (stock code: 601607), Chenguang Biotechnology Group Co., Ltd. (stock code: 300138), Guilin Lain Biotechnology Co., Ltd. (stock code: 002166), and Anhui Huaheng Biotechnology Co., Ltd. (stock code: 68863), and sorted out the technology layout and market trends in the fields of biomanufacturing and plant natural products.
| Enterprise | Focus on Plant Natural Products | The demand and layout for synthetic biology |
|---|---|---|
| Angel Yeast Co., Ltd | Increased attention should be directed to the utilization of natural products (e.g.,yeast derivatives, nucleotides, peptides, and functional sugars) in food and health applications. | It is crucial to engineer yeast chassis with synthetic biology to boost metabolite production and drive the shift to smart bioproduction. |
| Shanghai Pharmaceuticals Holding Co.,ltd. | Focus on high-value active pharmaceutical ingredients (e.g., paclitaxel, artemisinin), active components of traditional Chinese medicine, and their modernization. | To address shortages of natural medicinal materials, synthetic biology must be applied to drug optimization and green manufacturing. |
| Chenguang Biotech Group Co.,Ltd. | The focus lies on natural pigments (e.g., capsanthin, lutein, lycopene, curcumin) and functional extracts. | Focusing on synthetic biology and heterologous synthesis is key to reducing extraction costs and resource dependence. |
| Guilin Layn Natural Ingredients Corp. | The core is natural sweeteners (mogroside, stevioside) and functional ingredients (tea polyphenols, flavonoids) | Actively explore the application of synthetic biology in the synthesis of sweeteners and scarce functional ingredients to ensure stable supply |
| Anhui Huaheng Biotechnology Co., Ltd. | Amino Acid Production, Bio-based Materials | There is a strong technical demand for enhancing key enzyme activity and chassis strain compatibility |
Tab. 2 Biomanufacturing Enterprise Annual Report and Technical Requirements.
Impact on us
Our analysis of biomanufacturing company reports shows a strong demand for enzyme engineering and pathway optimization tools, especially plant protein design and Artificial Intelligence-driven synthetic biology platforms. This guided us to focus on plant enzyme design, aligning with industry needs and aiming to solve key challenges and speed up product development(Tab. 2).
Protein design tool demand survey
To better understand the scientific issues behind the urgent need of biomanufacturing companies for efficient enzyme engineering and metabolic pathway optimization tools, we decided to connect with industry experts and scholars to explore the key technical points to achieve these goals.
Why choose to communicate with this expert?
Associate Professor Fuqing Wu(Tsinghua University)develops PHA biosynthetic strains, extraction processes, and applications. With Professor Guoqiang Chen, China’s first IMES awardee, he co-founded Beijing Weigou Workshop Biotechnology Co., Ltd and built China’s first 10,000-ton PHA production line.
What did we discuss?
We asked Professor Wu about the current state of the biomanufacturing industry, the challenges it faces, and future development recommendations, as well as his perspectives on enzyme design, modification needs, and modification tools(Fig. 2).
Fig. 2 Academic presentation and personal interview with Associate Researcher Fuqing Wu at Tsinghua University.
a. The team invited Professor Wu Fuqing to
give an online presentation.
b. Team members visited and learned about Tsinghua University's
synthetic
biology platform.
c. Team members took a group photo with Professor Wu Fuqing during their
interview.
How did these discussions influence our project plans?
Professor Wu helped refine our focus, guiding us to target pharmaceutical natural products and plant pigments/sweeteners. We aim to deliver key enzyme engineering and low-cost pathway optimization solutions to companies like Shanghai Pharmaceuticals, Chenguang Bio, and Lain Bio. Our goal is to make protein design tools a “bridge” from research to industry, shortening enzyme engineering R&D cycles.
Why choose to communicate with this expert?
Professor Qipeng Yuan (Beijing University of Chemical Technology) specializes in isolating, biosynthesizing, and applying natural active ingredients, making him an ideal expert on cell factory construction challenges.
Fig. 3 Team members attended an academic conference to study Professor Qipeng Yuan’s report.
What did we learn?
YNNU-China members attended Professor Yuan’s talk on cell factory construction and applications, identifying key challenges such as missing enzymes or low catalytic activity that limit product synthesis and efficiency(Fig. 3).
How did these discussions influence our project plans?
Professor Yuan identified the lack of key enzymes or poor catalytic activity as the main barrier to cell factory development. He stressed balancing basic research with technology transfer, reminding us to design projects with both academic value and industrial application in mind to maximize social impact.
Why choose to communicate with this expert?
