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Yang J, Zhao Y, Qian L, Yu Y, Zhang Y, Zhang J. Modularization of dual recognized CRISPR/Cas12a system for the detection of Staphylococcus aureus assisted by hydrazone chemistry. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134877. [PMID: 38901249 DOI: 10.1016/j.jhazmat.2024.134877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024]
Abstract
In this work, a dual recognized CRISPR/Cas12a system has been proposed, in which the activation chain is cleverly divided into two parts that can serve for precise dual target recognition, and hydrazone chemistry is introduced for the formation of a whole activation chain. It has been further explored to construct a new method for the specific and sensitive detection of Staphylococcus aureus (SA) as one of the most common pathogens in infectious diseases. In virtue of proximity effect contributed by complementary base pairing, hydrazone chemistry accelerates the formation of the whole activation strand and improves the specificity of the CRISPR/Cas12a system, serving for the accurate analysis of SA. Moreover, the temporary aggregation of CRISPR/Cas12a around SA enhances its catalytical efficiency so as to further amplify signal. With high sensitivity, stability, reproducibility and specificity, the established method has been successfully applied to detect SA in complex substrates. Meanwhile, our established method can well evaluate the inhibition effect of chlorogenic acid and congo red in comparison with flow cytometry. ENVIRONMENTAL IMPLICATION: Bacterial pathogens exist widely in the environment and seriously threaten the safety of human health. Staphylococcus aureus (SA) is the most common pathogen of human suppurative infection, which can cause local suppurative infection, pneumonia, and even systemic infections such as sepsis. In this work, a dual recognized CRISPR/Cas12a system mediated by hydrazone chemistry has been proposed. With high sensitivity and low detection limit, the established method can specifically detect SA and effectively evaluate the antibacterial effect of inhibitors. This method is expected to be further developed into a detection method in different scenarios such as environmental monitoring and clinical diagnosis.
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Affiliation(s)
- Jingyi Yang
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yining Zhao
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Lelin Qian
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Ying Yu
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China; Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yuan Zhang
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair, Ministry of Education, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, PR China.
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Panda M, Kalita E, Singh S, Kumar K, Prajapati VK. Nanobody-peptide-conjugate (NPC) for passive immunotherapy against SARS-CoV-2 variants of concern (VoC): a prospective pan-coronavirus therapeutics. Mol Divers 2023; 27:2577-2603. [PMID: 36400898 PMCID: PMC9676808 DOI: 10.1007/s11030-022-10570-x] [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] [Received: 10/06/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
The COVID-19 crisis, incited by the zoonotic SARS-CoV-2 virus, has quickly escalated into a catastrophic public health issue and a grave threat to humankind owing to the advent of mutant viruses. Multiple pharmaceutical therapies or biologics envision stopping the virus from spreading further; however, WHO has voiced concerns about the variants of concern (VoCs) inability to respond. Nanobodies are a new class of antibody mimics with binding affinity and specificity similar to classical mAbs, as well as the privileges of a small molecular weight, ease of entry into solid tissues, and binding cryptic epitopes of the antigen. Herein, we investigated multiple putative anti-SARS-CoV-2 nanobodies targeting the Receptor binding domain of the WHO-listed SARS-CoV-2 variants of concern using a comprehensive computational immunoinformatics methodology. With affinity maturation via alanine scanning mutagenesis, we remodeled an ultrapotent nanobody with substantial breadth and potency, exhibiting pico-molar binding affinities against all the VoCs. An antiviral peptide with specificity for ACE-2 receptors was affixed to make it multispecific and discourage viral entry. Collectively, we constructed a broad-spectrum therapeutic biparatopic nanobody-peptide conjugate (NPC) extending coverage to SARS-CoV-2 VoCs RBDs. We PEGylated the biparatopic construct with 20kD maleimide-terminated PEG (MAL-(PEG)n-OMe) to improve its clinical efficacy limiting rapid renal clearance, and performed in silico cloning to facilitate future experimental studies. Our findings suggest that combining biparatopic nanobody conjugate with standard treatment may be a promising bivariate tool for combating viral entry during COVID-19 illness.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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Lin J, Anjum Huma F, Irfan A, Ali SS, Waheed Y, Mohammad A, Munir M, Khan A, Wei DQ. Structural plasticity of omicron BA.5 and BA.2.75 for enhanced ACE-dependent entry into cells. J Biomol Struct Dyn 2023; 41:10762-10773. [PMID: 36541923 DOI: 10.1080/07391102.2022.2158944] [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] [Received: 10/31/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
The current study investigated the binding variations among the wilt type, Omicron sub-variants BA.2.75 and BA.5, using protein-protein docking, protein structural graphs (P SG), and molecular simulation methods. HADDOCK predicted docking scores and dissociation constant (KD) revealed tighter binding of these sub-variants in contrast to the WT. Further investigation revealed variations in the hub residues, protein sub-networks, and GlobalMetapath in these variants as compared to the WT. A very unusual dynamic for BA.2.75 and BA.5 was observed, and secondary structure transition can also be witnessed in the loops (44-505). The results show that the flexibility of these three loops is increased by the mutations as an allosteric effect and thus enhances the chances of bonding with the nearby residues to connect and form a stable connection. Furthermore, the additional hydrogen bonding contacts steer the robust binding of these variants in contrast to the wild type. The total binding free energy for the wild type was calculated to be -61.38 kcal/mol, while for BA.2.75 and BA.5 variants the T BE was calculated to be -70.42 kcal/mol and 69.78 kcal/mol, respectively. We observed that the binding of BA.2.75 is steered by the electrostatic interactions while the BA.5 additional contacts are due to the vdW (Van der Waal) energy. From these findings, it can be observed the Spike (S) protein is undergoing structural adjustments to bind efficiently to the hACE2 (human angiotensin-converting enzyme 2) receptor and, in turn, increase entry to the host cells. The current study will aid the development of structure-based drugs against these variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Junqi Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | - Aiza Irfan
- Rawalpindi Medical University, Punjab, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation & Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
- Peng Cheng Laboratory, Nashan District, Shenzhen, Guangdong, P.R China
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Krivitsky V, Krivitsky A, Mantella V, Ben-Yehuda Greenwald M, Sankar DS, Betschmann J, Bader J, Zoratto N, Schreier K, Feiss S, Walker D, Dengjel J, Werner S, Leroux JC. Ultrafast and Controlled Capturing, Loading, and Release of Extracellular Vesicles by a Portable Microstructured Electrochemical Fluidic Device. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212000. [PMID: 37452635 DOI: 10.1002/adma.202212000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Extracellular vesicles (EVs) are secreted by all living cells and are found in body fluids. They exert numerous physiological and pathological functions and serve as cargo shuttles. Due to their safety and inherent bioactivity, they have emerged as versatile therapeutic agents, biomarkers, and potential drug carriers. Despite the growing interest in EVs, current progress in this field is, in part, limited by relatively inefficient isolation techniques. Conventional methods are indeed slow, laborious, require specialized laboratory equipment, and may result in low yield and purity. This work describes an electrochemically controlled "all-in-one" device enabling capturing, loading, and releasing of EVs. The device is composed of a fluidic channel confined within antibody-coated microstructured electrodes. It rapidly isolates EVs with a high level of purity from various biofluids. As a proof of principle, the device is applied to isolate EVs from skin wounds of healthy and diabetic mice. Strikingly, it is found that EVs from healing wounds of diabetic mice are enriched in mitochondrial proteins compared to those of healthy mice. Additionally, the device improves the loading protocol of EVs with polyplexes, and may therefore find applications in nucleic acid delivery. Overall, the electrochemical device can greatly facilitate the development of EVs-based technologies.
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Affiliation(s)
- Vadim Krivitsky
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Adva Krivitsky
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Valeria Mantella
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Maya Ben-Yehuda Greenwald
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | | | - Jil Betschmann
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Johannes Bader
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Nicole Zoratto
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Kento Schreier
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Sarah Feiss
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Dario Walker
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, 1700, Switzerland
| | - Sabine Werner
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
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Chen Y, Shi H. Rapid and Label-Free Analysis of Antigen-Antibody Dynamic Binding of Tumor Markers Using Piezoelectric Quartz Crystal Biosensor. BIOSENSORS 2023; 13:917. [PMID: 37887110 PMCID: PMC10605586 DOI: 10.3390/bios13100917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023]
Abstract
Quantitative biomacromolecular diagnosis is rapidly developing in molecular oncology. In this study, we developed a continuous flow immunoassay device based on a piezoelectric (PZ) quartz crystal biosensor fabricated with whole-electrode occupation for the quantitative molecular diagnosis of tumor markers such as alpha-fetoprotein (AFP). Only one face of the crystal was in contact with the serum sample during the assays. First, the characteristics of AFP and anti-AFP binding kinetics, such as the optimal time for immune response, the average antigen binding rate, the kinetic constants and the optimal standard curve, were investigated. The overall immunoreaction time was only 12 min, the average antigen binding rate of AFP was 45.9 ng/min, the concentration range of AFP detection was 18.8-1100 ng/mL and the association rate constant (kon), dissociation rate constant (koff) and equilibrium dissociation constant (KD) were 5.58×104 M-1s-1,1.79×10-5 s-1 and 3.21×10-10 M, respectively. This sensing system was further validated by detecting AFP values from clinical serum samples, which were obtained from pregnant women, liver and lung cancer patients and those undergoing liver cancer screening. No cross-reactivity with lung cancer markers were found, and the detection results were in good agreement with the radioimmunoassay (RIA) results, with a relative deviation of no more than 3.7% and correlation coefficient r of 0.9998. Therefore, the developed immunoassay device has the potential to be used in large-scale screening for cancers, as well as in novel high-affinity binding drug development.
