Doctor of Philosophy, University of California Los Angeles (2019)
Master of Arts, Washington University in St. Louis, Chemistry (2014)
Bachelor of Science, Jilin University, Chemistry & Biotechnology (2012)
Peter Kim, Postdoctoral Faculty Sponsor
Efficient evolution of human antibodies from general protein language models.
Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by suggesting mutations that are evolutionarily plausible, despite providing the model with no information about the target antigen, binding specificity or protein structure. We performed language-model-guided affinity maturation of seven antibodies, screening 20 or fewer variants of each antibody across only two rounds of laboratory evolution, and improved the binding affinities of four clinically relevant, highly mature antibodies up to sevenfold and three unmatured antibodies up to 160-fold, with many designs also demonstrating favorable thermostability and viral neutralization activity against Ebola and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudoviruses. The same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, including antibiotic resistance and enzyme activity, suggesting that these results generalize to many settings.
View details for DOI 10.1038/s41587-023-01763-2
View details for PubMedID 37095349
View details for PubMedCentralID 4410700
Designing epitope-focused vaccines via antigen reorientation.
bioRxiv : the preprint server for biology
A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.GRAPHICAL ABSTRACT: Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an "upside-down" configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.
View details for DOI 10.1101/2022.12.20.521291
View details for PubMedID 36597536
Multimerization of Ebola GPDeltamucin on protein nanoparticle vaccines has minimal effect on elicitation of neutralizing antibodies.
Frontiers in immunology
2022; 13: 942897
Ebola virus (EBOV), a member of the Filoviridae family of viruses and a causative agent of Ebola Virus Disease (EVD), is a highly pathogenic virus that has caused over twenty outbreaks in Central and West Africa since its formal discovery in 1976. The only FDA-licensed vaccine against Ebola virus, rVSV-ZEBOV-GP (Ervebo), is efficacious against infection following just one dose. However, since this vaccine contains a replicating virus, it requires ultra-low temperature storage which imparts considerable logistical challenges for distribution and access. Additional vaccine candidates could provide expanded protection to mitigate current and future outbreaks. Here, we designed and characterized two multimeric protein nanoparticle subunit vaccines displaying 8 or 20 copies of GPDeltamucin, a truncated form of the EBOV surface protein GP. Single-dose immunization of mice with GPDeltamucin nanoparticles revealed that neutralizing antibody levels were roughly equivalent to those observed in mice immunized with non-multimerized GPDeltamucin trimers. These results suggest that some protein subunit antigens do not elicit enhanced antibody responses when displayed on multivalent scaffolds and can inform next-generation design of stable Ebola virus vaccine candidates.
View details for DOI 10.3389/fimmu.2022.942897
View details for PubMedID 36091016
Enzyme Therapeutic for Ischemia and Reperfusion Injury in Organ Transplantation
2022; 34 (1): e2105670
Ischemia-reperfusion injury (IRI) remains as a critical challenge for organ transplantation. Herein, an enzyme therapeutic based on superoxide dismutase and catalase for effective mitigation of IRI and pathogen-induced liver injury is reported, providing a therapeutic for organ transplantation and other diseases.
View details for DOI 10.1002/adma.202105670
View details for Web of Science ID 000714899900001
View details for PubMedID 34617335
Systemic delivery of microRNA for treatment of brain ischemia
2021; 14 (9): 3319-3328
View details for DOI 10.1007/s12274-021-3413-8
View details for Web of Science ID 000644310800001
Dual redox mediators accelerate the electrochemical kinetics of lithium-sulfur batteries
2020; 11 (1): 5215
The sluggish electrochemical kinetics of sulfur species has impeded the wide adoption of lithium-sulfur battery, which is one of the most promising candidates for next-generation energy storage system. Here, we present the electronic and geometric structures of all possible sulfur species and construct an electronic energy diagram to unveil their reaction pathways in batteries, as well as the molecular origin of their sluggish kinetics. By decoupling the contradictory requirements of accelerating charging and discharging processes, we select two pseudocapacitive oxides as electron-ion source and drain to enable the efficient transport of electron/Li+ to and from sulfur intermediates respectively. After incorporating dual oxides, the electrochemical kinetics of sulfur cathode is significantly accelerated. This strategy, which couples a fast-electrochemical reaction with a spontaneous chemical reaction to bypass a slow-electrochemical reaction pathway, offers a solution to accelerate an electrochemical reaction, providing new perspectives for the development of high-energy battery systems.
