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Zhou L, Cai F, Li Y, Gao X, Wei Y, Fedorova A, Kirchhofer D, Hannoush RN, Zhang Y. Disulfide-constrained peptide scaffolds enable a robust peptide-therapeutic discovery platform. PLoS One 2024; 19:e0300135. [PMID: 38547109 PMCID: PMC10977697 DOI: 10.1371/journal.pone.0300135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/21/2024] [Indexed: 04/02/2024] Open
Abstract
Peptides present an alternative modality to immunoglobulin domains or small molecules for developing therapeutics to either agonize or antagonize cellular pathways associated with diseases. However, peptides often suffer from poor chemical and physical stability, limiting their therapeutic potential. Disulfide-constrained peptides (DCP) are naturally occurring and possess numerous desirable properties, such as high stability, that qualify them as drug-like scaffolds for peptide therapeutics. DCPs contain loop regions protruding from the core of the molecule that are amenable to peptide engineering via direct evolution by use of phage display technology. In this study, we have established a robust platform for the discovery of peptide therapeutics using various DCPs as scaffolds. We created diverse libraries comprising seven different DCP scaffolds, resulting in an overall diversity of 2 x 1011. The effectiveness of this platform for functional hit discovery has been extensively evaluated, demonstrating a hit rate comparable to that of synthetic antibody libraries. By utilizing chemically synthesized and in vitro folded peptides derived from selections of phage displayed DCP libraries, we have successfully generated functional inhibitors targeting the HtrA1 protease. Through affinity maturation strategies, we have transformed initially weak binders against Notch2 with micromolar Kd values to high-affinity ligands in the nanomolar range. This process highlights a viable hit-to-lead progression. Overall, our platform holds significant potential to greatly enhance the discovery of peptide therapeutics.
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Affiliation(s)
- Lijuan Zhou
- Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Fei Cai
- Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Yanjie Li
- Department of Peptide Therapeutics, Genentech, Inc., South San Francisco, California, United States of America
| | - Xinxin Gao
- Department of Peptide Therapeutics, Genentech, Inc., South San Francisco, California, United States of America
| | - Yuehua Wei
- Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Anna Fedorova
- Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Daniel Kirchhofer
- Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Yingnan Zhang
- Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America
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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024. [PMID: 38411572 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Liu C, Yan Q, Yi K, Hu T, Wang J, Zhang Z, Li H, Luo Y, Zhang D, Meng E. A secretory system for extracellular production of spider neurotoxin huwentoxin-I in Escherichia coli. Prep Biochem Biotechnol 2022; 53:914-922. [PMID: 36573266 DOI: 10.1080/10826068.2022.2158473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Due to their advantages in structural stability and versatility, cysteine-rich peptides, which are secreted from the venom glands of venomous animals, constitute a naturally occurring pharmaceutical arsenal. However, the correct folding of disulfide bonds is a challenging task in the prokaryotic expression system like Escherichia coli due to the reducing environment. Here, a secretory expression plasmid pSE-G1M5-SUMO-HWTX-I for the spider neurotoxin huwentoxin-I (HWTX-I) with three disulfides as a model of cysteine-rich peptides was constructed. By utilizing the signal peptide G1M5, the fusion protein 6 × His-SUMO-HWTX-I was successfully secreted into extracellular medium of BL21(DE3). After enrichment using cation-exchange chromatography and purification utilizing the Ni-NTA column, 6 × His-SUMO-HWTX-I was digested via Ulp1 kinase to release recombinant HWTX-I (rHWTX-I), which was further purified utilizing RP-HPLC. Finally, both impurities with low and high molecular weights were completely removed. The molecular mass of rHWTX-I was identified as being 3750.8 Da, which was identical to natural HWTX-I with three disulfide bridges. Furthermore, by utilizing whole-cell patch clamp, the sodium currents of hNav1.7 could be inhibited by rHWTX-I and the IC50 value was 419 nmol/L.
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Affiliation(s)
- Changjun Liu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Genetic Improvement and Multiple Utilization of Economic Crops in Hunan Province, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Qing Yan
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Ke Yi
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Tianhao Hu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Jianjie Wang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Zheyang Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Huimin Li
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Yutao Luo
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Dongyi Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
| | - Er Meng
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Genetic Improvement and Multiple Utilization of Economic Crops in Hunan Province, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, Hunan University of Science and Technology, Xiangtan, Hunan, PR China
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4
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Lai Z, Yuan X, Chen H, Zhu Y, Dong N, Shan A. Strategies employed in the design of antimicrobial peptides with enhanced proteolytic stability. Biotechnol Adv 2022; 59:107962. [PMID: 35452776 DOI: 10.1016/j.biotechadv.2022.107962] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
Due to the alarming developing rate of multidrug-resistant bacterial pathogens, the development and modification of antimicrobial peptides (AMPs) are unprecedentedly active. Despite the fact that considerable efforts have been expended on the discovery and design strategies of AMPs, the clinical translation of peptide antibiotics remains inadequate. A large number of articles and reviews credited the limited success of AMPs to their poor stability in the biological environment, particularly their poor proteolytic stability. In the past forty years, various design strategies have been used to improve the proteolytic stability of AMPs, such as sequence modification, cyclization, peptidomimetics, and nanotechnology. Herein, we focus our discussion on the progress made in improving the proteolytic stability of AMPs and the principle, successes, and limitations of various anti-proteolytic design strategies. It is of prospective significance to extend current insights into the degradation-related inactivation of AMPs and also alleviate/overcome the problem.
