Qingfei Zheng

The Ohio State University

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Wen Liu

Chinese Academy of Sciences

Yael David

Cornell University

Huapeng Li

The Ohio State University

Hai‐Yan Tian

Jinan University

Shruthi Kandalai

The Ohio State University

Haidong Peng

The Ohio State University

Farzana Hossain

The Ohio State University

Jiangjiang Zhu

The Ohio State University

Wen‐Cai Ye

Jinan University

Igor Maksimovic

Mayo Clinic

Cooperative Institutions

Chinese Academy of Sciences

The Ohio State University

University of Chinese Academy of Sciences

Shanghai Institute of Organic Chemistry

The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute

Jinan University

Memorial Sloan Kettering Cancer Center

Zhejiang University

Icahn School of Medicine at Mount Sinai

Peking University

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An enzymatic [4+2] cyclization cascade creates the pentacyclic core of pyrroindomycins

Nature Chemical Biology (2015)

Zhenhua Tian Peng Sun Yan Yan Zhuhua Wu Qingfei Zheng

Alkene

Tandem

Cascade reaction

10.1038/nchembio.1769

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Citations (131)

Multiplexing of Combinatorial Chemistry in Antimycin Biosynthesis: Expansion of Molecular Diversity and Utility

Angewandte Chemie (2013)

Yan Yan Jing Chen Lihan Zhang Qingfei Zheng Ying Han

Antimycin A

10.1002/ange.201305569

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Citations (20)

Chemical and Synthetic Biology Approaches for Cancer Vaccine Development

Molecules (2022)

Farzana Hossain Shruthi Kandalai Xiaozhuang Zhou Nan Zhang Qingfei Zheng

Cancer vaccines have been considered promising therapeutic strategies and are often constructed from whole cells, attenuated pathogens, carbohydrates, peptides, nucleic acids, etc. However, the use of whole organisms or pathogens can elicit unwanted immune responses arising from unforeseen reactions to the vaccine components. On the other hand, synthetic vaccines, which contain antigens that are conjugated, often with carrier proteins, can overcome these issues. Therefore, in this review we have highlighted the synthetic approaches and discussed several bioconjugation strategies for developing antigen-based cancer vaccines. In addition, the major synthetic biology approaches that were used to develop genetically modified cancer vaccines and their progress in clinical research are summarized here. Furthermore, to boost the immune responses of any vaccines, the addition of suitable adjuvants and a proper delivery system are essential. Hence, this review also mentions the synthesis of adjuvants and utilization of biomaterial scaffolds, which may facilitate the design of future cancer vaccines.

Bioconjugation

Cancer vaccine

Synthetic Biology

Cancer Immunotherapy

10.3390/molecules27206933

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Citations (2)

The thioredoxin system determines CHK1 inhibitor sensitivity via redox-mediated regulation of ribonucleotide reductase activity

Nature Communications (2024)

Chandra Bhushan Prasad Adrian Oo Yujie Liu Zhaojun Qiu Yaogang Zhong

Abstract Checkpoint kinase 1 (CHK1) is critical for cell survival under replication stress (RS). CHK1 inhibitors (CHK1i’s) in combination with chemotherapy have shown promising results in preclinical studies but have displayed minimal efficacy with substantial toxicity in clinical trials. To explore combinatorial strategies that can overcome these limitations, we perform an unbiased high-throughput screen in a non-small cell lung cancer (NSCLC) cell line and identify thioredoxin1 (Trx1), a major component of the mammalian antioxidant-system, as a determinant of CHK1i sensitivity. We establish a role for redox recycling of RRM1, the larger subunit of ribonucleotide reductase (RNR), and a depletion of the deoxynucleotide pool in this Trx1-mediated CHK1i sensitivity. Further, the TrxR inhibitor auranofin, an approved anti-rheumatoid arthritis drug, shows a synergistic interaction with CHK1i via interruption of the deoxynucleotide pool. Together, we show a pharmacological combination to treat NSCLC that relies on a redox regulatory link between the Trx system and mammalian RNR activity.

Ribonucleotide reductase

Auranofin

10.1038/s41467-024-48076-9

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Citations (2)

Catabolic protein degradation in marine sediments confined to distinct archaea

The ISME Journal (2022)

Xiuran Yin Guo‐Wei Zhou Mingwei Cai Qingzeng Zhu Tim Richter‐Heitmann

Abstract Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating 13C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.