View details for DOI 10.1038/s41467-020-19070-8
View details for Web of Science ID 000582681400027
View details for PubMedID 33060606
View details for PubMedCentralID PMC7567085
Enhanced Delivery of Rituximab Into Brain and Lymph Nodes Using Timed-Release Nanocapsules in Non-Human Primates
FRONTIERS IN IMMUNOLOGY
2020; 10: 3132
Tumor metastasis into the central nervous system (CNS) and lymph nodes (LNs) is a major obstacle for effective therapies. Therapeutic monoclonal antibodies (mAb) have revolutionized tumor treatment; however, their efficacy for treating metastatic tumors-particularly, CNS and LN metastases-is poor due to inefficient penetration into the CNS and LNs following intravenous injection. We recently reported an effective delivery of mAb to the CNS by encapsulating the anti-CD20 mAb rituximab (RTX) within a thin shell of polymer that contains the analogs of choline and acetylcholine receptors. This encapsulated RTX, denoted as n-RTX, eliminated lymphoma cells systemically in a xenografted humanized mouse model using an immunodeficient mouse as a recipient of human hematopoietic stem/progenitor cells and fetal thymus more effectively than native RTX; importantly, n-RTX showed notable anti-tumor effect on CNS metastases which is unable to show by native RTX. As an important step toward future clinical translation of this technology, we further analyzed the properties of n-RTX in immunocompetent animals, rats, and non-human primates (NHPs). Our results show that a single intravenous injection of n-RTX resulted in 10-fold greater levels in the CNS and 2-3-fold greater levels in the LNs of RTX, respectively, than the injection of native RTX in both rats and NHPs. In addition, we demonstrate the enhanced delivery and efficient B-cell depletion in lymphoid organs of NHPs with n-RTX. Moreover, detailed hematological analysis and liver enzyme activity tests indicate n-RTX treatment is safe in NHPs. As this nanocapsule platform can be universally applied to other therapeutic mAbs, it holds great promise for extending mAb therapy to poorly accessible body compartments.
View details for DOI 10.3389/fimmu.2019.03132
View details for Web of Science ID 000513689600001
View details for PubMedID 32047498
View details for PubMedCentralID PMC6996053
Sustained delivery and molecular targeting of a therapeutic monoclonal antibody to metastases in the central nervous system of mice
NATURE BIOMEDICAL ENGINEERING
2019; 3 (9): 706–16
Approximately 15-40% of all cancers develop metastases in the central nervous system (CNS), yet few therapeutic options exist to treat them. Cancer therapies based on monoclonal antibodies are widely successful, yet have limited efficacy against CNS metastases, owing to the low levels of the drug reaching the tumour site. Here, we show that the encapsulation of rituximab within a crosslinked zwitterionic polymer layer leads to the sustained release of rituximab as the crosslinkers are gradually hydrolysed, enhancing the CNS levels of the antibody by approximately tenfold with respect to the administration of naked rituximab. When the nanocapsules were functionalized with CXCL13-the ligand for the chemokine receptor CXCR5, which is frequently found on B-cell lymphoma-a single dose led to improved control of CXCR5-expressing metastases in a murine xenograft model of non-Hodgkin lymphoma, and eliminated lymphoma in a xenografted humanized bone marrow-liver-thymus mouse model. Encapsulation and molecular targeting of therapeutic antibodies could become an option for the treatment of cancers with CNS metastases.
View details for DOI 10.1038/s41551-019-0434-z
View details for Web of Science ID 000485111600009
View details for PubMedID 31384008
View details for PubMedCentralID PMC6736720
Real-Time Quantification of Cell Internalization Kinetics by Functionalized Bioluminescent Nanoprobes.
Advanced materials (Deerfield Beach, Fla.)
Cells transport mass dynamically, crossing cell membranes to maintain metabolism and systemic homeostasis, through which biomolecules are also delivered to cells for gene editing, cell reprograming, therapy, and other purposes. Quantifying the translocation kinetics is fundamentally and clinically essential, but remains limited by fluorescence-based technologies, which are semi-quantitative and only provide kinetics information at cellular level or in discrete time. Herein, a real-time method of quantifying cell internalization kinetics is reported using functionalized firefly-luciferase nanocapsules as the probe. This quantitative assay will facilitate the rational design of delivery vectors and enable high-throughput screening of peptides and other functional molecules, constituting an effective tool for broad applications, including drug development and cancer therapy.
