(3ga) Development of a Systematic and Rational Design Approach for Antibody-Antimicrobial Peptide-Linked Therapeutics

I have extensive experience in protein design and engineering and mechanistic study for biological systems using both computational and experimental approaches. In my doctoral and postdoctoral research, I gained experience in performing molecular dynamics (MD) simulations, machine learning and mutagenesis methods to engineer therapeutic proteins including antimicrobial peptides (AMPs) and antibodies. I have published significant research papers in the area of protein engineering and molecular modeling. In addition, I have a solid foundation in statistical thermodynamics, mathematical modeling and physics from my engineering training. I also have a strong ability to collaborate on interdisciplinary research projects with academia and industry. My ultimate goal is to combine computational and experimental approaches for designing novel therapeutic protein modalities to treat infectious diseases.

The emergence of antimicrobial resistance is a crucial public health problem. AMPs are promising alternatives to traditional antibiotics. One of the most desirable advantages of AMPs is that bacterial resistance would evolve much more slowly than against antibiotics. However, AMPs can exhibit undesirable properties as drugs, including short circulating half-life, poor stability and toxicity to animals and humans. The AMP therapeutics development is still hindered by several challenges including potential toxicity to animal cells, high manufacturing cost, and lack of a robust guideline for rational design. Therefore, novel approaches are needed to be developed to make AMPs less toxic for human while maintaining or improving their potency to eliminate bacteria and reduce the production cost.

Monoclonal antibodies (mAbs) have been used as therapeutic drugs for over 30 years. The majority of mAbs approved or in clinical trials are for the treatment of cancer or rheumatic diseases. In contrast, only three antibacterial mAbs have been approved for infectious diseases. The small number of antibacterial mAbs is surprising because it is well known that antibodies are induced through natural infection to attack bacteria. This could be due to the success of small-molecule antibiotics, obviating the need to develop alternative therapeutics, or lack of economic incentive to the pharmaceutical industry. As antibiotic development slows down, antibacterial antibodies have attracted renewed interest. The long biological half-lives and high specificity of antibodies are remarkable advantages.

Despite their therapeutic potential, multiple challenges need to be overcome. First, proper selection of bacterial targets remains with a lot of challenging uncertainties. The highly conserved outer membrane proteins may be masked by exopolysaccharides, impeding mAb binding. Although mAbs can bind to exopolysaccharides, their epitopes are not typically conserved. This requires designing multiple mAbs to bind to a variety of bacterial serotypes. Second, most mAbs do not exhibit direct bactericidal activities and rely on the involvement of the host immune system. This could lead to undesirable inflammatory responses and complex pharmacokinetics and pharmacodynamics behaviors. Third, the production cost for mAbs is very high, and the stability of mAbs varies, making the developability assessment difficult in early stage design.

With my experience with AMPs and antibodies, my research goal is to combine the benefits of both types of biomolecules to overcome their weakness. The goal of my future research program is to genetically engineer antibody-AMP fusion proteins to target bacteria. The antibodies are used to deliver highly potent AMPs to the targets with high specificity, and to reduce the risk of off-target toxicity. In addition, these fusion proteins exert antimicrobial activities through AMPs and do not require antibodies to be bactericidal, avoiding the need for inducing host immune response. This construct also increases the half-life of the AMPs. The antibodies and AMPs are both proteins; therefore, recombinant DNA techniques can be applied to produce fusion proteins, preventing costly chemical synthesis.

Three projects will be conducted. The first project is the engineering and characterization of the fusion proteins. The fundamental problem in this project is how to design fusion orientation and linker length so that antibodies and AMPs can both properly function without interfering each other. The second project is the selection of bacterial targets and the mechanistic studies of the binding process. The fundamental problem in this project is to test if the fusion proteins can increase target selection and overcome the barrier to the targets. Most of the mAbs are only used to block toxin-secreting membrane proteins. The fusion protein contains AMP for bactericidal activity; therefore, we are not limited to toxin-secreting membrane proteins for antibody targets. The third project is the evaluation of the biophysical properties of the fusion proteins for drug development. It is of critical importance to understand the effects on the stability behaviors in the presence of the fusion partners. These fundamental problems require the understanding of the structure of the fusion proteins and the interaction with their targets at the molecular level. My strong capacity of computational molecular engineering and experience of bioengineering equip me with robust skill set to achieve this goal. I am excited to study the synergistic effects of the fusion proteins and design them based on fundamental principles, bridging experimental and computational techniques. Eventually, I will make significant contributions to advance the field of antibacterial therapy.

Teaching interests

Chemical engineering is a multidiscipline subject involving chemistry, physics, mathematics and biology to design and produce product that we use in daily life. There are numerous mathematical models to describe fundamental thermodynamics, kinetics, transport phenomena and process control in chemical engineering discipline. From my learning and teaching experience, there are four essential components to practically understand these concepts. The four crucial components are mathematical model, physical meaning, calculation and application. The mathematical models connect phenomena with quantitative measurement. Understanding the physical meaning of the mathematical models allows students to describe complex situations from basic principles. The ability to approximate or solve the mathematical models is also essential for prediction and product design. The application of these concepts to real-world problems indicates true understanding of the subject. My teaching philosophy is to cultivate students’ ability for these skills. My intended learning outcomes (ILOs) will also align with these goals.

Teaching methods

In addition to traditional lecturing, I will incorporate active learning strategies in class to facilitate the learning process. Active learning focuses on student engagement, which has been proven to be more effective for learning. The first strategy is peer teaching. Before class, I will assign pre-reading assignment covering several topics I plan to teach in the class. These readings discuss the basic concept of each topic. In the beginning of the class, I will divide students into small groups and assign topics to students to teach each other. After the peer teaching, I will ask if the students have any question about the content and lead the discussion. After this activity, I will start with some presentations about the theories and mathematical models underlying these concepts. The second active learning activity is brainstorming. I will ask the students to think about some real-world examples that applies these concepts and write them down on the board. This motivates them to learn more about the subject. The third activity is to go through some worked examples. This activity illustrates how to approximate and estimate parameters in the mathematical models, which is a very important skill in future research and in industry. The students will work on some problems similar to the worked examples for practice to sharpen their calculation skills and deepen their understanding.

Assessment of student learning

In the beginning of the class, I will assign a quiz to evaluate the understanding of the students which cover the content from previous session and the pre-reading assignment. During the lectures, I will incorporate plickers to test and get instant feedback about the learning outcomes for each topic. After class, I will assign students with problem sets that are relevant to the real-world examples discussed in the class. This helps to assess the students’ ability to apply new concepts to real-world problems. The midterm and final exams will be open book, which focuses on conceptual questions and not on memorization. In the middle of the semester, I will assign a group project for students to combine the concepts learned in the class to more complicated and practical problems. This project helps to evaluate the ability to conduct real-world application, which aligns with the teaching goals.

Class environment

An inclusive classroom is beneficial for student’s learning experience. In the beginning of the semester, I will ask the students to write a short introduction and specify the motivation and expectation for this class and try to adjust my teaching content accordingly. In class, I will encourage students to express their ideas. My office hours will be flexible so that students have equal opportunities to discuss with me. I will often ask for feedback after class to get an idea about students’ feeling and learning progress. To reduce bias and conflict between students, I will take some strategies. In class discussion, I will randomly assign students into groups and not based on any racial, gender and other identities. I will also give examples about some common biases and discriminations in the past to let the students aware of these behaviors and situations.