Yuansheng Liu, engineer and Vice President of Yunnan Lishi Group, offered valuable market insights. Unlike our earlier focus on academic experts and reports, Lishi Group, a leader in agricultural processing and food manufacturing, provided practical industry perspectives.
What did we discuss?
Vice President Yuansheng Liu shared the market research methods for corporate products before project launch, namely the three major parts of consumer group characteristics analysis, market size and trend analysis, and brand competition landscape analysis.
How did these discussions influence our project plans?
We recognize that for research tools to be implemented, they must be closely aligned with real-world needs. Just as businesses target consumer groups through user profiles, we also need to conduct systematic research to identify industry needs and the strengths and weaknesses of competing tools in order to develop tools with practical application value. our tools can help promote greener and more efficient synthesis of natural products, they will meet the needs of businesses and society for healthy and sustainable development.
Literature Research
| PROSS | FuncLib | ProteinMPNN | |
|---|---|---|---|
| Crystal structure | YES | YES | No |
| Design site | Surface Backbone | Active Center |
Surface Active center Backbone |
| Library size | +++++ | +++++ | +++++ |
| Experimental burden | +++++ | +++++ | +++ |
| Dependance on computing resources | +++++ | +++++ | +++ |
| Time consumption | +++++ | +++++ | ++ |
| Computer knowledge | Few | Few | Many* |
| Major application field | Industrial enzyme for themostability | Industrial enzyme for themostability | Industrial enzyme for themostability |
Tab. 3 Comparison of protein design platform characteristics.
*Building your own service requires both strong computer and Rosetta knowledge. + represents the level, the more + represents the higher the level.
Through interviews with scholars, industry experts, and marketing directors, we identified the core barrier to industrialization: improving the activity and stability of heterologous enzymes(Tab. 3). We analyzed existing protein design tools, clarified their strengths and weaknesses, and designed questionnaires for the public and researchers to gather insights on heterologous synthesis, technical challenges, and expectations, ensuring our tool meets real scientific and industrial needs.
Questionnaire survey of the public and scientific researchers
We collected 204 valid responses, covering demographics, knowledge of biosynthetic drug ingredients, researcher needs, and acceptance of enzyme engineering tools. The survey audience matched our target users, supporting the social relevance of our project(Fig. 4). Key findings are as follows:
Fig. 4 Overview of YNNU-China questionnaire survey results.
a and b. Public attitude towards heterologous synthesis of natural products. c and d. Difficulties faced by researchers in heterologous synthesis of natural products. e and f. The need for protein engineering tools.
Public Perception and Project Value
In the trust and preference survey, 51.47% still trust wild medicinal plants, but “price” is the key factor (Fig. 4a). 77.94% would accept microbially synthesized products if they have the same efficacy but lower cost (Fig. 4b).
Research Needs and Protein Design
61.67% of researchers report low enzyme efficiency as their main challenge (Fig. 4c). Most rely on rational design (58.33%) (Fig. 4d), but only 26.79% have stable workflows. Key weaknesses of current tools are poor integration with experiments (36.67%) and complexity (25%) (Figs. 4e,f).
Survey-Backed Project Feasibility
The results confirm high public acceptance of biosynthesis and researchers’ demand for enzyme engineering tools, validating the project’s necessity. The survey’s alignment with our target audience and tool design further supports its feasibility.
Protein design technical consultation
Through policy analysis, enterprise research, expert consultation, and surveys, we identified low enzyme activity and poor stability as major bottlenecks in heterologous plant natural product synthesis. To address this, we interviewed Professors Yuan Zhou, Liu Haiyan, and Huang Bin, discussing strategies to improve plant enzyme performance through protein design tools.
Why choose to communicate with this expert?
Professor Yuan Zhou (Huazhong University of Science and Technology) specializes in heterologous enzyme design and modification for natural product biosynthesis, with extensive experience in pathway analysis and synthesis of complex products like cucurbitacin.
What did we discuss?
Research strategies for heterologous synthesis include pathway analysis, identification of rate-limiting enzymes, protein modification, and industrial feasibility evaluation. Associate Professor Zhou highlighted two major challenges: screening for rate-limiting enzymes and poor heterologous adaptability. He suggested combining co-evolutionary analysis with semi-rational modification to quickly locate optimal sites and reduce trial-and-error (Fig. 5).
Fig. 5 Interview with Associate Professor Yuan Zhou by the YNNU-China team.
How did these discussions influence our project plans?
The interview helped us realize that projects should cover the full chain—from pathway analysis to enzyme identification and expression optimization—rather than focusing on a single enzyme. Associate Professor Zhou also stressed considering “industrial value,” prompting us to evaluate both scientific difficulty and market potential when choosing target enzymes.
Why choose to communicate with this expert?