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Affiliation(s)
- Yan Chen
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Huashan Shi
- Department of Biological Therapy, West China Hospital, Sichuan University, Chengdu 610047, China;
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Kosoy G, Miller BL. Two Decades of Arrayed Imaging Reflectometry for Sensitive, High-Throughput Biosensing. BIOSENSORS 2023; 13:870. [PMID: 37754104 PMCID: PMC10526495 DOI: 10.3390/bios13090870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
Arrayed imaging reflectometry (AIR), first introduced in 2004, is a thin-film interference sensor technique that optimizes optical properties (angle of incidence, polarization, substrate refractive index, and thickness) to create a condition of total destructive interference at the surface of a silicon substrate. The advantages of AIR are its sensitivity, dynamic range, multiplex capability, and high-throughput compatibility. AIR has been used for the detection of antibodies against coronaviruses, influenza viruses, Staphylococcus aureus, and human autoantigens. It has also shown utility in detection of cytokines, with sensitivity comparable to bead-based and ELISA assays. Not limited to antibodies or antigens, mixed aptamer and protein arrays as well as glycan arrays have been employed in AIR for differentiating influenza strains. Mixed arrays using direct and competitive inhibition assays have enabled simultaneous measurement of cytokines and small molecules. Finally, AIR has also been used to measure affinity constants, kinetic and at equilibrium. In this review, we give an overview of AIR biosensing technologies and present the latest AIR advances.
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Affiliation(s)
- Gabrielle Kosoy
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14526, USA;
| | - Benjamin L. Miller
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14526, USA;
- Department of Dermatology, University of Rochester, Rochester, NY 14526, USA
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7
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Alhassan AM, Shirure VS, Luo J, Nguyen BB, Rollins ZA, Shergill BS, Zhu X, Baumgarth N, George SC. A microfluidic strategy to capture antigen-specific high affinity B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548739. [PMID: 37503139 PMCID: PMC10369944 DOI: 10.1101/2023.07.12.548739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Assessing B cell affinity to pathogen-specific antigens prior to or following exposure could facilitate the assessment of immune status. Current standard tools to assess antigen-specific B cell responses focus on equilibrium binding of the secreted antibody in serum. These methods are costly, time-consuming, and assess antibody affinity under zero-force. Recent findings indicate that force may influence BCR-antigen binding interactions and thus immune status. Here, we designed a simple laminar flow microfluidic chamber in which the antigen (hemagglutinin of influenza A) is bound to the chamber surface to assess antigen-specific BCR binding affinity of five hemagglutinin-specific hybridomas under 65- to 650-pN force range. Our results demonstrate that both increasing shear force and bound lifetime can be used to enrich antigen-specific high affinity B cells. The affinity of the membrane-bound BCR in the flow chamber correlates well with the affinity of the matched antibodies measured in solution. These findings demonstrate that a microfluidic strategy can rapidly assess BCR-antigen binding properties and identify antigen-specific high affinity B cells. This strategy has the potential to both assess functional immune status from peripheral B cells and be a cost-effective way of identifying individual B cells as antibody sources for a range of clinical applications.
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Affiliation(s)
- Ahmed M. Alhassan
- Department of Biomedical Engineering, University of California, Davis
| | | | - Jean Luo
- Department of Pathology, Microbiology, and Immunology, University of California, Davis
| | - Bryan B. Nguyen
- Department of Biomedical Engineering, University of California, Davis
| | | | | | - Xiangdong Zhu
- Department of Physics and Astronomy, University of California, Davis
| | - Nicole Baumgarth
- Department of Pathology, Microbiology, and Immunology, University of California, Davis
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health and Department of Molecular and Comparative Pathobiology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Steven C. George
- Department of Biomedical Engineering, University of California, Davis
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8
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Electrochemical magneto-immunoassay for detection of zika virus antibody in human serum. Talanta 2023; 256:124277. [PMID: 36738622 DOI: 10.1016/j.talanta.2023.124277] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/29/2022] [Accepted: 01/14/2023] [Indexed: 01/22/2023]
Abstract
Zika virus (ZIKV) is a flavivirus transmitted by infected Aedes genus mosquitoes. An infected person may be asymptomatic or present symptoms such as fever, arthralgia, and in pregnancy it may lead to neurological disorders in the fetus, such as microcephaly. Based on the high dissemination potential of ZIVK and its similar antigen composition to other arboviruses, new approaches for selective virus detection are urgently needed. This work reports the development of an electrochemical immunoassay for detection of anti-ZIKV antibodies, using magnetic beads functionalized with recombinant protein derived from the non-structural protein 1 (ΔNS1-ZIKV) and anti-IgG antibodies labeled with horseradish peroxidase (HRP) enzyme. The magneto-immunoassay uses disposable microfluidic devices for detection of anti-ZIKV in serum samples. A linear response was obtained for a wide concentration range from 0.01 to 9.80 × 105 pg mL-1 (r2 = 0.982), with a limit of detection of 0.48 pg mL-1. The proposed immunoassay proved to be highly efficient for the detection of anti-ZIKV antibodies in serum, offering promising perspectives for the development of fast, simple, and affordable point-of-care diagnosis devices for ZIKV.
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Chen YL, Zhang MH, Su LL, Sun LC, Qiu XJ, Lin D, Zhang LJ, Jin T, Cao MJ. Relationships of Matrix Metalloproteinase 1 and a Tissue Inhibitor of Metalloproteinase to Collagen Metabolism in Haliotis discus hannai. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14886-14897. [PMID: 36398610 DOI: 10.1021/acs.jafc.2c05931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In response to physical, chemical, and/or biological stimuli, considerable tissue self-degradation occurs in abalone, causing severe post-harvest quality loss. During this process, the extracellular matrix (ECM) is greatly degraded by endogenous proteases. The main component of the ECM is collagen, primarily type I collagen. Although the activity of matrix metalloproteinases (MMPs), which can specifically degrade collagen, is precisely regulated by tissue inhibitors of MPs (TIMPs), indicating that MMPs and TIMPs play crucial roles in the regulation of tissue self-degradation, few studies have reported the interaction between MMPs and TIMPs. In this study, we reveal collagenases to participate in postmortem tissue self-degradation of Haliotis discus hannai by degrading type I collagen. The recombinant MMP-1 catalytic domain (rMMP1c) of abalone with high purity and enzyme activity is expressed using a prokaryotic expression system. The optimum temperature and pH for rMMP1c are 37 °C and 7.0, respectively. The thermal denaturation temperature of rMMP1c is 67.0 ± 0.9 °C. Ethylenediamine tetraacetic acid (EDTA) and 1,10-phenanthroline can completely inhibit rMMP1c activity, while Ba2+, Ca2+, and Mg2+ can significantly elevate it. TIMP is also expressed using HEK 293F cells. Recombinant TIMP (rTIMP) shows good inhibitory activity toward rMMP1c. Inhibition kinetics analyses reveal rTIMP to be a competitive inhibitor of rMMP1c. Biolayer interferometry reveals that rTIMP can effectively bind with rMMP1c, with an equilibrium dissociation constant value of 263 nM. rMMP1c effectively degrades type I collagen γ-β-α chains in turn, and rTIMP can significantly inhibit rMMP1c degradation activity. These results provide a theoretical basis for the study of MMP and TIMP interaction and elucidate the possible mechanism for abalone tissue self-degradation.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Ming-Hui Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Le-Le Su
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Le-Chang Sun
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xu-Jian Qiu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Duanquan Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Tengchuan Jin
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Collaborative Innovation Center of Marine Food Deep Processing, Dalian Polytechnic University, Dalian 116034, China
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10
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Plikusiene I, Maciulis V, Juciute S, Ramanavicius A, Balevicius Z, Slibinskas R, Kucinskaite-Kodze I, Simanavicius M, Balevicius S, Ramanaviciene A. Investigation of SARS-CoV-2 nucleocapsid protein interaction with a specific antibody by combined spectroscopic ellipsometry and quartz crystal microbalance with dissipation. J Colloid Interface Sci 2022; 626:113-122. [PMID: 35780545 PMCID: PMC9233548 DOI: 10.1016/j.jcis.2022.06.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 11/26/2022]
Abstract
Detailed evaluations of the antigen and antibody interaction rate and strength of the immune complex formed are very important for medical and bioanalytical applications. These data are crucial for the development of sensitive and fast immunosensors suitable for continuous measurements. Therefore, combined spectroscopic ellipsometry (SE) and quartz crystal microbalance with dissipation (QCM-D) technique (SE/QCM-D) was used for the evaluation: (i) of covalent immobilization of SARS-CoV-2 nucleocapsid protein (SCoV2-N) on QCM-D sensor disc modified by self-assembled monolayer based on 11-mercaptoundecanoic acid and (ii) interaction of immobilized SCoV2-N with specific polyclonal anti-SCoV2-N antibodies followed by immune complex formation process. The results show that the SCoV2-N monolayer is rigid due to the low energy dissipation registered during the QCM-D measurement. In contrast, the anti-SCoV2-N layer produced after interaction with the immobilized SCoV2-N formed a soft and viscous layer. It was determined, that the sparse distribution of SCoV2-N on the surface affected the spatial arrangement of the antibody during the formation of immune complexes. The hinge-mediated flexibility of the antibody Fab fragments allows them to reach the more distantly located SCoV2-N and establish a bivalent binding between proteins in the formed SCoV2-N/anti-SCoV2-N complex. It was noted that the SE/QCM-D method can provide more precise quantitative information about the flexibility and conformational changes of antibody during the formation of the immune complex on the surface over time.