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Affiliation(s)
- Zhenheng Lai
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xiaojie Yuan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Hongyu Chen
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Yunhui Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Na Dong
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China.
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5
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Identification and characterization of a wolfberry carboxypeptidase inhibitor from Lycium barbarum. Food Chem 2021; 351:129338. [PMID: 33647700 DOI: 10.1016/j.foodchem.2021.129338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/22/2021] [Accepted: 02/06/2021] [Indexed: 01/13/2023]
Abstract
Hyperstable cysteine-rich peptides (CRPs) represent an underexplored superfamily of bioactives in functional foods. An example is wolfberry of the Lycium barbarum family. Previously, we discovered a CRP, designated α-lybatide, from L. barbarum bark. Herein, we report the discovery of β-lybatide, a novel carboxypeptidase inhibitor belonging to a different CRP family from the wolfberry plant. Proteomic and transcriptomic analyses showed that β-lybatide contains 36 amino acids with six cysteine residues. NMR spectroscopy revealed that β-lybatide displays a knottin-like structure that renders it highly resistant to thermal, chemical and enzymatic degradation, conditions important for keeping its structural integrity in gastrointestinal tract. Biochemical assays showed that β-lybatide is a potent carboxypeptidase inhibitor which could contribute to the wolfberry biological activities. Bioinformatics analysis revealed an additional 49 β-lybatide-like plant carboxypeptidase inhibitors. Together, our results show that β-lybatide is the first and the smallest plant-derived hyperstable carboxypeptidase inhibitor discovered from a functional food.
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Parsley NC, Williams OL, Hicks LM. Exploring the Diversity of Cysteine-Rich Natural Product Peptides via MS/MS Fingerprint Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1833-1843. [PMID: 32872784 PMCID: PMC7816094 DOI: 10.1021/jasms.0c00078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Natural product extracts present inherently complex matrices in which the identification of novel bioactive peptide species is challenged by low-abundance masses and significant structural and sequence diversity. Additionally, discovery efforts often result in the re-identification of known compounds, where modifications derived in vivo or during sample handling may obscure true sequence identity. Herein, we identify mass spectral (MS2) "fingerprint" ions characteristic of cyclotides, a diverse and biologically active family of botanical cysteine-rich peptides, based on regions of high sequence homology. We couple mass shift analysis with MS2 spectral fingerprint ions cross referenced with CyBase-a cyclotide database-to discern unique mass species in Viola communis extracts from mass species that are likely already characterized and those with common modifications. The approach is extended to a related class of cysteine-rich peptides, the trypsin inhibitors, using the characterized botanical species Lagenaria siceraria. Coupling the observation of highly abundant MS2 ions with mass shift analysis, we identify a new set of small, highly disulfide-bound cysteine-rich L. siceraria peptides.
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Affiliation(s)
| | | | - Leslie M. Hicks
- Address Correspondence to: Leslie M. Hicks, 125 South Road, CB#3290, Kenan Laboratories, C045, Chapel Hill, NC 27599, [T] 919-843-6903, [E]
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7
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Barashkova AS, Rogozhin EA. Isolation of antimicrobial peptides from different plant sources: Does a general extraction method exist? PLANT METHODS 2020; 16:143. [PMID: 33110440 PMCID: PMC7585225 DOI: 10.1186/s13007-020-00687-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/17/2020] [Indexed: 05/06/2023]
Abstract
Plants are good sources of biologically active compounds with antimicrobial activity, including polypeptides. Antimicrobial peptides (AMPs) represent one of the main barriers of plant innate immunity to environmental stress factors and are attracting much research interest. There are some extraction methods for isolation of AMPs from plant organs based on the type of extractant and initial fractionation stages. But most methods are directed to obtain some specific structural types of AMPs and do not allow to understand the molecular diversity of AMP inside a whole plant. In this mini-review, we suggest an optimized scheme of AMP isolation from plants followed by obtaining a set of peptides belonging to various structural families. This approach can be performed for large-scale screening of plants to identify some novel or homologous AMPs for fundamental and applied studies.