View details for DOI 10.1002/adma.201902469
View details for PubMedID 31402525
Efficient Delivery of Nerve Growth Factors to the Central Nervous System for Neural Regeneration.
Advanced materials (Deerfield Beach, Fla.)
The central nervous system (CNS) plays a central role in the control of sensory and motor functions, and the disruption of its barriers can result in severe and debilitating neurological disorders. Neurotrophins are promising therapeutic agents for neural regeneration in the damaged CNS. However, their penetration across the blood-brain barrier remains a formidable challenge, representing a bottleneck for brain and spinal cord therapy. Herein, a nanocapsule-based delivery system is reported that enables intravenously injected nerve growth factor (NGF) to enter the CNS in healthy mice and nonhuman primates. Under pathological conditions, the delivery of NGF enables neural regeneration, tissue remodeling, and functional recovery in mice with spinal cord injury. This technology can be utilized to deliver other neurotrophins and growth factors to the CNS, opening a new avenue for tissue engineering and the treatment of CNS disorders and neurodegenerative diseases.
View details for DOI 10.1002/adma.201900727
View details for PubMedID 31125138
A Bioinspired Platform for Effective Delivery of Protein Therapeutics to the Central Nervous System.
Advanced materials (Deerfield Beach, Fla.)
Central nervous system (CNS) diseases are the leading cause of morbidity and mortality; their treatment, however, remains constrained by the blood-brain barrier (BBB) that impedes the access of most therapeutics to the brain. A CNS delivery platform for protein therapeutics, which is achieved by encapsulating the proteins within nanocapsules that contain choline and acetylcholine analogues, is reported herein. Mediated by nicotinic acetylcholine receptors and choline transporters, such nanocapsules can effectively penetrate the BBB and deliver the therapeutics to the CNS, as demonstrated in mice and non-human primates. This universal platform, in general, enables the delivery of any protein therapeutics of interest to the brain, opening a new avenue for the treatment of CNS diseases.
View details for PubMedID 30803073
Systemic Delivery of Monoclonal Antibodies to the Central Nervous System for Brain Tumor Therapy.
Advanced materials (Deerfield Beach, Fla.)
As an essential component of immunotherapy, monoclonal antibodies (mAbs) have emerged as a class of powerful therapeutics for treatment of a broad range of diseases. For central nervous system (CNS) diseases, however, the efficacy remains limited due to their inability to enter the CNS. A platform technology is reported here that enables effective delivery of mAbs to the CNS for brain tumor therapy. This is achieved by encapsulating the mAbs within nanocapsules that contain choline and acetylcholine analogues; such analogues facilitate the penetration of the nanocapsules through the brain-blood barrier and the delivery of mAbs to tumor sites. This platform technology uncages the therapeutic power of mAbs for various CNS diseases that remain poorly treated.
View details for PubMedID 30773720
Nanocapsules of oxalate oxidase for hyperoxaluria treatment
2018; 11 (5): 2682–88
View details for DOI 10.1007/s12274-017-1898-3
View details for Web of Science ID 000431999700033
Fabrication of Hybrid Silicate Coatings by a Simple Vapor Deposition Method for Lithium Metal Anodes
ADVANCED ENERGY MATERIALS
2018; 8 (6)
View details for DOI 10.1002/aenm.201701744
View details for Web of Science ID 000426152400010
A Hepatocyte-Mimicking Antidote for Alcohol Intoxication.
Advanced materials (Deerfield Beach, Fla.)
2018; 30 (22): e1707443
Alcohol intoxication causes serious diseases, whereas current treatments are mostly supportive and unable to remove alcohol efficiently. Upon alcohol consumption, alcohol is sequentially oxidized to acetaldehyde and acetate by the endogenous alcohol dehydrogenase and aldehyde dehydrogenase, respectively. Inspired by the metabolism of alcohol, a hepatocyte-mimicking antidote for alcohol intoxication through the codelivery of the nanocapsules of alcohol oxidase (AOx), catalase (CAT), and aldehyde dehydrogenase (ALDH) to the liver, where AOx and CAT catalyze the oxidation of alcohol to acetaldehyde, while ALDH catalyzes the oxidation of acetaldehyde to acetate. Administered to alcohol-intoxicated mice, the antidote rapidly accumulates in the liver and enables a significant reduction of the blood alcohol concentration. Moreover, blood acetaldehyde concentration is maintained at an extremely low level, significantly contributing to liver protection. Such an antidote, which can eliminate alcohol and acetaldehyde simultaneously, holds great promise for the treatment of alcohol intoxication and poisoning and can provide therapeutic benefits.