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11
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Ahmad H, Khan A, Umbreen S, Khan T, Xuewei Z, Wei DQ, Tian Z. Structural and Dynamic Investigation of non-synonymous variations in Renin-AGT complex revealed altered binding via hydrogen bonding network reprogramming to accelerate the hypertension pathway. Chem Biol Drug Des 2022; 100:730-746. [PMID: 35730263 DOI: 10.1111/cbdd.14107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/13/2022] [Accepted: 06/19/2022] [Indexed: 11/28/2022]
Abstract
Hypertension is one of the major issues worldwide and one of the main factors involved in heart and kidney failure. Angiotensinogen and renin are key components of the renin-angiotensin-aldosterone system (RAAS), which plays an indispensable role in hypertension. The aimed of this study to find out the non-synonymous mutations and structure-based mutation-function correlation in the Renin-AGT complex and reveal the most deleterious mutations to accelerated hypertension. In the current study, we employed computational modelling and molecular simulation approaches to demonstrate the impact of specific mutations in the REN-AGT interface in hypertension. Computational algorithms i.e. PhD-SNP, PolyPhen-1, MAPP, SIFT, SNAP, PredictSNP, PolyPhen-2, and PANTHER predicted 20 mutations as deleterious in AGT while only five mutations were conformed as deleterious in the Renin protein. Investigation of the bonding analysis revealed that two mutations S107L and V193F in Renin altered the hydrogen-bonding paradigm at the interface site. Furthermore, exploration of structural-dynamic behaviors demonstrated by that these mutations also increases the structural stability to regulate the expression of disease pathway. The flexibility index of each residues and structural compactness analysis further validated the findings by portraying the difference in the dynamic behavior in contrast to the wild type. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) methods were used which further established the binding differences between the wild type, S107L, and V193F mutant variants. The total binding energy for wild type, S107L, and V193F were reported to be -27.79 kcal/mol, -47.72 kcal/mol, and -38.25 kcal/mol respectively. In conclusion, these two mutations increase the binding free energy alongside the docking score to enhance the binding between Renin and AGT to overexpress this pathway in a hypertension disease condition. Patients with these mutations may be screened for potential therapeutic intervention.
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Affiliation(s)
- Hussain Ahmad
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, 700149 Xi'an, China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zheng Xuewei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, 700149 Xi'an, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, P.R. China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Zhongmin Tian
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, 700149 Xi'an, China
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12
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Through the looking-glass - Recent developments in reflectometry open new possibilities for biosensor applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Xu L, Ramadan S, Akingbade OE, Zhang Y, Alodan S, Graham N, Zimmerman KA, Torres E, Heslegrave A, Petrov PK, Zetterberg H, Sharp DJ, Klein N, Li B. Detection of Glial Fibrillary Acidic Protein in Patient Plasma Using On-Chip Graphene Field-Effect Biosensors, in Comparison with ELISA and Single-Molecule Array. ACS Sens 2022; 7:253-262. [PMID: 34908400 PMCID: PMC8805154 DOI: 10.1021/acssensors.1c02232] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Glial
fibrillary
acidic protein (GFAP) is a discriminative blood
biomarker for many neurological diseases, such as traumatic brain
injury. Detection of GFAP in buffer solutions using biosensors has
been demonstrated, but accurate quantification of GFAP in patient
samples has not been reported, yet in urgent need. Herein, we demonstrate
a robust on-chip graphene field-effect transistor (GFET) biosensing
method for sensitive and ultrafast detection of GFAP in patient plasma.
Patients with moderate–severe traumatic brain injuries, defined
by the Mayo classification, are recruited to provide plasma samples.
The binding of target GFAP with the specific antibodies that are conjugated
on a monolayer GFET device triggers the shift of its Dirac point,
and this signal change is correlated with the GFAP concentration in
the patient plasma. The limit of detection (LOD) values of 20 fg/mL
(400 aM) in buffer solution and 231 fg/mL (4 fM) in patient plasma
have been achieved using this approach. In parallel, for the first
time, we compare our results to the state-of-the-art single-molecule
array (Simoa) technology and the classic enzyme-linked immunosorbent
assay (ELISA) for reference. The GFET biosensor shows competitive
LOD to Simoa (1.18 pg/mL) and faster sample-to-result time (<15
min), and also it is cheaper and more user-friendly. In comparison
to ELISA, GFET offers advantages of total detection time, detection
sensitivity, and simplicity. This GFET biosensing platform holds high
promise for the point-of-care diagnosis and monitoring of traumatic
brain injury in GP surgeries and patient homes.
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Affiliation(s)
- Lizhou Xu
- Department of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Sami Ramadan
- Department of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Oluwatomi E. Akingbade
- Department of Brain Sciences, Imperial College London, London W12 0BZ, U.K
- Care Research & Technology Centre, UK Dementia Research Institute, London W12 0BZ, U.K
| | - Yuanzhou Zhang
- Department of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Sarah Alodan
- Department of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Neil Graham
- Department of Brain Sciences, Imperial College London, London W12 0BZ, U.K
- Care Research & Technology Centre, UK Dementia Research Institute, London W12 0BZ, U.K
| | - Karl A. Zimmerman
- Department of Brain Sciences, Imperial College London, London W12 0BZ, U.K
- Care Research & Technology Centre, UK Dementia Research Institute, London W12 0BZ, U.K
| | - Elias Torres
- Graphenea Semiconductor, Paseo Mikeletegi 83, San Sebastián 20009, Spain
| | - Amanda Heslegrave
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, U.K
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1E 6BT, U.K
| | - Peter K. Petrov
- Department of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Henrik Zetterberg
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, U.K
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1E 6BT, U.K
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal 43141, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 43141, Sweden
- Hong Kong Centre for Neurodegenerative Diseases, Hong Kong 999077, China
| | - David J. Sharp
- Department of Brain Sciences, Imperial College London, London W12 0BZ, U.K
- Care Research & Technology Centre, UK Dementia Research Institute, London W12 0BZ, U.K
| | - Norbert Klein
- Department of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Bing Li
- Department of Brain Sciences, Imperial College London, London W12 0BZ, U.K
- Care Research & Technology Centre, UK Dementia Research Institute, London W12 0BZ, U.K
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14
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Khan A, Gui J, Ahmad W, Haq I, Shahid M, Khan AA, Shah A, Khan A, Ali L, Anwar Z, Safdar M, Abubaker J, Uddin NN, Cao L, Wei DQ, Mohammad A. The SARS-CoV-2 B.1.618 variant slightly alters the spike RBD-ACE2 binding affinity and is an antibody escaping variant: a computational structural perspective. RSC Adv 2021; 11:30132-30147. [PMID: 35480256 PMCID: PMC9040812 DOI: 10.1039/d1ra04694b] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Continuing reports of new SARS-CoV-2 variants have caused worldwide concern and created a challenging situation for clinicians. The recently reported variant B.1.618, which possesses the E484K mutation specific to the receptor-binding domain (RBD), as well as two deletions of Tyr145 and His146 at the N-terminal binding domain (NTD) of the spike protein, must be studied in depth to devise new therapeutic options. Structural variants reported in the RBD and NTD may play essential roles in the increased pathogenicity of this SARS-CoV-2 new variant. We explored the binding differences and structural-dynamic features of the B.1.618 variant using structural and biomolecular simulation approaches. Our results revealed that the E484K mutation in the RBD slightly altered the binding affinity through affecting the hydrogen bonding network. We also observed that the flexibility of three important loops in the RBD required for binding was increased, which may improve the conformational optimization and consequently binding of the new variant. Furthermore, we found that deletions of Tyr145 and His146 at the NTD reduced the binding affinity of the monoclonal antibody (mAb) 4A8, and that the hydrogen bonding network was significantly affected consequently. This data show that the new B.1.618 variant is an antibody-escaping variant with slightly altered ACE2-RBD affinity. Moreover, we provide insights into the binding and structural-dynamics changes resulting from novel mutations in the RBD and NTD. Our results suggest the need for further in vitro and in vivo studies that will facilitate the development of possible therapies for new variants such as B.1.618.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Jianjun Gui
- Department of Emergency, Shiyan People's Hospital Bao'an District Shenzhen China
| | - Waqar Ahmad
- Department of Microbiology, Abdul Wali Khan University Mardan Khyber Pakhtunkhwa Pakistan
| | - Inamul Haq
- Department of Animal Sciences, Jeonbuk National University 567 Baekji-Daero, Deokjin-gu Jeonju-si Jeollabuk-do 54896 Republic of Korea
| | - Marukh Shahid
- Department of Botany, University of Okara Okara Punjab Pakistan
| | | | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University Dir Sheringal Pakistan
| | - Arsala Khan
- Department of Pathology, University of Veterinary and Animal Sciences Lahore Punjab Pakistan
| | - Liaqat Ali
- Department of Biosciences, COMSATS University Islamabad 45550 Pakistan
| | - Zeeshan Anwar
- Department of Pharmacy, Abdul Wali Khan University Mardan Khyber Pakhtunkhwa Pakistan
| | - Muhammad Safdar
- Faculty of Pharmacy, Gomal University DI Khan Khyber Pakhtunkhwa Pakistan
| | - Jehad Abubaker
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute Kuwait
| | - N Nizam Uddin
- Biomedical Engineering Department, HITEC University Taxila Punjab Pakistan
| | - Liqiang Cao
- Henan University of Technology (HAUT) Zhengzhou P. R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P. R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200030 P. R. China
- Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nashan District Shenzhen Guangdong 518055 P. R China
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute Kuwait
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15
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Delamarche E, Pereiro I, Kashyap A, Kaigala GV. Biopatterning: The Art of Patterning Biomolecules on Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9637-9651. [PMID: 34347483 DOI: 10.1021/acs.langmuir.1c00867] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Patterning biomolecules on surfaces provides numerous opportunities for miniaturizing biological assays; biosensing; studying proteins, cells, and tissue sections; and engineering surfaces that include biological components. In this Feature Article, we summarize the themes presented in our recent Langmuir Lecture on patterning biomolecules on surfaces, miniaturizing surface assays, and interacting with biointerfaces using three key technologies: microcontact printing, microfluidic networks, and microfluidic probes.