Catabolism

Stable-isotope probing

10.1038/s41396-022-01210-1

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Citations (18)

Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis

Angewandte Chemie (2015)

Lihan Zhang Takahiro Mori Qingfei Zheng Takayoshi Awakawa Yan Yan

Abstract Bioengineering of natural product biosynthesis is a powerful approach to expand the structural diversity of bioactive molecules. However, in polyketide biosynthesis, the modification of polyketide extender units, which form the carbon skeletons, has remained challenging. Herein, we report the rational control of polyketide extender units by the structure‐based engineering of a crotonyl‐CoA carboxylase/reductase (CCR), in the biosynthesis of antimycin. Site‐directed mutagenesis of the CCR enzyme AntE, guided by the crystal structure solved at 1.5 Å resolution, expanded its substrate scope to afford indolylmethylmalonyl‐CoA by the V350G mutation. The mutant A182L selectively catalyzed carboxylation over the regular reduction. Furthermore, the combinatorial biosynthesis of heterocycle‐ and substituted arene‐bearing antimycins was achieved by an engineered Streptomyces strain bearing AntE V350G . These findings deepen our understanding of the molecular mechanisms of the CCRs, which will serve as versatile biocatalysts for the manipulation of building blocks, and set the stage for the rational design of polyketide biosynthesis.

Polyketide synthase

Rational design

Protein Engineering

10.1002/ange.201506899

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Citations (7)

Nature-inspired protein ligation and its applications

Nature Reviews Chemistry (2023)

Rasmus Pihl Qingfei Zheng Yael David

Native chemical ligation

Chemical Biology

Chemical Ligation

10.1038/s41570-023-00468-z

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Citations (38)

Isolation and identification ofl/d-lactate-conjugated bufadienolides from toad eggs revealing lactate racemization in amphibians

Organic & Biomolecular Chemistry (2017)

Shiwen Zhou Qingfei Zheng Xiuyong Huang Yong Wang Sifan Luo

Three pairs of bufadienolidel/d-lactate epimers (1–6) were isolated from the eggs of the toadBufo bufo gargarizans.

Racemization

Isolation

10.1039/c7ob01055a

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Citations (9)

Bidirectional histone monoaminylation dynamics regulate neural rhythmicity

Nature (2025)

Qingfei Zheng Benjamin H. Weekley David A. Vinson Shuai Zhao Ryan M. Bastle

Abstract Histone H3 monoaminylations at Gln5 represent an important family of epigenetic marks in brain that have critical roles in permissive gene expression 1–3 . We previously demonstrated that serotonylation 4–10 and dopaminylation 9,11–13 of Gln5 of histone H3 (H3Q5ser and H3Q5dop, respectively) are catalysed by transglutaminase 2 (TG2), and alter both local and global chromatin states. Here we found that TG2 additionally functions as an eraser and exchanger of H3 monoaminylations, including H3Q5 histaminylation (H3Q5his), which displays diurnally rhythmic expression in brain and contributes to circadian gene expression and behaviour. We found that H3Q5his, in contrast to H3Q5ser, inhibits the binding of WDR5, a core member of histone H3 Lys4 (H3K4) methyltransferase complexes, thereby antagonizing methyltransferase activities on H3K4. Taken together, these data elucidate a mechanism through which a single chromatin regulatory enzyme has the ability to sense chemical microenvironments to affect the epigenetic states of cells, the dynamics of which have critical roles in the regulation of neural rhythmicity.

10.1038/s41586-024-08371-3

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Citations (2)

Chemical Labeling and Enrichment of Histone Glyoxal Adducts

ACS Chemical Biology (2022)

Devin M. Ray Erin Q. Jennings Igor Maksimovic Xander Chai James J. Galligan

Because of their long half-lives and highly nucleophilic tails, histones are particularly susceptible to accumulating nonenzymatic covalent modifications, such as glycation. The resulting modifications can have profound effects on cellular physiology due to the regulatory role histones play in all DNA-templated processes; however, the complexity of Maillard chemistry on proteins makes tracking and enriching for glycated proteins a challenging task. Here, we characterize glyoxal (GO) modifications on histones using quantitative proteomics and an aniline-derived GO-reactive probe. In addition, we leverage this chemistry to demonstrate that the glycation regulatory proteins DJ-1 and GLO1 reduce levels of histone GO adducts. Finally, we employ a two-round pull-down method to enrich histone H3 GO glycation and map these adducts to specific chromatin regions.

Glyoxal

10.1021/acschembio.1c00864

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Citations (23)