Professor Haiyan Liu(University of Science and Technology of China) has made major contributions to protein backbone design, function-oriented design, and AI model optimization. We consulted her to address the challenges of protein design and modification rules encountered in REvoDesign development.
What did we discuss?
Professor Liu reviewed the evolution of protein design, emphasizing the paradigm shift brought by AI—from fragment-based “building block” design to “de novo generation.” He warned that energy minimization does not always mean physical feasibility; energy functions should serve as quality checks, not optimization targets. He stressed that incorporating MSA (multiple sequence alignment) information is essential for maintaining enzyme activity, and that experimental validation remains critical because AI models still have biases. AI should be a powerful assistant, not a black box replacing scientists(Fig. 6). Key recommendations for our tool:
Function-Oriented Design – Add evolutionary conservation constraints during site screening to protect active sites, and combine function and stability predictions to avoid performance loss.
Multi-Dimensional Iteration – Use energy functions for late-stage verification, adopt cross-model screening, and form a DBTL (design-build-test-learn) loop for rapid iteration.
Fig. 6 Interview with Professor Haiyan Liu by YNNU-China team members.
How did these discussions influence our project plans?
Our next focus will be to enhance MSA integration to retain enzyme activity, streamline workflows by removing redundant preprocessing, improve interpretability and visualization for expert review, and add a “question-guided” module to help users set scientific modification goals.
Why choose to communicate with this expert?
Professor Bin Huang (Yunnan Normal University) is a rising leader in protein de novo design. His SCUBA tool, published in Nature, enables protein backbone design independent of natural templates. Since our project focuses on adapting plant-derived enzymes in microbes, involving backbone plasticity and local structural optimization, he was an ideal expert.
What did we discuss?
Professor Huang shared two key insights: Before optimizing mutations, assess whether the backbone’s catalytic efficiency has an upper limit. In the future, redesign the backbone at the domain or local level if needed.Combinations of single-point mutations may not have additive effects; nonlinear interactions must be considered. He recommended building a mutation-combination prediction module(Fig. 7).
Fig. 7: YNNU-China team interview with Professor Bin Huang.
a. Team members report on project plans and progress.
b. Professor Bin Huang offers
suggestions
for
the project.
c. Team members pose for a photo with Professor Bin Huang.
How did these discussions influence our project plans?
His advice expanded our perspective from local point mutations to backbone-level global optimization. We plan to introduce multi-model evaluation to raise design success rates. Professor Huang’s input helped us move beyond the narrow idea that “single-point mutations improve activity,” pushing Protein design tool toward becoming an intelligent, user-friendly platform for advanced protein design.
Development of the REvoDesign tool
Through interviews with experts and companies, we discovered common pain points: poor adaptability of plant-derived enzymes in the microbial chassis, the need to modify key rate-limiting enzymes, high research and development costs, and long experimental cycles. Therefore, our team developed a semi-rational modification workflow for key enzymes in plant natural products, along with an initial version of a visualization tool based on co-evolutionary analysis and rational protein design. The tool characteristically integrates computational tools with conserved and co-evolutionary data to engineer very limited residues from the protein surface and active center, achieving synergistic improvements in stability and activity with minimal experimental testing efforts, as well as alleviating epistasis effects due to spatially independent mutations (Fig. 8).
Fig. 8 REvoDesign program framework design.
Guided by the of "social responsibility as a core value of scientific design," the development of synthetic biology must not only pursue technological breakthroughs but also focus on practical impacts on human health, environmental sustainability, and social equity. Based on this, the team developed REvoDesign, a visualization tool for enzyme modification, with the core goal of addressing the difficulties, low yields, and high costs of obtaining high-value-added medicinal natural products. By enhancing the catalytic activity of key enzymes and the adaptability of microbial chassis, it promotes biosynthesis as an alternative to traditional production methods, embodying both technological innovation and social responsibility.
Plant products for treating diseases
To test REvoDesign’s ability to improve plant enzyme “fitness” in microbial systems and address real-world problems, we analyzed both biomanufacturing challenges and the global disease burden. We visited the clinical frontlines, interviewing cardiovascular and oncology doctors at Fuwai Yunnan Hospital(Chinese Academy of Medical Sciences) and Yunnan Cancer Hospital(Peking University Cancer Hospital Yunnan) to understand the clinical use and challenges of plant natural products.