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Affiliation(s)
- Emmanuel Delamarche
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Iago Pereiro
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Aditya Kashyap
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Govind V Kaigala
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
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16
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Khan. A, Wei D, Kousar K, Abubaker J, Ahmad S, Ali J, Al‐Mulla F, Ali SS, Nizam‐Uddin N, Mohammad Sayaf A, Mohammad A. Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. Chembiochem 2021; 22:2641-2649. [PMID: 34160124 PMCID: PMC8426803 DOI: 10.1002/cbic.202100191] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/23/2021] [Indexed: 01/05/2023]
Abstract
The evolution of new SARS-CoV-2 variants around the globe has made the COVID-19 pandemic more worrisome, further pressuring the health care system and immunity. Novel variations that are unique to the receptor-binding motif (RBM) of the receptor-binding domain (RBD) spike glycoprotein, i. e. L452R-E484Q, may play a different role in the B.1.617 (also known as G/452R.V3) variant's pathogenicity and better survival compared to the wild type. Therefore, a thorough analysis is needed to understand the impact of these mutations on binding with host receptor (RBD) and to guide new therapeutics development. In this study, we used structural and biomolecular simulation techniques to explore the impact of specific mutations (L452R-E484Q) in the B.1.617 variant on the binding of RBD to the host receptor ACE2. Our analysis revealed that the B.1.617 variant possesses different dynamic behaviours by altering dynamic-stability, residual flexibility and structural compactness. Moreover, the new variant had altered the bonding network and structural-dynamics properties significantly. MM/GBSA technique was used, which further established the binding differences between the wild type and B.1.617 variant. In conclusion, this study provides a strong impetus to develop novel drugs against the new SARS-CoV-2 variants.
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Affiliation(s)
- Abbas Khan.
- State Key Laboratory of Microbial MetabolismShanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial ResistancesJoint Laboratory of International Cooperation in Metabolic and Developmental SciencesMinistry of Education and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200030P. R. China
- Department of Bioinformatics and Biological StatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Dong‐Qing Wei
- State Key Laboratory of Microbial MetabolismShanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial ResistancesJoint Laboratory of International Cooperation in Metabolic and Developmental SciencesMinistry of Education and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200030P. R. China
- Department of Bioinformatics and Biological StatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I, Building 8Xili Street, Nashan DistrictShenzhenGuangdong518055P. R. China
| | - Kafila Kousar
- Atta ur Rahman School of Applied BiosciencesNational University of Science and Technology (NUST)IslamabadPakistan
| | - Jehad Abubaker
- Department of Biochemistry and Molecular BiologyDasman Diabetes Institute (Kuwait)
| | - Sajjad Ahmad
- Department of Health and Biological SciencesAbasyn UniversityKhyber PakhtunkhwaPakistan
| | - Javaid Ali
- Swat Institute of Nuclear Medicine Oncology and Radiotherapy (SINOR) HospitalSaidu SharifKhyber PakhtunkhwaPakistan
| | - Fahd Al‐Mulla
- Department of Genetics and BioinformaticsDasman Diabetes Institute (Kuwait)
| | - Syed Shujait Ali
- Center for Biotechnology and MicrobiologyUniversity of SwatSwat, KPPakistan
| | - N. Nizam‐Uddin
- Biomedical Engineering DepartmentHITEC UniversityTaxilaPakistan
| | | | - Anwar Mohammad
- Department of Biochemistry and Molecular BiologyDasman Diabetes Institute (Kuwait)
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17
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Hong T, Miyazaki T, Matsumoto A, Koji K, Miyahara Y, Anraku Y, Cabral H. Phosphorylcholine-Installed Nanocarriers Target Pancreatic Cancer Cells through the Phospholipid Transfer Protein. ACS Biomater Sci Eng 2021; 7:4439-4445. [PMID: 34351746 DOI: 10.1021/acsbiomaterials.1c00730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphorylcholine (PC) has been used to improve the water solubility and biocompatibility of biomaterials. Here, we show that PC can also work as a ligand for targeting cancer cells based on their increased phospholipid metabolism. PC-installed multiarm poly(ethylene glycol)s and polymeric micelles achieved high and rapid internalization in pancreatic cancer cells. This enhanced cellular uptake was drastically reduced when the cells were incubated with excess free PC or at 4 °C, as well as by inhibiting the phospholipid transfer protein (PLTP) on the surface of cancer cells, indicating an energy dependent active transport mediated by PLTP.
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Affiliation(s)
- Taehun Hong
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takuya Miyazaki
- Kanagawa Institute of Industrial Science and Technology (KISTEC), 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan.,Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Akira Matsumoto
- Kanagawa Institute of Industrial Science and Technology (KISTEC), 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan.,Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kyoko Koji
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yasutaka Anraku
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Horacio Cabral
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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18
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Abrogation of SARS-CoV-2 interaction with host (NRP1) neuropilin-1 receptor through high-affinity marine natural compounds to curtail the infectivity: A structural-dynamics data. Comput Biol Med 2021; 141:104714. [PMID: 34772509 PMCID: PMC8324387 DOI: 10.1016/j.compbiomed.2021.104714] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/27/2021] [Indexed: 01/07/2023]
Abstract
The evolution of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants around the globe has made the coronavirus disease 2019 (COVID-19) pandemic more worrisome, pressuring the health care system and resulting in an increased mortality rate. Recent studies recognized neuropilin-1 (NRP1) as a key facilitator in the invasion of the new SARS-CoV-2 into the host cell. Therefore, it is considered an imperative drug target for the treatment of COVID-19. Hence, a thorough analysis was needed to understand the impact and to guide new therapeutics development. In this study, we used structural and biomolecular simulation techniques to identify novel marine natural products which could block this receptor and stop the virus entry. We discovered that the binding affinity of CMNPD10175, CMNPD10017, CMNPD10114, CMNPD10115, CMNPD10020. CMNPD10018, CMNPD10153, CMNPD10149 CMNPD10464 and CMNPD10019 were substantial during the virtual screening (VS). We further explored these compounds by analyzing their absorption, distribution, metabolism, and excretion and toxicity (ADMET) properties and structural-dynamics features. Free energy calculations further established that all the compounds exhibit stronger binding energy for NRP1. Consequently, we hypothesized that these compounds might be the best lead candidates for therapeutic interventions hindering virus binding to the host cell. This study provides a strong impetus to develop novel drugs against the SARS-CoV-2 by targeting NRP1.
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19
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Khan A, Zia T, Suleman M, Khan T, Ali SS, Abbasi AA, Mohammad A, Wei DQ. Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. J Cell Physiol 2021; 236:7045-7057. [PMID: 33755190 PMCID: PMC8251074 DOI: 10.1002/jcp.30367] [Citation(s) in RCA: 236] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
The evolution of the SARS‐CoV‐2 new variants reported to be 70% more contagious than the earlier one is now spreading fast worldwide. There is an instant need to discover how the new variants interact with the host receptor (ACE2). Among the reported mutations in the Spike glycoprotein of the new variants, three are specific to the receptor‐binding domain (RBD) and required insightful scrutiny for new therapeutic options. These structural evolutions in the RBD domain may impart a critical role to the unique pathogenicity of the SARS‐CoV‐2 new variants. Herein, using structural and biophysical approaches, we explored that the specific mutations in the UK (N501Y), South African (K417N‐E484K‐N501Y), Brazilian (K417T‐E484K‐N501Y), and hypothetical (N501Y‐E484K) variants alter the binding affinity, create new inter‐protein contacts and changes the internal structural dynamics thereby increases the binding and eventually the infectivity. Our investigation highlighted that the South African (K417N‐E484K‐N501Y), Brazilian (K417T‐E484K‐N501Y) variants are more lethal than the UK variant (N501Y). The behavior of the wild type and N501Y is comparable. Free energy calculations further confirmed that increased binding of the spike RBD to the ACE2 is mainly due to the electrostatic contribution. Further, we find that the unusual virulence of this virus is potentially the consequence of Darwinian selection‐driven epistasis in protein evolution. The triple mutants (South African and Brazilian) may pose a serious threat to the efficacy of the already developed vaccine. Our analysis would help to understand the binding and structural dynamics of the new mutations in the RBD domain of the Spike protein and demand further investigation in in vitro and in vivo models to design potential therapeutics against the new variants.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Tauqir Zia
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber-Pakhtunkhwa, Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Khyber-Pakhtunkhwa, Pakistan
| | - Aamir Ali Abbasi
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, Shanghai Jiao Tong University, Shanghai, P.R. China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Guangdong, Shenzhen, P.R. China
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20
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Rubén LC, Laura MR, Almudena FB, Emilio GM. Glycan array analysis of Pholiota squarrosa lectin and other fucose-oriented lectins. Glycobiology 2020; 31:459-476. [PMID: 33021632 DOI: 10.1093/glycob/cwaa093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
The α(1,6)fucose residue attached to the N-glycoprotein core is suspected to play an essential role in the progression of several types of cancer. Lectins remain the first choice for probing glycan modifications, although they may lack specificity. Thus, efforts have been made to identify new lectins with a narrower core fucose (CF) detection profile. Here, we present a comparison of the classical Aleuria aurantia lectin (AAL), Lens culinaris agglutinin (LCA) and Aspergillus oryzae lectin (AOL) with the newer Pholiota squarrosa lectin (PhoSL), which has been described as being specific for core fucosylated N-glycans. To this end, we studied the binding profiles of the four lectins using mammalian glycan arrays from the Consortium of Functional Glycomics. To validate their glycan specificity, we probed AOL, LCA and PhoSL in western-blot assays using protein extracts from eight common colorectal cancer (CRC) lines and colorectal biopsies from a small cohort of patients with CRC. The results showed that (i) LCA and PhoSL were the most specific lectins for detecting the presence of CF in a concentration-dependent manner; (ii) PhoSL exhibited the highest N-glycan sequence restriction, with preferential binding to core fucosylated paucimannosidic-type N-glycans, (iii) the recognition ability of PhoSL was highly influenced by the presence of terminal N-acetyl-lactosamine; (iv) LCA bound to paucimannosidic, bi-antennary and tri-antennary core fucosylated N-glycans and (v) AOL and AAL exhibited broader specificity towards fucosylation. Together, our results support the choice of LCA as the most appropriate lectin for CF detection, as validated in protein extracts from CRC cell lines and tissue specimens from patients with CRC.