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Affiliation(s)
- Anna S. Barashkova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, ul. Miklukho-Maklaya, 16/10, Moscow, Russia 117997
| | - Eugene A. Rogozhin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, ul. Miklukho-Maklaya, 16/10, Moscow, Russia 117997
- Gause Institute of New Antibiotics, ul. Bolshaya Pirogovskaya, 11, Moscow, Russia 119021
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Chen Y, Yang Y, Qian Y, Gblinwon RT, Jiao Z, Chen L, Lin L, Zheng Y, Yang H, Shen Y. Harnessing multiplex PCR assay targeting specific mitochondrial DNA elements for simultaneous identification of antelope species in Cornu Saigae Tataricae. Mitochondrial DNA B Resour 2019; 4:3222-3226. [PMID: 33365929 PMCID: PMC7707849 DOI: 10.1080/23802359.2019.1666667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
A multiplex PCR assay was developed to simultaneously differentiate four antelope species and identify adulteration in Cornu Saigae Tataricae. Four novel primer sets were designed with high inter-species specificity and intra-species stability. Limit of detection was estimated to be 10 ng of genomes. When a mixture of antelope hornand fake species was assayed, it exhibited powerful differentiation capability. 5 out of 12 batches of commercialproducts were identified to be counterfeited or adulterated with Ovis aries Linnaeus and/or Capra hircus Linnaeus. It is readily applicable in routine analysis for identification of sham or adulterants of Cornu Saigae Tataricae.
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Affiliation(s)
- Yufei Chen
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yaya Yang
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yinhuan Qian
- Department of Pharmacy, Zhenjiang Hospital of Traditional Chinese Medicine, Zhenjiang, Jiangsu, China
| | | | - Zhaoqun Jiao
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Liqun Chen
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ling Lin
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yang Zheng
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Huan Yang
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuping Shen
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu, China
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Huang J, Wong KH, Tay SV, How A, Tam JP. Cysteine-Rich Peptide Fingerprinting as a General Method for Herbal Analysis to Differentiate Radix Astragali and Radix Hedysarum. FRONTIERS IN PLANT SCIENCE 2019; 10:973. [PMID: 31417590 PMCID: PMC6684776 DOI: 10.3389/fpls.2019.00973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/11/2019] [Indexed: 05/23/2023]
Abstract
Species misidentification and adulteration are major concerns in authenticating herbal medicines. Radix Astragali (RA), the roots of Astragalus membranaceus, is a traditional herbal medicine used for treating diabetes. However, it is often substituted by Radix Hedysarum (RH), the roots of Hedysarum polybotrys from the same plant family Fabaceae, which possesses different bioactivities. Current authentication methods, focusing on the chemical composition differences of herbal medicines based on small molecules, have limitations when these chemical markers are found in many species. Herein, we describe a rapid and general method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), coupled with multivariate analyses to differentiate herbal medicines. We used cysteine-rich peptide (CRP) fingerprinting, a method that exploits an underexplored chemical space between 2 to 6 kDa and which is populated by highly stable CRPs. To show the generality of the method, we screened 100 medicinal plant extracts and showed that CRP fingerprints are unique chemical markers. In addition, CRP fingerprinting was many-fold faster than the conventional authentication method using ultra-performance liquid chromatography (UPLC). Multivariate analyses showed that it has comparable classification accuracy as UPLC fingerprinting. Together, our findings revealed that CRP fingerprinting coupled with multivariate analyses is a rapid and general method for authentication and quality control for natural products in medicinal plants.
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Dutta B, Huang J, To J, Tam JP. LIR Motif-Containing Hyperdisulfide β-Ginkgotide is Cytoprotective, Adaptogenic, and Scaffold-Ready. Molecules 2019; 24:E2417. [PMID: 31262066 PMCID: PMC6651024 DOI: 10.3390/molecules24132417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/24/2022] Open
Abstract
Grafting a bioactive peptide onto a disulfide-rich scaffold is a promising approach to improve its structure and metabolic stability. The ginkgo plant-derived β-ginkgotide β-gB1 is a highly unusual molecule: Small, hyperdisulfide, and found only in selected ancient plants. It also contains a conserved 16-amino-acid core with three interlocking disulfides, as well as a six-amino-acid inter-cysteine loop 2 suitable for grafting peptide epitopes. However, very little is known about this recently-discovered family of molecules. Here, we report the biophysical and functional characterizations of the β-ginkgotide β-gB1 from G. biloba. A circular dichroism spectroscopy analysis at 90 °C and proteolytic treatments of β-gB1 supported that it is hyperstable. Data mining revealed that the β-gB1 loop 2 contains the canonical LC3 interacting region (LIR) motif crucial for selective autophagy. Cell-based assays and pull-down experiments showed that β-gB1 is an adaptogen, able to maintain cellular homeostasis through induced autophagosomes formation and to protect cells by targeting intracellular proteins from stress-mediated damage against hypoxia and the hypoxia-reoxygenation of induced cell death. This is the first report of an LIR-containing peptide natural product. Together, our results suggest that the plant-derived β-ginkgotide is cytoprotective, capable of targeting intracellular proteins, and holds promise as a hyperdisulfide scaffold for engineering peptidyl therapeutics with enhanced structural and metabolic stability.
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Affiliation(s)
- Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jiayi Huang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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