Fig. 9 YNNU-China members interviewed doctors at cardiovascular disease hospitals.
| Research scenario | Key findings | Inspiration |
|---|---|---|
| Cardiovascular disease treatment(Fuwai Yunnan Hospital) | It mainly relies on chemical drugs such as nifedipine, atorvastatin, and aspirin, with food-drug homologs and natural products as auxiliary interventions. | Antioxidant products such as anthocyanins and carotenoids can be used for personalized intervention. |
| Cancer treatment(Yunnan Cancer Hospital) | Plant-derived products are highly effective in tumor treatment but have significant side effects and individual differences. | Focus on products such as taxanes, vinca alkaloids and camptothecin. |
| Drug accessibility issues | Paclitaxel drugs and antioxidant natural products are difficult for patients to use due to their high prices. | Microbial synthesis of high-value natural products can alleviate patients' difficulties in taking medication. |
Tab. 4 Hospital field research and inspiration.
What did we discuss?
These interviews provided first-hand insights into drug therapy, food-drug homologous interventions, and the potential of synthetic biology for drug production(Fig. 9). Doctors highlighted that many patients abandon treatment due to high drug costs, echoing the UN Sustainable Development Goals and our survey findings(Fig. 10).
Fig. 10 YNNU-China members interviewed doctors at the cancer hospital
a. Q&A interview with a doctor.
b. Group photo of team members at the cancer hospital
How did these discussions influence our project plans?
Based on this research, we selected high-value natural products for cancer and cardiovascular treatments as optimization targets(Tab. 4). Using REvoDesign, we aimed to enhance their expression and catalytic efficiency in microbial chassis, validating the tool’s usability and practical value.
During hospital research, we learned about differences in individualized treatment and drug side effects. To better understand these issues, we consulted experts on human health and immunity to explore the links between diseases, drugs, and individual response differences, and shared this knowledge to raise public health awareness.
Why choose to communicate with this expert?
Researcher Yancong Zhang (Agricultural Genomics Institute at Shenzhen, CAAS) studies functional annotation of microbial “dark genes” and the interactions between microbiota, drugs, and immunity.
What did we discuss?
She emphasized that the microbiome shapes drug metabolism and immune responses, engineered bacteria face colonization and safety challenges, and individual microbiome differences drive the development of precision medicine(Fig. 11).
Fig. 11 YNNU-China team interviews researcher Yancong Zhang.
How did these discussions influence our project plans?
This interview has promoted the dissemination of knowledge about disease treatment and individual differences. We should focus on the needs of biomanufacturing companies, and projects should focus on improving the catalytic activity of plant-derived enzymes.
Early reports, hospital visits, and expert interviews confirmed the clinical value of plant natural products and identified poor heterologous enzyme expression and low catalytic activity as key bottlenecks. To ensure REvoDesign meets real-world needs, we studied industry requirements, regulatory standards, and commercialization barriers. At the 9th China-South Asia Expo, we visited KPC Pharmaceuticals, Yunnan Phyto Pharmaceutical, and Kunming LongJin Pharmaceutical to discuss biosynthesis prospects with senior executives and technical experts(Fig.12 and 13).
Fig. 12: YNNU-China members communicate with KPC Pharmaceuticals Group staff.
a. Team members introduce the project and corporate development consultation.
b. Team members pose
for a group photo with Kunming Pharmaceutical Group.
| Research topics | Enterprise feedback | Inspiration for us |
|---|---|---|
| Current status of drug production and raw material supply | The company has a full production and supply chain. Raw materials are mainly from planting and procurement, and costs are relatively low. | Focus on whether biosynthesis can truly beat planting in cost to ensure industry adoption. |
| Attitude towards biosynthesis | The companys is developing biosynthesis projects (e.g., Breviscapine, Notoginsenoside, Artemisinin) and sees it as the future trend. | Confirmed strong market demand, boosting our confidence. |
| Market acceptance and regulatory barriers of microbial plant products | Companies stress strict pharmacopeia standards for source and composition. Biosynthetic drugs must pass traceability checks and clinical trials, which take time. | Ensure our designs support traceability and meet compliance needs. |
| Cost and commercial potential | Efficient biosynthesis can cut costs and boost efficiency, but must keep efficacy, earn trust, and meet regulations. | Strengthened our focus on “quality consistency” and “standardized verification.” |
| Feedback on REvoDesign | The technical director affirmed our focus on enzyme activity and adaptability, saying it can shorten early screening. | Encouraged us to improve the tool interface and user experience. |
Tab. 5 Research and inspiration on plant product pharmaceutical companies.
Fig. 13 YNNU-Chian members interact with Yunnan Phyto Pharmaceutical, and Kunming LongJin Pharmaceutical.
a. Team members discuss with pharmaceutical company representatives
a. Team members introduce their projects and consult with the companies on their technical development
needs, their attitudes toward, and plans for, heterologous natural product synthesis.
b. Team
members
pose for a group photo after interacting with company executives.
How did these discussions influence our project plans?