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Affiliation(s)
- López-Cortés Rubén
- Doctoral Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, Vigo, Pontevedra, Galicia ES36310, Spain
| | - Muinelo-Romay Laura
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), CIBERONC, Travesía da Choupana, Santiago de Compostela, A Coruña, Galicia ES15706, Spain
| | - Fernández-Briera Almudena
- Molecular Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, Vigo, Pontevedra, Galicia ES36310, Spain
| | - Gil Martín Emilio
- Nutrition and Food Science Group, Department of Biochemistry, Genetics and Immunology, Faculty of Biology, Universidade de Vigo. Campus Lagoas-Marcosende, Vigo, Pontevedra, Galicia ES36310, Spain
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21
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Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc AM, Mohammed Y, Aguilar‐Mahecha A, Poetz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH. Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells. Proteomics Clin Appl 2020; 14:e2000034. [PMID: 32643306 PMCID: PMC7539945 DOI: 10.1002/prca.202000034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/13/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Immuno-MALDI (iMALDI) combines immuno-enrichment of biomarkers with MALDI-MS for fast, precise, and specific quantitation, making it a valuable tool for developing clinical assays. iMALDI assays are optimized for the PI3-kinase signaling pathway members phosphatase and tensin homolog (PTEN) and PI3-kinase catalytic subunit alpha (p110α), with regard to sensitivity, robustness, and throughput. A standardized template for developing future iMALDI assays, including automation protocols to streamline assay development and translation, is provided. EXPERIMENTAL DESIGN Conditions for tryptic digestion and immuno-enrichment (beads, bead:antibody ratios, incubation times, direct vs. indirect immuno-enrichment) are rigorously tested. Different strategies for calibration and data readout are compared. RESULTS Digestion using 1:2 protein:trypsin (wt:wt) for 1 h yielded high and consistent peptide recoveries. Direct immuno-enrichment (antibody-bead coupling prior to antigen-enrichment) yielded 30% higher peptide recovery with a 1 h shorter incubation time than indirect enrichment. Immuno-enrichment incubation overnight yielded 1.5-fold higher sensitivities than 1 h incubation. Quantitation of the endogenous target proteins is not affected by the complexity of the calibration matrix, further simplifying the workflow. CONCLUSIONS AND CLINICAL RELEVANCE This optimized and automated workflow will facilitate the clinical translation of high-throughput sensitive iMALDI assays for quantifying cell-signaling proteins in individual tumor samples, thereby improving patient stratification for targeted treatment.
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Affiliation(s)
- Bjoern C. Froehlich
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCV8P 5C2Canada
| | - Robert Popp
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
| | - Constance A. Sobsey
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Andre M. LeBlanc
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Yassene Mohammed
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeiden2333 ZAThe Netherlands
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscow121205Russia
| | - Adriana Aguilar‐Mahecha
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute University of TuebingenReutlingen72770Germany
- SIGNATOPE GmbHReutlingen72770Germany
| | - Michael X. Chen
- Department of Pathology and Laboratory MedicineFaculty of MedicineUniversity of British ColumbiaVancouverCanada
| | - Alan Spatz
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Mark Basik
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Gerald Batist
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQCH4A3T2Canada
| | - René P. Zahedi
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscow121205Russia
| | - Christoph H. Borchers
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQCH4A3T2Canada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscow121205Russia
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22
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Crawford BM, Wang HN, Stolarchuk C, von Furstenberg RJ, Strobbia P, Zhang D, Qin X, Owzar K, Garman KS, Vo-Dinh T. Plasmonic nanobiosensors for detection of microRNA cancer biomarkers in clinical samples. Analyst 2020; 145:4587-4594. [PMID: 32436503 PMCID: PMC9532004 DOI: 10.1039/d0an00193g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
MicroRNAs (miRNAs) play an important role in the regulation of biological processes and have demonstrated great potential as biomarkers for the early detection of various diseases, including esophageal adenocarcinoma (EAC) and Barrett's esophagus (BE), the premalignant metaplasia associated with EAC. Herein, we demonstrate the direct detection of the esophageal cancer biomarker, miR-21, in RNA extracted from 17 endoscopic tissue biopsies using the nanophotonics technology our group has developed, termed the inverse molecular sentinel (iMS) nanobiosensor, with surface-enhanced Raman scattering (SERS) detection. The potential of this label-free, homogeneous biosensor for cancer diagnosis without the need for target amplification was demonstrated by discriminating esophageal cancer and Barrett's esophagus from normal tissue with notable diagnostic accuracy. This work establishes the potential of the iMS nanobiosensor for cancer diagnostics via miRNA detection in clinical samples without the need for target amplification, validating the potential of this assay as part of a new diagnostic strategy. Combining miRNA diagnostics with the nanophotonics technology will result in a paradigm shift in achieving a general molecular analysis tool that has widespread applicability for cancer research as well as detection of cancer. We anticipate further development of this technique for future use in point-of-care testing as an alternative to histopathological diagnosis as our method provides a quick result following RNA isolation, allowing for timely treatment.
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23
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Liu H, Moura-Alves P, Pei G, Mollenkopf HJ, Hurwitz R, Wu X, Wang F, Liu S, Ma M, Fei Y, Zhu C, Koehler AB, Oberbeck-Mueller D, Hahnke K, Klemm M, Guhlich-Bornhof U, Ge B, Tuukkanen A, Kolbe M, Dorhoi A, Kaufmann SH. cGAS facilitates sensing of extracellular cyclic dinucleotides to activate innate immunity. EMBO Rep 2019; 20:embr.201846293. [PMID: 30872316 DOI: 10.15252/embr.201846293] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/26/2022] Open
Abstract
Cyclic dinucleotides (CDNs) are important second messenger molecules in prokaryotes and eukaryotes. Within host cells, cytosolic CDNs are detected by STING and alert the host by activating innate immunity characterized by type I interferon (IFN) responses. Extracellular bacteria and dying cells can release CDNs, but sensing of extracellular CDNs (eCDNs) by mammalian cells remains elusive. Here, we report that endocytosis facilitates internalization of eCDNs. The DNA sensor cGAS facilitates sensing of endocytosed CDNs, their perinuclear accumulation, and subsequent STING-dependent release of type I IFN Internalized CDNs bind cGAS directly, leading to its dimerization, and the formation of a cGAS/STING complex, which may activate downstream signaling. Thus, eCDNs comprise microbe- and danger-associated molecular patterns that contribute to host-microbe crosstalk during health and disease.
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Affiliation(s)
- Haipeng Liu
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Pedro Moura-Alves
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Gang Pei
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hans-Joachim Mollenkopf
- Department of Immunology, Microarray Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Robert Hurwitz
- Protein Purification Core Facility, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Xiangyang Wu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fei Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siyu Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Mingtong Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yiyan Fei
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Fudan University, Shanghai, China
| | - Chenggang Zhu
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Fudan University, Shanghai, China
| | - Anne-Britta Koehler
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | | | - Karin Hahnke
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Marion Klemm
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Ute Guhlich-Bornhof
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | | | - Michael Kolbe
- Max Planck Institute for Infection Biology, Structural Systems Biology, Berlin, Germany.,Department of Structural Infection Biology, Center for Structural Systems Biology, Hamburg, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany.,Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Anca Dorhoi
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany .,Institute of Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Griefswald-Insel Riems, Germany.,Faculty of Mathematics and Natural Sciences, University of Greifswald, Greifswald, Germany
| | - Stefan He Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany .,Faculty Fellow of the Hagler Institute for Advanced Study at Texas A&M University, College Station, TX, USA
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24
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Nuclear cGAS suppresses DNA repair and promotes tumorigenesis. Nature 2018; 563:131-136. [PMID: 30356214 DOI: 10.1038/s41586-018-0629-6] [Citation(s) in RCA: 395] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/22/2018] [Indexed: 12/24/2022]
Abstract
Accurate repair of DNA double-stranded breaks by homologous recombination preserves genome integrity and inhibits tumorigenesis. Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that activates innate immunity by initiating the STING-IRF3-type I IFN signalling cascade1,2. Recognition of ruptured micronuclei by cGAS links genome instability to the innate immune response3,4, but the potential involvement of cGAS in DNA repair remains unknown. Here we demonstrate that cGAS inhibits homologous recombination in mouse and human models. DNA damage induces nuclear translocation of cGAS in a manner that is dependent on importin-α, and the phosphorylation of cGAS at tyrosine 215-mediated by B-lymphoid tyrosine kinase-facilitates the cytosolic retention of cGAS. In the nucleus, cGAS is recruited to double-stranded breaks and interacts with PARP1 via poly(ADP-ribose). The cGAS-PARP1 interaction impedes the formation of the PARP1-Timeless complex, and thereby suppresses homologous recombination. We show that knockdown of cGAS suppresses DNA damage and inhibits tumour growth both in vitro and in vivo. We conclude that nuclear cGAS suppresses homologous-recombination-mediated repair and promotes tumour growth, and that cGAS therefore represents a potential target for cancer prevention and therapy.
