Pei Zhou

Overview:

Protein-protein interactions play a pivotal role in the regulation of various cellular processes. The formation of higher order protein complexes is frequently accompanied by extensive structural remodeling of the individual components, varying from domain re-orientation to induced folding of unstructured elements. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for macromolecular structure determination in solution. It has the unique advantage of being capable of elucidating the dynamic behavior of proteins during the process of recognition. Recent advances in NMR techniques have enabled the study of significantly larger proteins and protein complexes. These innovations have also led to faster and more accurate structure determination. My research interests focus on the exploration of molecular recognition and conformation variability of protein complexes in crucial biomedical processes using state-of-the-art NMR techniques.

Positions:

Professor of Biochemistry

Biochemistry
School of Medicine

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Education:

Ph.D. 1998

Harvard University

Post-Doct Fellow, Biological Chemistry

Harvard University

Grants:

Structural Biology and Biophysics Training Program

Administered By
Basic Science Departments
Awarded By
National Institutes of Health
Role
Mentor
Start Date
End Date

Biochemical and functional investigation of the novel enzymatic activities of MESH1

Administered By
Molecular Genetics and Microbiology
Awarded By
National Institutes of Health
Role
Co-Principal Investigator
Start Date
End Date

Regulation of Germline Stem Cell Division in Drosophila

Administered By
Cell Biology
Awarded By
National Institutes of Health
Role
Consultant
Start Date
End Date

Discovery and validation of broadly effective LpxH inhibitors as novel therapeutics against multi-drug resistant Gram-negative pathogens

Administered By
Biochemistry
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Discovery and validation of broadly effective LpxH inhibitors as novel therapeutics against multi-drug resistant Gram-negative pathogens

Administered By
Biochemistry
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Publications:

Synthesis and evaluation of sulfonyl piperazine LpxH inhibitors.

The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is essential in lipid A biosynthesis and has emerged as a promising target for the development of novel antibiotics against multidrug-resistant Gram-negative pathogens. Recently, we reported the crystal structure of Klebsiella pneumoniae LpxH in complex with 1 (AZ1), a sulfonyl piperazine LpxH inhibitor. The analysis of the LpxH-AZ1 co-crystal structure and ligand dynamics led to the design of 2 (JH-LPH-28) and 3 (JH-LPH-33) with enhanced LpxH inhibition. In order to harness our recent findings, we prepared and evaluated a series of sulfonyl piperazine analogs with modifications in the phenyl and N-acetyl groups of 3. Herein, we describe the synthesis and structure-activity relationship of sulfonyl piperazine LpxH inhibitors. We also report the structural analysis of an extended N-acyl chain analog 27b (JH-LPH-41) in complex with K. pneumoniae LpxH, revealing that 27b reaches an untapped polar pocket near the di-manganese cluster in the active site of K. pneumoniae LpxH. We expect that our findings will provide designing principles for new LpxH inhibitors and establish important frameworks for the future development of antibiotics against multidrug-resistant Gram-negative pathogens.
Authors
Kwak, S-H; Cochrane, CS; Ennis, AF; Lim, WY; Webster, CG; Cho, J; Fenton, BA; Zhou, P; Hong, J
MLA Citation
Kwak, Seung-Hwa, et al. “Synthesis and evaluation of sulfonyl piperazine LpxH inhibitors.Bioorg Chem, vol. 102, June 2020, p. 104055. Pubmed, doi:10.1016/j.bioorg.2020.104055.
URI
https://scholars.duke.edu/individual/pub1452342
PMID
32663666
Source
pubmed
Published In
Bioorg Chem
Volume
102
Published Date
Start Page
104055
DOI
10.1016/j.bioorg.2020.104055

Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.

The UDP-2,3-diacylglucosamine pyrophosphate hydrolase LpxH is an essential lipid A biosynthetic enzyme that is conserved in the majority of gram-negative bacteria. It has emerged as an attractive novel antibiotic target due to the recent discovery of an LpxH-targeting sulfonyl piperazine compound (referred to as AZ1) by AstraZeneca. However, the molecular details of AZ1 inhibition have remained unresolved, stymieing further development of this class of antibiotics. Here we report the crystal structure of Klebsiella pneumoniae LpxH in complex with AZ1. We show that AZ1 fits snugly into the L-shaped acyl chain-binding chamber of LpxH with its indoline ring situating adjacent to the active site, its sulfonyl group adopting a sharp kink, and its N-CF3-phenyl substituted piperazine group reaching out to the far side of the LpxH acyl chain-binding chamber. Intriguingly, despite the observation of a single AZ1 conformation in the crystal structure, our solution NMR investigation has revealed the presence of a second ligand conformation invisible in the crystalline state. Together, these distinct ligand conformations delineate a cryptic inhibitor envelope that expands the observed footprint of AZ1 in the LpxH-bound crystal structure and enables the design of AZ1 analogs with enhanced potency in enzymatic assays. These designed compounds display striking improvement in antibiotic activity over AZ1 against wild-type K. pneumoniae, and coadministration with outer membrane permeability enhancers profoundly sensitizes Escherichia coli to designed LpxH inhibitors. Remarkably, none of the sulfonyl piperazine compounds occupies the active site of LpxH, foretelling a straightforward path for rapid optimization of this class of antibiotics.
Authors
Cho, J; Lee, M; Cochrane, CS; Webster, CG; Fenton, BA; Zhao, J; Hong, J; Zhou, P
MLA Citation
Cho, Jae, et al. “Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.Proc Natl Acad Sci U S A, vol. 117, no. 8, Feb. 2020, pp. 4109–16. Pubmed, doi:10.1073/pnas.1912876117.
URI
https://scholars.duke.edu/individual/pub1431154
PMID
32041866
Source
pubmed
Published In
Proc Natl Acad Sci U S A
Volume
117
Published Date
Start Page
4109
End Page
4116
DOI
10.1073/pnas.1912876117

MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis.