REvoDesign aims to boost catalytic efficiency, reduce byproducts, and generate traceable records for drug registration. We are optimizing the interface and modular outputs to help companies quickly identify candidate mutations and shorten R&D cycles. Future testing will focus on purity, byproduct profiles, and alignment with pharmacopoeial standards to guide regulatory compliance(Tab. 5).
Regarding the selection of high-value natural products, pharmaceutical companies recommended that we select single products with large market scale and high product value as case studies for tool application. To gain diverse insights, we conducted in-depth research on high-value natural products at research institutes, universities, and Fortune 500 companies.
High-value plant product research
Why choose to communicate with this expert?
Yunnan, known as the "Kingdom of Plants," has unique geography and climate, making it a key hub for Chinese medicinal materials. To explore high-value plant products for our project, we visited the Institute of Medicinal Plants at the Dali Academy of Agricultural Sciences and held discussions with Director Kunhong Yang and his team.
Fig. 14 YNNU-China members visit the medicinal plant resource garden of the Dali Academy of Agricultural Sciences.
a b c Members visit the germplasm resource garden. d Books on specialty medicinal plants and management techniques published by the Dali Academy of Agricultural Sciences.
What did we discuss?
Northwest Yunnan hosts valuable herbs like Paris polyphylla , Taxuschnensis var. mairei , and Fritillaria thunbergii . Wild varieties often contain higher levels of active metabolites than cultivated ones, highlighting the challenge of resource scarcity(Fig. 14). Heterologous synthesis of key active ingredients may offer a solution(Fig. 15).
Fig. 15 YNNU-China members present their project at the Dali Academy of Agricultural Sciences.
a. Team members introduce the REvoDesign tool.
b. Team members pose for a group photo with the
Dali
Institute of Medicinal Plants.
How did these discussions influence our project plans?
This study helped us identify potential research targets and pathways, with well-studied species such as Taxuschnensis var. mairei, Angelica sinensis, and Fritillaria thunbergii providing a basis for future enzyme engineering and drug development efforts.
Why choose to communicate with this company?
Shanghai Pharmaceuticals Holding Co., Ltd. is a leader in Chinese yew cultivation and paclitaxel industrialization, covering planting, processing, and sales. We investigated the paclitaxel raw material supply chain to identify challenges and trends, providing industry context for selecting enzyme-modification tools to boost production efficiency.
Fig. 16 Visiting the planting base of Shanghai Pharmaceuticals Holding Co., Ltd.
a Yew forest (aerial view). b Yew plants. c The company's yew primary processing plant. d Yew fruiting.
What did we discuss?
The company extracts Baccatin III from yew for paclitaxel semi-synthesis but faces long growth cycles and unstable yields(Fig. 16). Manager Cao encouraged leveraging Yunnan’s unique metabolites and synthetic biology to improve Baccatin III production, aiming for cost, performance, and safety advantages while promoting industry-academia-research collaboration (Fig. 17).
Fig. 17 YNNU-Chian team members communicate with General Manager Feng Cao.
These insights guided us to focus on enhancing Baccatin III synthesis and validating REvoDesign using paclitaxel’s rate-limiting enzyme. We will emphasize scalability and industrial adaptability, collaborate with companies to collect production data, and develop REvoDesign into a standardized, easy-to-adopt industrial tool.
Why choose to communicate with this expert?
Professor Min Xu (Kunming University of Science and Technology) ocuses on molecular discovery, structural engineering, and innovative drug development from southwestern ethnic medicinal resources. Her team’s plant-based small-molecule anti-HBV drug Phyllanthus urinariae is entering preclinical trials. We sought her feedback on REvoDesign and potential collaboration opportunities.
Fig. 18 YNNU-China members report their projects to Professor Min Xu and interview experts.
What did we discuss?
Professor Xu shared her strategy of combining Structure-Based Molecular Networking (SBMN) and Nature Fragment-Based Drug Design (NFBDD) to accelerate natural molecule discovery and modification, successfully identifying novel anti-HBV leads. She highlighted the importance of a “precise search + efficient modification” closed loop for new drug discovery.
She noted that REvoDesign complements her upstream molecular discovery work. Although the biosynthetic pathway of phyllanthrin is still unclear, she expressed interest in future collaboration on key enzyme modification and large-scale production, helping translate Yunnan’s unique medicinal resources from lab to industry(Fig. 18).
How did these discussions influence our project plans?
Inspired by her metaphor of a “hotbed,” we plan to build a multi-stage validation pathway, positioning REvoDesign as both a research tool and a bridge for real-world application.
Why choose to communicate with this expert?