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25
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Affiliation(s)
- Limor Cohen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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26
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Li Y, Liu W, Jin G, Niu Y, Chen Y, Xie M. Label-Free Sandwich Imaging Ellipsometry Immunosensor for Serological Detection of Procalcitonin. Anal Chem 2018; 90:8002-8010. [DOI: 10.1021/acs.analchem.8b00888] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yike Li
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
| | - Wei Liu
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China
- NML, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Gang Jin
- NML, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
- School of Engineering Science, University of Chinese Academy of Science, Beijing 100049, China
| | - Yu Niu
- NML, Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yiping Chen
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Mengxia Xie
- Analytical and Testing Center of Beijing Normal University, Beijing 100875, China
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27
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McAllister TE, Yeh TL, Abboud MI, Leung IKH, Hookway ES, King ONF, Bhushan B, Williams ST, Hopkinson RJ, Münzel M, Loik ND, Chowdhury R, Oppermann U, Claridge TDW, Goto Y, Suga H, Schofield CJ, Kawamura A. Non-competitive cyclic peptides for targeting enzyme-substrate complexes. Chem Sci 2018; 9:4569-4578. [PMID: 29899950 PMCID: PMC5969509 DOI: 10.1039/c8sc00286j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 01/19/2023] Open
Abstract
Affinity reagents are of central importance for selectively identifying proteins and investigating their interactions. We report on the development and use of cyclic peptides, identified by mRNA display-based RaPID methodology, that are selective for, and tight binders of, the human hypoxia inducible factor prolyl hydroxylases (PHDs) - enzymes crucial in hypoxia sensing. Biophysical analyses reveal the cyclic peptides to bind in a distinct site, away from the enzyme active site pocket, enabling conservation of substrate binding and catalysis. A biotinylated cyclic peptide captures not only the PHDs, but also their primary substrate hypoxia inducible factor HIF1-α. Our work highlights the potential for tight, non-active site binding cyclic peptides to act as promising affinity reagents for studying protein-protein interactions.
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Affiliation(s)
- T E McAllister
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - T-L Yeh
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M I Abboud
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - I K H Leung
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
| | - E S Hookway
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - O N F King
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - B Bhushan
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - S T Williams
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - R J Hopkinson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M Münzel
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - N D Loik
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - R Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - U Oppermann
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - T D W Claridge
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Y Goto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
- JST , CREST , The University of Tokyo , Tokyo 113-0033 , Japan
| | - C J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - A Kawamura
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
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28
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Label-free Microarray-based Binding Affinity Constant Measurement with Modified Fluidic Arrangement. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2102-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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29
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Malovichko G, Zhu X. Single Amino Acid Substitution in the Vicinity of a Receptor-Binding Domain Changes Protein-Peptide Binding Affinity. ACS OMEGA 2017; 2:5445-5452. [PMID: 31457812 PMCID: PMC6644533 DOI: 10.1021/acsomega.7b00963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/24/2017] [Indexed: 06/10/2023]
Abstract
Using a microarray-based assay, we studied how the substitution of amino acids in the immediate vicinity of the receptor-binding domain on a peptide affects its binding to a protein. Replicates of 802 linear peptides consisting of the variants of WTHPQFAT and LQWHPQAGK, GKFPIPLGKQSG, and NGQFQVWIPGAQK, different by one amino acid, were synthesized on a glass slide with a maskless photolithography. Using a microarray-compatible label-free optical sensor, we measured the binding curves of streptavidin with the synthesized peptides and extracted the streptavidin-peptide affinity constants. We found that (a) the substitution of one residue in the HPQ motif reduces the affinity constant K a from 108 M-1 by at least 3-4 orders of magnitude, with an exception of HPM; (b) substitution of the immediate flanking residue on the Gln side also causes the affinity to decrease by up to 3-4 orders of magnitude, depending on the substituting residue and the second-neighboring flanking residue; (c) substitution of the flanking residues on the His side has no significant effect on the affinity, possibly due to the strong binding of streptavidin to HPQF and HPQAG motifs. We also found that some of amino acid residues located close to the C-terminus (and the solid surface) improve the yield of peptide synthesis on a glass surface and can be exploited in the fabrication of peptide microarrays.
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30
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Malaspina DC, Longo G, Szleifer I. Behavior of ligand binding assays with crowded surfaces: Molecular model of antigen capture by antibody-conjugated nanoparticles. PLoS One 2017; 12:e0185518. [PMID: 28957393 PMCID: PMC5619776 DOI: 10.1371/journal.pone.0185518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022] Open
Abstract
Ligand-receptor binding is of utmost importance in several biologically related disciplines. Ligand binding assays (LBA) use the high specificity and high affinity of ligands to detect, target or measure a specific receptors. One particular example of ligand binding assays are Antibody conjugated Nanoparticles (AcNPs), edge-cutting technologies that are present in several novel biomedical approaches for imaging, detection and treatment of diseases. However, the nano-confinement in AcNPs and LBA nanostructures introduces extra complexity in the analysis of ligand-receptor equilibriums. Because antibodies are large voluminous ligands, the effective affinity in AcNPs is often determined by antibody orientation and surface coverage. Moreover, antibodies have two binding sites introducing an extra ligand-receptor binding equilibrium. As consequence of all this, experimental or theoretical studies providing a guidelines for the prediction of the binding behavior in AcNPs are scarce. In this work, we present a set of theoretical calculations to shed light into the complex binding behavior of AcNPs and its implications in biomedical applications. To investigate the ligand-receptor binding on AcNPs, we have used a molecular theory that predicts the probability of different molecular conformations of the system depending on the local environment. We have considered two different pathways for designing these devices: covalently conjugated antibodies and streptavidin-biotin conjugated antibodies. We also explore the effects of surface coverage, bulk concentrations, nanoparticle size and antibody-antigen affinity. Overall, this work offers a series of theoretical predictions that can be used as a guide in the design of antibody conjugated nanoparticles for different applications.
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Affiliation(s)
- David C. Malaspina
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, United States of America
| | - Gabriel Longo
- Instituto de Investigaciones Fisicoquímicas, Teóricas y Aplicadas (INIFTA), UNLP, CONICET, La Plata, Argentina
| | - Igal Szleifer
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, United States of America
- Chemistry Department and Chemistry of Life Processes Institute, Evanston, Illinois, United States of America
- * E-mail:
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31
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Wang J, Zhu C, Song D, Xia R, Yu W, Dang Y, Fei Y, Yu L, Wu J. Epigallocatechin-3-gallate enhances ER stress-induced cancer cell apoptosis by directly targeting PARP16 activity. Cell Death Discov 2017; 3:17034. [PMID: 28698806 PMCID: PMC5502302 DOI: 10.1038/cddiscovery.2017.34] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/12/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) are ADP-ribosylating enzymes and play important roles in a variety of cellular processes. Most small-molecule PARP inhibitors developed to date have been against PARP1, a poly-ADP-ribose transferase, and suffer from poor selectivity. PARP16, a mono-ADP-ribose transferase, has recently emerged as a potential therapeutic target, but its inhibitor development has trailed behind. Here we newly characterized epigallocatechin-3-gallate (EGCG) as a potential inhibitor of PARP16. We found that EGCG was associated with PARP16 and dramatically inhibited its activity in vitro. Moreover, EGCG suppressed the ER stress-induced phosphorylation of PERK and the transcription of unfolded protein response-related genes, leading to dramatically increase of cancer cells apoptosis under ER stress conditions, which was dependent on PARP16. These findings newly characterized EGCG as a potential inhibitor of PARP16, which can enhance the ER stress-induced cancer cell apoptosis, suggesting that a combination of EGCG and ER stress-induced agents might represent a novel approach for cancer therapy or chemoprevention.
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Affiliation(s)
- Juanjuan Wang
- The State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Science, Fudan University, Shanghai, PR China
| | - Chenggang Zhu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, PR China
| | - Dan Song
- The State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Science, Fudan University, Shanghai, PR China
| | - Ruiqi Xia
- The State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Science, Fudan University, Shanghai, PR China
| | - Wenbo Yu
- The State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Science, Fudan University, Shanghai, PR China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, The Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, PR China
| | - Long Yu
- The State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Science, Fudan University, Shanghai, PR China
| | - Jiaxue Wu
- The State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Science, Fudan University, Shanghai, PR China
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32
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Ivan T, Enkvist E, Sinijarv H, Uri A. Competitive ligands facilitate dissociation of the complex of bifunctional inhibitor and protein kinase. Biophys Chem 2017. [PMID: 28651101 DOI: 10.1016/j.bpc.2017.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Dissociation of the complex of a ligand and a protein usually follows the kinetic profile of the first order process and the rate of dissociation is not affected by the presence of competitive ligands. We discovered that dissociation of the complex between a bifunctional ligand and a protein kinase (the catalytic subunit of cAMP-dependent protein kinase), an enzyme possessing 2 different substrate binding sites, was accelerated (facilitated) over 50-fold in the presence of competitive ligands at higher concentrations. Structurally diverse compounds revealed >10-fold different efficiency for acceleration of dissociation of the complex. These results show that the kinetic behavior of flexible biomolecular complexes possessing two spatially separated contact areas is highly dynamic. This property of biomolecular complexes should be carefully considered for effective application of bifunctional ligands for regulation of activity of target proteins in cells.
