In the stage of exploring the topic of our project, we visited our PI, Prof. Jiong Hong. Prof. Jiong Hong is a professor in our School of Life Sciences, and has made great achievements in the field of synthetic biology.

During the conversation, he mentioned that recently he had been leading several students to do research related to designing biosynthetic pathways. But a problem occurred that there is often no proven enzyme readily available in the database to catalyze an unknown reaction. So they often had to do a lot of repetitive experiments based on their own knowledge and experience. This process tended to time-consuming and often clueless at the beginning.

However, existing software for predicting metabolic pathways often produced results that are not the type of response they wanted. Naturally an idea occurred to our mind that we may be able to do something to make the research process easier.

Fig.1 Communication with Prof. Jiong Hong

In late May, we USTC-Software and USTC participated together in the science and technology week held by our school. We set up a shed on the campus so that students could get closer to biology knowledge.

The participants were mostly middle and high school students from nearby schools, as well as elementary students. We helped them do hands-on experiments together and spread some knowledge about synthetic biology. They all showed great interest and some even asked us questions about it.

Fig.2 The students are taking part in our activities

After MEI was basically completed, we designed brochures about our project and related knowledge. The brochures provides a comprehensive overview of synthetic biology, from its development history, research content and practical applications. Besides, it also introduces the relevant knowledge of enzymes and enzyme kinetics we used in our project.

By distributing the brochures in USTC campus, we spread the basic knowledge of enzyme theory and synthetic biology to students, and received many positive feedbacks.

Fig.3 The booklet provides an overview of synthetic biology

Anhui Lianchuang Biological Medicine Co., LTD is committed to the efficient conversion of chiral ketones and alcohols. They had put a lot of effort into deep research in screening enzymes, and put this into large-scale industrial production. After communicating with their research leaders, we visited their factories and communicated with their researchers.

Knowing that we were developing a platform to predict screening enzymes and expected to use it in practice, They were delighted. They said that in practical industrial production, enzyme activity is an important factor to consider when screening enzymes. If the enzyme activity is not high, not only the product conversion rate is not high, it is also difficult to separate and purify the products after the reaction, which often leads to a lot of waste and high cost. In addition, the concentration of product isomers, enzyme stability and other factors also need to be considered.

We had a long conversation with their research leader. Naturally, we decided to incorporate more practical considerations into the original software. For example, using enzyme kinetics, we decided to add the activity of the enzyme to the standard of evaluating the quality of the results.

Fig.4 visiting to Anhui Lianchuang Biological Medicine Co., LTD

Through the online sharing during CCIC, we learned that the project of Tongji-Software from Tongji University is to predict antiCRISPR protein. And our team developed a platform to screen and predict the enzyme. So we thought we could communicate and discuss on specific search and prediction algorithms. But due to the impact of the epidemic, the cost of offline communication increased, so we decided to communicate online with them.

We hosted an online meetup with Tongji-Software, and we introduced the project to each other in detail. We shared the modeling ideas and prediction algorithms and members of both teams discussed the specific algorithms used and the flaws. The Tongji-Software team provided us with many valuable suggestions to make our software more stable and robust.

Fig.5 Online meeting with Tongji-Software

Although we have done a lot of research, it is not clear what researchers in synthetic biology-related fields actually need when they use the software Therefore, we approached Senior Cao from the School of Life Sciences. He had represented the school in the IDEC International Directed Evolution Competition and got good marks for his project on improving key enzymes in metabolism.

We showed him the platform we have built so far and its functional implementation. Mr. Cao was very satisfied with the interactive interface of our platform and thought it basically met the need of users. We also explained the algorithm basis of our project to him. After listening to it, Mr. Cao thought that there would be a big boost if we take both auxiliary reaction and coupling reaction into consideration. We appreciated his suggestion and decided to incorporate those reactions into our software.

After the first period of building our project, we invited NNU to test our tools. They used our platform, made predictions, and compared our results with the enzyme that they actually used. Besides, they gave us a lot of advice on how to upgrade our program. They said we had a very friendly UI; with simple and clear input interface.

They believe that our platform can greatly improve the efficiency of enzyme screening and has strong practicality. Also, they gave us some feedback that we still had some defects, and gave us some advice. The screening of our platform is established in brenda database, which is highly dependent and only limited to the case that substrate and product differ by one group. They suggested the screening range should be further improved to achieve accurate positioning. We sincerely appreciate their feedback.

Team USTC has always been enthusiastic to help us test our tool and improve our project.

In addition, due to their project, which is to select the most productive enzyme after transfection, we invited them to test our platform. They tested their manual screening results of enzymes on our website and confirmed their choice.

After that, they also retrieved several similar enzymes with equal function and predicted some enzymes for future research During the test, they also suggested a lot of improvements to our project, such as adding some common protection groups on the input interface and adding a button for users to design groups themselves.

During our visit to Anhui Lianchuang Biological Medicine Co., LTD, we discussed with the researchers about enzyme screening. And they were approved to provide us with the data information of their industrial enzymes and reactions that had been put into mass production. And thanks to that, we can test our software and do better iterations.