Associate Professor Aili Zhang (Yunnan University of Chinese Medicine), an expert in TCM health product development, has extensive experience in discovering and synthesizing active ingredients from traditional Chinese medicine. She helped us identify key scientific issues from both academic and industrial perspectives.
What did we discuss?
TCM active ingredients are complex secondary metabolites with long synthesis pathways. Steps like hydroxylation and glycosylation are major bottlenecks. Engineering microbial synthesis can improve accessibility and lower costs, but breakthroughs are needed in key enzyme analysis, multi-gene expression optimization, and robust industrial production to advance TCM modernization(Fig. 19).
Fig. 19 Interview with Associate Professor Aili Zhang by YNNU-Chian members.
How did these discussions influence our project plans?
Her feedback sharpened our focus on key enzyme analysis and optimization, highlighting that REvoDesign’s value lies in precisely modifying difficult enzymes such as P450s and UGTs for efficient heterologous expression. We realized that true industrial breakthroughs require integrating REvoDesign with pathway optimization, multi-gene coordination, and chassis engineering to build a closed-loop system from design to production.
Why choose to communicate with this expert?
Professor Junbo Gou (Hubei University of Chinese Medicine), first author of the Taxuschnensis var. mairei genome sequence, researches synthetic biology, drug development, and functional botanical products. Our discussion aimed to understand key challenges in synthetic biology, identify rate-limiting enzymes in T. chinensis, and assess REvoDesign’s practical value and collaboration potential.
What did we discuss?
Industrialization of plant natural product biosynthesis prioritizes yield, purity, and cost. Future breakthroughs will rely on AI-assisted enzyme design, organelle engineering, and genome-scale metabolic optimization. P450 enzymes remain the main bottleneck in paclitaxel synthesis. Optimization requires both external chaperone enhancement (e.g., CPR, b5, cofactor supply) and internal improvements to transmembrane regions, substrate access, and surface properties to boost folding and catalytic efficiency(Fig. 20).
Fig.20 YNNU-Chian members interviewed Professor Junbo Gou.
How did these discussions influence our project plans?
Microbes lack paclitaxel precursors such as baccatin III, and the first rate-limiting step involves taxadiene synthase (TS) and taxadiene-5α-hydroxylase (T5αH), the latter having low catalytic activity. Inspired by Professor Gou, we will apply REvoDesign to P450 enzymes in paclitaxel biosynthesis to showcase its broad applicability and contribution to industrialization.
To ensure our REvoDesign tool meets real industry needs, we interviewed numerous institutions and experts to explore the challenges of heterologous synthesis and commercialization of high-value plant natural products. The industry's key pain points are bottlenecks in key enzymes. Paclitaxel has a long pathway with numerous bottleneck enzymes, particularly P450 enzymes (such as T5αH), which exhibit poor activity in heterologous hosts, creating obstacles to heterologous synthesis. Similar challenges exist in the nutritional and health industry, for example, where the substrate specificity and catalytic efficiency of cyclases in the lycopene biosynthesis pathway affect lycopene production. Experts recommended avoiding a focus on a single product and emphasized the need for tools to be universal and scalable, applicable across diverse plant natural product pathways.
We selected lycopene (nutrition and health) and paclitaxel (pharmaceuticals) as case studies to demonstrate REvoDesign’s broad applicability. Lycopene offers fewer regulatory hurdles and high industrial value, while paclitaxel addresses major medical needs.
After tool development and validation, REvoDesign successfully improved the catalytic efficiency of T5αH and lycopene cyclase, providing a new technical path for efficient natural product synthesis. We then revisited our academic collaborators ( China Agricultural University, Beijing University of Chemical Technology ) and consulted protein design experts and industry scholars to evaluate results, refine functionality, and explore future applications.
Evaluation and Feedback
Why did we choose to talk to this company?
Chenguang Biotech Group Co.,Ltd is a global leader in plant extracts, dominating the market for lycopene, lutein, and capsaicin. We chose Chenguang because its industrial needs align closely with our project. Its expertise in process scale-up, quality control, and market access offered a real-world testing ground for REvoDesign.
Fig. 21 YNNU-Chian members visit the R&D center of Chenguang Biotechnology.
a. Dr. Hao Wang introduces the development history of Chenguang Biotechnology.
b. Team members
visit
the company's layout in the field of natural product utilization.
What did we discuss?
Chenguang Biotech Vice President shared the company’s strategy to expand into medicinal plant extracts and health foods(Fig. 21). We presented REvoDesign’s successful application in modifying lycopene cyclase and taxol P450 (T5αH) through co-evolutionary analysis and precision mutation libraries. Technical discussions covered carbon source utilization, culture optimization, product calibration, and conversion rate improvements in Yarrowia lipolytica, aiming to cut costs and boost efficiency(Fig. 22).