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Affiliation(s)
- Taavi Ivan
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Hedi Sinijarv
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
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Sun YS, Landry JP, Zhu XD. Evaluation of Kinetics Using Label-Free Optical Biosensors. INSTRUMENTATION SCIENCE & TECHNOLOGY 2017; 45:486-505. [PMID: 30906180 PMCID: PMC6430235 DOI: 10.1080/10739149.2016.1277535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Optical biosensors provide a platform for qualitatively and quantitatively analyzing various biomolecular interactions. In addition to advantages such as label-free and high-throughput detection, these devices are also capable of measuring real-time binding curves in response to changes in optical properties of biomolecules. These kinetic data may be fitted to models to extract binding affinities such as association rates, dissociation rates, and equilibrium dissociation constants. In these biosensors, one of the binding pair is usually immobilized on a solid substrate for capturing the other. Due to the nature of these surface-based methods, mass transport effects and immobilization heterogenetity may cause problems when fitting the kinetic curves with the simple one-to-one Langmuir model. Here real-time binding curves of various antibody-antigen reactions were obtained by using an ellipsometry-based biosensor, and the results were fitted to the simple one-to-one model as well as a more sophisticated approach. The results show that the one-to-two model fitted much better to the curves than the one-to-one model. The two-site model may be explained by assuming two immobilization configurations on the surface. In summary, in fitting real-time curves obtained from optical biosensors, more sophisticated models are usually required to take surface-related issues, such as immobilization heterogenetity and mass transport effects within targets, into account.
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Affiliation(s)
- Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - James P. Landry
- Department of Physics, University of California at Davis, Davis, CA, USA
| | - X. D. Zhu
- Department of Physics, University of California at Davis, Davis, CA, USA
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Abstract
Microarrays of biological molecules such as DNAs, proteins, carbohydrates, and small molecules provide a high-throughput platform for screening tens of thousands of biomolecular interactions simultaneously, facilitating the functional characterization of these biomolecules in areas of genomics, proteomics, glycomics, and cytomics. Routinely, analysis of binding reactions between solution-phased probes and surface-immobilized targets involves some kinds of fluorescence-based detection methods. Even though these methods have advantages of high sensitivity and wide dynamic range, labeling probes and/or targets inevitably changes their innate properties and in turn affects probe-target interactions in often uncharacterized ways. Therefore, in recent years, various label-free sensing technologies have been developed for characterizing biomolecular interactions in microarray format. These biosensors, to a certain extent, take the place of fluorescent methods by providing a comparable sensitivity as well as retaining the conformational and functional integrality of biomolecules to be investigated. More importantly, some of these biosensors are capable of real-time monitoring probe-target interactions, providing the binding affinities of these reactions. Using label-free biosensors in microarrays has become a current trend in developing high-throughput screening platforms for drug discoveries and applications in all areas of "-omics." This article is aimed to provide principles and recent developments in label-free sensing technologies applicable to microarrays, with special attentions being paid to surface plasmon resonance microscopy and oblique-incidence reflectivity difference microscopy.
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Affiliation(s)
- Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New Taipei City, Taiwan, 24205.
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Sun YS, Zhu X. Characterization of Bovine Serum Albumin Blocking Efficiency on Epoxy-Functionalized Substrates for Microarray Applications. ACTA ACUST UNITED AC 2016; 21:625-31. [DOI: 10.1177/2211068215586977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Indexed: 01/21/2023]
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36
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Guo X, Deng Y, Zhu C, Cai J, Zhu X, Landry JP, Zheng F, Cheng X, Fei Y. Characterization of protein expression levels with label-free detected reverse phase protein arrays. Anal Biochem 2016; 509:67-72. [PMID: 27372609 DOI: 10.1016/j.ab.2016.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 01/12/2023]
Abstract
In reverse-phase protein arrays (RPPA), one immobilizes complex samples (e.g., cellular lysate, tissue lysate or serum etc.) on solid supports and performs parallel reactions of antibodies with immobilized protein targets from the complex samples. In this work, we describe a label-free detection of RPPA that enables quantification of RPPA data and thus facilitates comparison of studies performed on different samples and on different solid supports. We applied this detection platform to characterization of phosphoserine aminotransferase (PSAT) expression levels in Acanthamoeba lysates treated with artemether and the results were confirmed by Western blot studies.
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Affiliation(s)
- Xuexue Guo
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China
| | - Yihong Deng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Chenggang Zhu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China
| | - Junlong Cai
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiangdong Zhu
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - James P Landry
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - Fengyun Zheng
- Institutes of Biomedical Science, Fudan University, Shanghai, 200032, China
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China.
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Hsiao JJ, Smits MM, Ng BH, Lee J, Wright ME. Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription. J Biol Chem 2016; 291:18818-42. [PMID: 27365400 PMCID: PMC5009256 DOI: 10.1074/jbc.m116.732313] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant androgen receptor (AR)-dependent transcription is a hallmark of human prostate cancers. At the molecular level, ligand-mediated AR activation is coordinated through spatial and temporal protein-protein interactions involving AR-interacting proteins, which we designate the “AR-interactome.” Despite many years of research, the ligand-sensitive protein complexes involved in ligand-mediated AR activation in prostate tumor cells have not been clearly defined. Here, we describe the development, characterization, and utilization of a novel human LNCaP prostate tumor cell line, N-AR, which stably expresses wild-type AR tagged at its N terminus with the streptavidin-binding peptide epitope (streptavidin-binding peptide-tagged wild-type androgen receptor; SBP-AR). A bioanalytical workflow involving streptavidin chromatography and label-free quantitative mass spectrometry was used to identify SBP-AR and associated ligand-sensitive cytosolic proteins/protein complexes linked to AR activation in prostate tumor cells. Functional studies verified that ligand-sensitive proteins identified in the proteomic screen encoded modulators of AR-mediated transcription, suggesting that these novel proteins were putative SBP-AR-interacting proteins in N-AR cells. This was supported by biochemical associations between recombinant SBP-AR and the ligand-sensitive coatomer protein complex I (COPI) retrograde trafficking complex in vitro. Extensive biochemical and molecular experiments showed that the COPI retrograde complex regulates ligand-mediated AR transcriptional activation, which correlated with the mobilization of the Golgi-localized ARA160 coactivator to the nuclear compartment of prostate tumor cells. Collectively, this study provides a bioanalytical strategy to validate the AR-interactome and define novel AR-interacting proteins involved in ligand-mediated AR activation in prostate tumor cells. Moreover, we describe a cellular system to study how compartment-specific AR-interacting proteins influence AR activation and contribute to aberrant AR-dependent transcription that underlies the majority of human prostate cancers.
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Affiliation(s)
- Jordy J Hsiao
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Melinda M Smits
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Brandon H Ng
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Jinhee Lee
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
| | - Michael E Wright
- From the Department of Molecular Physiology and Biophysics, Carver College of Medicine, Iowa City, Iowa 52242
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Zhu C, Zhu X, Landry JP, Cui Z, Li Q, Dang Y, Mi L, Zheng F, Fei Y. Developing an Efficient and General Strategy for Immobilization of Small Molecules onto Microarrays Using Isocyanate Chemistry. SENSORS (BASEL, SWITZERLAND) 2016; 16:E378. [PMID: 26999137 PMCID: PMC4813953 DOI: 10.3390/s16030378] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 01/06/2023]
Abstract
Small-molecule microarray (SMM) is an effective platform for identifying lead compounds from large collections of small molecules in drug discovery, and efficient immobilization of molecular compounds is a pre-requisite for the success of such a platform. On an isocyanate functionalized surface, we studied the dependence of immobilization efficiency on chemical residues on molecular compounds, terminal residues on isocyanate functionalized surface, lengths of spacer molecules, and post-printing treatment conditions, and we identified a set of optimized conditions that enable us to immobilize small molecules with significantly improved efficiencies, particularly for those molecules with carboxylic acid residues that are known to have low isocyanate reactivity. We fabricated microarrays of 3375 bioactive compounds on isocyanate functionalized glass slides under these optimized conditions and confirmed that immobilization percentage is over 73%.
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Affiliation(s)
- Chenggang Zhu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China.
| | - Xiangdong Zhu
- Department of Physics, University of California, Davis, CA 95616, USA.
| | - James P Landry
- Department of Physics, University of California, Davis, CA 95616, USA.
| | - Zhaomeng Cui
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Quanfu Li
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China.
| | - Fengyun Zheng
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200433, China.
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Jalali-Yazdi F, Huong Lai L, Takahashi TT, Roberts RW. High-Throughput Measurement of Binding Kinetics by mRNA Display and Next-Generation Sequencing. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Farzad Jalali-Yazdi
- Department of Chemical Engineering and Materials Science; University of Southern California; Los Angeles CA 90089 USA
| | - Lan Huong Lai
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Terry T. Takahashi
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Richard W. Roberts
- Department of Chemical Engineering and Materials Science; University of Southern California; Los Angeles CA 90089 USA
- Department of Molecular Computational Biology; USC Norris Comprehensive Cancer Center; University of Southern California; Los Angeles CA 90089 USA
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Jalali-Yazdi F, Lai LH, Takahashi TT, Roberts RW. High-Throughput Measurement of Binding Kinetics by mRNA Display and Next-Generation Sequencing. Angew Chem Int Ed Engl 2016; 55:4007-10. [PMID: 26914638 DOI: 10.1002/anie.201600077] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/02/2016] [Indexed: 01/23/2023]
Abstract
There is great demand for high-throughput methods to characterize ligand affinity. By combining mRNA display with next-generation sequencing, we determined the kinetic on- and off-rates for over twenty thousand ligands without the need for synthesis or purification of individual members. Our results are reproducible and as accurate as those obtained with other methods of affinity measurement.
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Affiliation(s)
- Farzad Jalali-Yazdi
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lan Huong Lai
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Richard W Roberts
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA. .,Department of Molecular Computational Biology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.