View details for PubMedID 29638019
View details for PubMedCentralID PMC6386471
Nanocapsules of therapeutic proteins with enhanced stability and long blood circulation for hyperuricemia management.
Journal of controlled release : official journal of the Controlled Release Society
2017; 255: 54–61
Among a broad spectrum of medical treatments, protein therapeutics holds tremendous opportunities for the treatment of metabolic disorders, cancer, autoimmune diseases and etc. Broad adaption of protein therapeutics, however, still remain challenging, not only because of poor protein stability, but they also experience fast clearance after administrated and elicit immune responses, resulting in undesirable biodistribution and short blood residence time. In this study, we demonstrate a novel protein delivery method via encapsulating therapeutic proteins within thin shells of poly(N-vinylpyrrolidone) (PVP), which leads to significantly improved protein stability, reduced macrophage uptake, prolonged circulation time and reduced immunogenicity. Exemplified with urate oxidase (UOx), the enzyme used for hyperuricemia treatment, as-formed UOx nanocapsules, n(UOx), exhibits enhanced stability, more significant therapeutic effects, and a more than 10-fold improvement in circulation time when compared with native UOx. This technology not only demonstrates the use of UOx nanocapsules for hyperuricemia management, but also provides a general approach for a broad spectrum of therapeutic proteins for in vivo applications.
View details for PubMedID 28288895
Prolonging the plasma circulation of proteins by nano-encapsulation with phosphorylcholine-based polymer
2016; 9 (8): 2424–32
View details for DOI 10.1007/s12274-016-1128-4
View details for Web of Science ID 000380726200021
An intracellular protein delivery platform based on glutathione-responsive protein nanocapsules.
Chemical communications (Cambridge, England)
2016; 52 (93): 13608–11
An efficient strategy for the intracellular delivery of proteins was developed based on assembling proteins with a self-crosslinkable polymer. Such a disulfide-crosslinking structure enhances the stability of the protein-polymer assembly, and also allows effective dissociation of the assembly in response to glutathione, which allows effective delivery of various proteins with high intracellular bioactivity.
View details for PubMedID 27808287
Structural insight into the type-II mitochondrial NADH dehydrogenases
2012; 491 (7424): 478-+
The single-component type-II NADH dehydrogenases (NDH-2s) serve as alternatives to the multisubunit respiratory complex I (type-I NADH dehydrogenase (NDH-1), also called NADH:ubiquinone oxidoreductase; EC 188.8.131.52) in catalysing electron transfer from NADH to ubiquinone in the mitochondrial respiratory chain. The yeast NDH-2 (Ndi1) oxidizes NADH on the matrix side and reduces ubiquinone to maintain mitochondrial NADH/NAD(+) homeostasis. Ndi1 is a potential therapeutic agent for human diseases caused by complex I defects, particularly Parkinson's disease, because its expression restores the mitochondrial activity in animals with complex I deficiency. NDH-2s in pathogenic microorganisms are viable targets for new antibiotics. Here we solve the crystal structures of Ndi1 in its substrate-free, NADH-, ubiquinone- and NADH-ubiquinone-bound states, to help understand the catalytic mechanism of NDH-2s. We find that Ndi1 homodimerization through its carboxy-terminal domain is critical for its catalytic activity and membrane targeting. The structures reveal two ubiquinone-binding sites (UQ(I) and UQ(II)) in Ndi1. NADH and UQ(I) can bind to Ndi1 simultaneously to form a substrate-protein complex. We propose that UQ(I) interacts with FAD to act as an intermediate for electron transfer, and that NADH transfers electrons through this FAD-UQ(I) complex to UQ(II). Together our data reveal the regulatory and catalytic mechanisms of Ndi1 and may facilitate the development or targeting of NDH-2s for potential therapeutic applications.
View details for DOI 10.1038/nature11541
View details for Web of Science ID 000311031600053
View details for PubMedID 23086143