Fig. 22 YNNU-Chian team members present project to Chenguang Bio executives.
a. REvoDesign tool progress report.
b. Team members pose for a group photo with Chenguang Bio
executives.
Evaluation of projects and tools and intended cooperation
REvoDesign Evaluation
Vice President Wei Gao and Dr. Hao Wang praised REvoDesign for its clear innovation, interpretability, and ability to solve key industry pain points, particularly in enzyme adaptability and reducing high-throughput screening costs.
Collaboration Intentions
Chenguang expressed strong interest in collaborating with YNNU-China to optimize key enzymes for lycopene synthesis, validate the modified cyclase pathway in pilot production, and explore heterologous synthesis for other high-value natural products.
Why did we choose to talk to this company?
Hubei Meiqi Health Technology Co., Ltd is a comprehensive enterprise integrating R&D, incubation, industrialization, and commercialization of health and medical beauty products. We chose to engage with them because of their comprehensive R&D, industrialization, and market transformation capabilities in the healthcare industry and functional ingredients, providing real-world industry demand scenarios for our REvoDesign tool.
What did we discuss?
During the visit, we introduced REvoDesign’s development background, design principles, and applications, highlighting its success in modifying paclitaxel’s key enzyme T5αH and lycopene cyclase. Together with the company’s management and technical teams, we discussed applying REvoDesign to functional health ingredients, covering target selection, base-strain optimization, pilot-scale transition, and potential patent strategies.
Fig. 23 The YNNU-China signed a project cooperation agreement with Hubei Meiqi Health Co., Ltd.
Evaluation of projects and tools and intended cooperation
Hubei Meiqi expressed strong interest, recognizing REvoDesign’s ability to address poor heterologous enzyme compatibility and low catalytic efficiency, lowering costs and improving product competitiveness. This led to a three-party collaboration agreement with Hubei Meiqi, our team, and the Institute of Agricultural Genomics, CAAS(Fig. 23). We will jointly conduct pilot research and strain optimization, while the company will handle scale-up and process development, establishing a clear path for patents, tech transfer, and commercialization.
Why choose to communicate with this expert?
We invited REvoDesign’s first users for follow-up feedback. Doctoral students Wenjie Geng and Jiannan Shi from Associate Professor Feng Jiang’s team( China Agricultural University ) represented advanced and beginner protein engineering researchers, helping us evaluate the tool from different user perspectives.
What did we discuss?
Users praised REvoDesign’s efficiency and educational value. Jiangnan Shi suggested goal-oriented guides, tiered versions (basic/advanced), and video tutorials to lower the learning curve. Wenjie Geng recommended improving stability, optimizing error feedback, and creating a user-developer communication platform to support continuous updates(Fig. 24 and Tab. 6).
Fig. 24 YNNU-China team members visit REvoDesign users.
a. Answering user questions. b. User and team members pose for a photo.
How did these discussions influence our project plans?
| User feedback | Improvement measures | Impact on the project |
|---|---|---|
| Purpose-oriented user manual | A guide to research goal-driven | Lower the learning threshold and help more beginners get started |
| Simple/advanced version | Design layered functional interface | Expand the audience of the tool (classroom teaching/research work) |
| Tutorial Video | Create a short video demo and embed it in the wiki and tool homepage | Shorten the learning time cost of new users and improve promotion efficiency |
| Error feedback mechanism | Enhance error reporting and add log download function | Improve tool stability and reduce user frustration |
| Technical exchange platform | Plan to establish a WeChat group/forum to collect user suggestions | Form a two-way interaction between developers and users to promote continuous upgrading of tools |
Tab. 6 REvoDesign user usage follow-up survey.
Why choose to communicate with this expert?
Professor Xiaolin Shen (Beijing University of Chemical Technology) specializes in synthetic biology and metabolic engineering, focusing on efficient biosynthesis of aromatic compounds. As an early REvoDesign user, he offered valuable feedback on its scientific and industrial applications.
What did we discuss?