Critical to the bacterial stringent response is the rapid relocation of resources from proliferation toward stress survival through the respective accumulation and degradation of (p)ppGpp by RelA and SpoT homologues. While mammalian genomes encode MESH1, a homologue of the bacterial (p)ppGpp hydrolase SpoT, neither (p)ppGpp nor its synthetase has been identified in mammalian cells. Here, we show that human MESH1 is an efficient cytosolic NADPH phosphatase that facilitates ferroptosis. Visualization of the MESH1-NADPH crystal structure revealed a bona fide affinity for the NADPH substrate. Ferroptosis-inducing erastin or cystine deprivation elevates MESH1, whose overexpression depletes NADPH and sensitizes cells to ferroptosis, whereas MESH1 depletion promotes ferroptosis survival by sustaining the levels of NADPH and GSH and by reducing lipid peroxidation. The ferroptotic protection by MESH1 depletion is ablated by suppression of the cytosolic NAD(H) kinase, NADK, but not its mitochondrial counterpart NADK2. Collectively, these data shed light on the importance of cytosolic NADPH levels and their regulation under ferroptosis-inducing conditions in mammalian cells.
Authors
Ding, C-KC; Rose, J; Sun, T; Wu, J; Chen, P-H; Lin, C-C; Yang, W-H; Chen, K-Y; Lee, H; Xu, E; Tian, S; Akinwuntan, J; Zhao, J; Guan, Z; Zhou, P; Chi, J-T
MLA Citation
Ding, Chien-Kuang Cornelia, et al. “MESH1 is a cytosolic NADPH phosphatase that regulates ferroptosis.Nature Metabolism, vol. 2, no. 3, Mar. 2020, pp. 270–77. Epmc, doi:10.1038/s42255-020-0181-1.
URI
https://scholars.duke.edu/individual/pub1435738
PMID
32462112
Source
epmc
Published In
Nature Metabolism
Volume
2
Published Date
Start Page
270
End Page
277
DOI
10.1038/s42255-020-0181-1

Metabolic engineering of Escherichia coli to produce a monophosphoryl lipid A adjuvant.

Monophosphoryl lipid A (MPLA) species, including MPL (a trade name of GlaxoSmithKline) and GLA (a trade name of Immune Design, a subsidiary of Merck), are widely used as an adjuvant in vaccines, allergy drugs, and immunotherapy to boost the immune response. Even though MPLA is a derivative of lipopolysaccharide (LPS), a component of the outer membrane of Gram-negative bacteria, bacterial strains producing MPLA have not been found in nature nor engineered. In fact, MPLA generation involves expensive and laborious procedures based on synthetic routes or chemical transformation of precursors isolated from Gram-negative bacteria. Here, we report the engineering of an Escherichia coli strain for in situ production and accumulation of MPLA. Furthermore, we establish a succinct method for purifying MPLA from the engineered E. coli strain. We show that the purified MPLA (named EcML) stimulates the mouse immune system to generate antigen-specific IgG antibodies similarly to commercially available MPLA, but with a dramatically reduced manufacturing time and cost. Our system, employing the first engineered E. coli strain that directly produces the adjuvant EcML, could transform the current standard of industrial MPLA production.
Authors
Ji, Y; An, J; Hwang, D; Ha, DH; Lim, SM; Lee, C; Zhao, J; Song, HK; Yang, EG; Zhou, P; Chung, HS
MLA Citation
Ji, Yuhyun, et al. “Metabolic engineering of Escherichia coli to produce a monophosphoryl lipid A adjuvant.Metab Eng, vol. 57, Jan. 2020, pp. 193–202. Pubmed, doi:10.1016/j.ymben.2019.11.009.
URI
https://scholars.duke.edu/individual/pub1423417
PMID
31786244
Source
pubmed
Published In
Metab Eng
Volume
57
Published Date
Start Page
193
End Page
202
DOI
10.1016/j.ymben.2019.11.009

Backprojection and Related Methods

© The Royal Society of Chemistry 2017. The sampling of the NMR time domain along radial spokes allows one to obtain projections of an NMR spectrum at various angles. These projections encode information about the positions, intensities, and lineshapes of the peaks in the spectrum, and this information can be recovered using suitable reconstruction methods. Here, we describe the technique of radial data collection and outline an intuitive framework for approaching reconstruction. We then survey the theory of tomographic reconstruction, and use that theory to analyze reconstruction methods and the information available from radial sampling. Finally, we survey past applications of projection-reconstruction methodology in NMR, including its use in 3-D and 4-D NMR data including NOESY.
Authors
Coggins, BE; Zhou, P
MLA Citation
Coggins, B. E., and P. Zhou. “Backprojection and Related Methods.” New Developments in NMR, vol. 2017-January, 2017, pp. 119–68. Scopus, doi:10.1039/9781782628361-00119.
URI
https://scholars.duke.edu/individual/pub1262145
Source
scopus
Volume
2017-January
Published Date
Start Page
119
End Page
168
DOI
10.1039/9781782628361-00119