Professor Shen emphasized that enzyme engineering is the most direct and cost-effective way to overcome the “feasible in lab but hard to scale up” bottleneck. She affirmed REvoDesign’s efficiency, noting that 27% of candidate mutants for acetaminophen biosynthesis outperformed the wild type, with the best showing a 68% activity increase, significantly reducing screening effort. She suggested adding multi-objective optimization ( activity, stability, solubility ) and multi-enzyme modeling to improve pathway balance and intermediate transfer. She also recommended better visualization, adjustable parameters, and clearer evaluation metrics. She stressed focusing on design logic during early research and cost/yield during industrialization.
| Expert feedback | Improvement measures | Impact on the project |
|---|---|---|
| Enhance protein multi-objective optimization capabilities | Introducing a comprehensive scoring module for activity, solubility, and stability in REvoDesign | Make the tool closer to real production needs and help obtain more comprehensive and usable mutants |
| Adding a multi-enzyme system perspective | It is planned to integrate multi-enzyme collaborative modeling function in the next iteration | Enables tools to assist in the optimization of multi-step cascade reactions and improve the overall yield of the pathway |
| Improved user experience and visualization | Added candidate mutant heat map, score ranking table, and optimized error prompts | Improve the analysis efficiency of scientific researchers and shorten the cycle from design to decision-making |
Tab. 7 REvoDesign user usage follow-up survey-Professor Shen.
How did these discussions influence our project plans?
She feedback clarified REvoDesign’s future direction: balancing scientific exploration with industrial needs, supporting both early-stage research and reliable industrial design. The next phase will emphasize multi-objective and multi-enzyme optimization, enhancing the tool’s universality and making it an “accelerator” for synthetic biology applications(Tab. 7).
Why choose to communicate with this expert?
Associate Researcher Yuan Liu (Peking University) studies computational biology and protein design. We interviewed him because REvoDesign aims to offer modular, low-threshold tools for semi-rational enzyme design by combining classical and AI-driven approaches for both efficiency and reliability.
What did we discuss?
Yuan Liu highlighted REvoDesign’s value in enzyme evolution and recommended using active learning to optimize iterative paths. He stressed that semi-rational design remains promising but needs experimental feedback for model calibration. He also emphasized the potential of natural language interfaces for conversational design, which could improve usability and success rates. While AI boosts efficiency, he noted that physical models like Rosetta remain essential for mechanistic interpretation.
How did these discussions influence our project plans?
From this discussion, we concluded that REvoDesign should integrate machine learning with physical energy functions for speed and interpretability, support active learning, and provide natural language interfaces and visual documentation. Semi-rational design should bridge de novo design and high-throughput screening, enabling low-cost, rapid iteration. These insights guided us to position REvoDesign as an “intelligent, interpretable, and low-threshold” platform that bridges computation and experiment.
Why choose to communicate with this expert?
Professor Long Liu (Jiangnan University) specializes in synthetic biology and food biomanufacturing. He has advanced the industrial production of functional sugars, vitamins, and milk oligosaccharides, and built collaborations with 30+ leading companies. We sought his advice to refine REvoDesign and accelerate application.
What did we discuss?
We presented REvoDesign to Professor Liu. The tool uses coevolutionary analysis and rational design to build precise, small-scale mutant libraries, reducing dependence on high-throughput screening. It has successfully optimized lycopene cyclase and paclitaxel P450 enzyme T5αH. Professor Liu recognized its potential to bridge research and industry. He recommended prioritizing efficient metabolic pathways, using QM/MM analysis to reveal molecular mechanisms, and focusing on scalability and cost control to meet industry needs(Tab. 8 and Fig. 25).
How did these discussions influence our project plans?
| Expertfeedback | Improvementmeasures | Impactontheproject |
|---|---|---|
| Prioritize synthetic pathways with low energy consumption and short steps | Perform metabolic flux analysis on the lycopene and paclitaxel pathways, evaluate pathway efficiency, and prioritize reconstruction of short pathway versions | Improve the overall productivity of cell factories, reduce energy burden, and lay the foundation for future industrial expansion |
| Introducing QM/MM calculations to explain mutation mechanisms | We plan to integrate the QM/MM calculation module in subsequent iterations to conduct mechanistic analysis of the key mutations recommended by REvoDesign. | Enhance the interpretability of design results, improve the persuasiveness of scientific research papers and the academic influence of tools |
| Focus on industry orientation while taking into account feasibility | Incorporate industry indicators such as output, stability, and raw material costs into tool optimization goals | Make REvoDesign design results more practical and meet the actual needs of food and drug production |
Tab. 8 REvoDesign user usage follow-up survey-Professor Liu.
Fig. 25 YNNU-China team members report project progress to Professor Liu Long.
a and b. Report the project progress to Mr. Liu Long and listen to his comments and feedback on REvoDesign. c. Team members take a group photo with Mr. Liu Long.
Conclusion
Through research and expert interviews, we identified key bottlenecks in heterologous natural product synthesis and used them to guide the development of REvoDesign, a co-evolution-driven enzyme engineering tool. REvoDesign has already optimized paclitaxel T5αH and lycopene cyclase, gaining strong recognition from experts and industry partners. It offers a new path for green, efficient natural product synthesis and expands the role of synthetic biology in advancing health and sustainability.