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41
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DeLoid GM, Cohen JM, Pyrgiotakis G, Pirela SV, Pal A, Liu J, Srebric J, Demokritou P. Advanced computational modeling for in vitro nanomaterial dosimetry. Part Fibre Toxicol 2015; 12:32. [PMID: 26497802 PMCID: PMC4619515 DOI: 10.1186/s12989-015-0109-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/12/2015] [Indexed: 12/27/2022] Open
Abstract
Background Accurate and meaningful dose metrics are a basic requirement for in vitro screening to assess potential health risks of engineered nanomaterials (ENMs). Correctly and consistently quantifying what cells “see,” during an in vitro exposure requires standardized preparation of stable ENM suspensions, accurate characterizatoin of agglomerate sizes and effective densities, and predictive modeling of mass transport. Earlier transport models provided a marked improvement over administered concentration or total mass, but included assumptions that could produce sizable inaccuracies, most notably that all particles at the bottom of the well are adsorbed or taken up by cells, which would drive transport downward, resulting in overestimation of deposition. Methods Here we present development, validation and results of two robust computational transport models. Both three-dimensional computational fluid dynamics (CFD) and a newly-developed one-dimensional Distorted Grid (DG) model were used to estimate delivered dose metrics for industry-relevant metal oxide ENMs suspended in culture media. Both models allow simultaneous modeling of full size distributions for polydisperse ENM suspensions, and provide deposition metrics as well as concentration metrics over the extent of the well. The DG model also emulates the biokinetics at the particle-cell interface using a Langmuir isotherm, governed by a user-defined dissociation constant, KD, and allows modeling of ENM dissolution over time. Results Dose metrics predicted by the two models were in remarkably close agreement. The DG model was also validated by quantitative analysis of flash-frozen, cryosectioned columns of ENM suspensions. Results of simulations based on agglomerate size distributions differed substantially from those obtained using mean sizes. The effect of cellular adsorption on delivered dose was negligible for KD values consistent with non-specific binding (> 1 nM), whereas smaller values (≤ 1 nM) typical of specific high-affinity binding resulted in faster and eventual complete deposition of material. Conclusions The advanced models presented provide practical and robust tools for obtaining accurate dose metrics and concentration profiles across the well, for high-throughput screening of ENMs. The DG model allows rapid modeling that accommodates polydispersity, dissolution, and adsorption. Result of adsorption studies suggest that a reflective lower boundary condition is appropriate for modeling most in vitro ENM exposures. Electronic supplementary material The online version of this article (doi:10.1186/s12989-015-0109-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Glen M DeLoid
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.
| | - Joel M Cohen
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Georgios Pyrgiotakis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Sandra V Pirela
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Anoop Pal
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA
| | - Jiying Liu
- Department of Architectural Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,School of Thermal Engineering, Shandong Jianzhu University, 1000 Fengming Rd, Jinan, China
| | - Jelena Srebric
- Department of Architectural Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.
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de Guzman RC, Tsuda SM, Ton MTN, Zhang X, Esker AR, Van Dyke ME. Binding Interactions of Keratin-Based Hair Fiber Extract to Gold, Keratin, and BMP-2. PLoS One 2015; 10:e0137233. [PMID: 26317522 PMCID: PMC4552821 DOI: 10.1371/journal.pone.0137233] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/14/2015] [Indexed: 11/22/2022] Open
Abstract
Hair-derived keratin biomaterials composed mostly of reduced keratin proteins (kerateines) have demonstrated their utility as carriers of biologics and drugs for tissue engineering. Electrostatic forces between negatively-charged keratins and biologic macromolecules allow for effective drug retention; attraction to positively-charged growth factors like bone morphogenetic protein 2 (BMP-2) has been used as a strategy for osteoinduction. In this study, the intermolecular surface and bulk interaction properties of kerateines were investigated. Thiol-rich kerateines were chemisorbed onto gold substrates to form an irreversible 2-nm rigid layer for surface plasmon resonance analysis. Kerateine-to-kerateine cohesion was observed in pH-neutral water with an equilibrium dissociation constant (KD) of 1.8 × 10(-4) M, indicating that non-coulombic attractive forces (i.e. hydrophobic and van der Waals) were at work. The association of BMP-2 to kerateine was found to be greater (KD = 1.1 × 10(-7) M), within the range of specific binding. Addition of salts (phosphate-buffered saline; PBS) shortened the Debye length or the electrostatic field influence which weakened the kerateine-BMP-2 binding (KD = 3.2 × 10(-5) M). BMP-2 in bulk kerateine gels provided a limited release in PBS (~ 10% dissociation in 4 weeks), suggesting that electrostatic intermolecular attraction was significant to retain BMP-2 within the keratin matrix. Complete dissociation between kerateine and BMP-2 occurred when the PBS pH was lowered (to 4.5), below the keratin isoelectric point of 5.3. This phenomenon can be attributed to the protonation of keratin at a lower pH, leading to positive-positive repulsion. Therefore, the dynamics of kerateine-BMP-2 binding is highly dependent on pH and salt concentration, as well as on BMP-2 solubility at different pH and molarity. The study findings may contribute to our understanding of the release kinetics of drugs from keratin biomaterials and allow for the development of better, more clinically relevant BMP-2-conjugated systems for bone repair and regeneration.
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Affiliation(s)
- Roche C. de Guzman
- School of Biomedical Engineering and Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Shanel M. Tsuda
- School of Biomedical Engineering and Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Minh-Thi N. Ton
- School of Biomedical Engineering and Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Xiao Zhang
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Alan R. Esker
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Mark E. Van Dyke
- School of Biomedical Engineering and Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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Laguna M, Holgado M, Hernandez AL, Santamaría B, Lavín A, Soria J, Suarez T, Bardina C, Jara M, Sanza FJ, Casquel R. Antigen-Antibody Affinity for Dry Eye Biomarkers by Label Free Biosensing. Comparison with the ELISA Technique. SENSORS 2015; 15:19819-29. [PMID: 26287192 PMCID: PMC4570398 DOI: 10.3390/s150819819] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/03/2023]
Abstract
The specificity and affinity of antibody-antigen interactions is a fundamental way to achieve reliable biosensing responses. Different proteins involved with dry eye dysfunction: ANXA1, ANXA11, CST4, PRDX5, PLAA and S100A6; were validated as biomarkers. In this work several antibodies were tested for ANXA1, ANXA11 and PRDX5 to select the best candidates for each biomarker. The results were obtained by using Biophotonic Sensing Cells (BICELLs) as an efficient methodology for label-free biosensing and compared with the Enzyme-Linked Immuno Sorbent Assay (ELISA) technique.
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Affiliation(s)
- Maríafe Laguna
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
- Department of Applied Physics and Material, Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid, Jose Gutiérrez Abascal, 2. 28006 Madrid, Spain.
| | - Miguel Holgado
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
- Department of Applied Physics and Material, Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid, Jose Gutiérrez Abascal, 2. 28006 Madrid, Spain.
| | - Ana L Hernandez
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Beatriz Santamaría
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
- BioOpticalDetection, Centro de Empresas de la UPM, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Alvaro Lavín
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
- Department of Applied Physics and Material, Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid, Jose Gutiérrez Abascal, 2. 28006 Madrid, Spain.
| | - Javier Soria
- Bioftalmik. Parque Tecnológico Zamudio Ed. 800 2ª Planta 48160, Bizkaia, Spain.
| | - Tatiana Suarez
- Bioftalmik. Parque Tecnológico Zamudio Ed. 800 2ª Planta 48160, Bizkaia, Spain.
| | - Carlota Bardina
- AntibodyBcn, MRB 104 Modul b UAB Campus, 08193 Bellaterra, Barcelona, Spain.
| | - Mónica Jara
- AntibodyBcn, MRB 104 Modul b UAB Campus, 08193 Bellaterra, Barcelona, Spain.
| | - Francisco J Sanza
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
- BioOpticalDetection, Centro de Empresas de la UPM, Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Rafael Casquel
- Center for Biomedical Technology, Optics, Photonics and Biophotonics Lab, Universidad Politécnica de Madrid. Campus Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain.
- Department of Applied Physics and Material, Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid, Jose Gutiérrez Abascal, 2. 28006 Madrid, Spain.
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Sun YS. Use of Microarrays as a High-Throughput Platform for Label-Free Biosensing. ACTA ACUST UNITED AC 2015; 20:334-53. [DOI: 10.1177/2211068215577570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/28/2022]
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45
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Fei Y, Sun YS, Li Y, Yu H, Lau K, Landry JP, Luo Z, Baumgarth N, Chen X, Zhu X. Characterization of Receptor Binding Profiles of Influenza A Viruses Using An Ellipsometry-Based Label-Free Glycan Microarray Assay Platform. Biomolecules 2015; 5:1480-98. [PMID: 26193329 PMCID: PMC4598760 DOI: 10.3390/biom5031480] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 06/09/2015] [Accepted: 07/06/2015] [Indexed: 12/11/2022] Open
Abstract
A key step leading to influenza viral infection is the highly specific binding of a viral spike protein, hemagglutinin (HA), with an extracellular glycan receptor of a host cell. Detailed and timely characterization of virus-receptor binding profiles may be used to evaluate and track the pandemic potential of an influenza virus strain. We demonstrate a label-free glycan microarray assay platform for acquiring influenza virus binding profiles against a wide variety of glycan receptors. By immobilizing biotinylated receptors on a streptavidin-functionalized solid surface, we measured binding curves of five influenza A virus strains with 24 glycans of diverse structures and used the apparent equilibrium dissociation constants (avidity constants, 10–100 pM) as characterizing parameters of viral receptor profiles. Furthermore by measuring binding kinetic constants of solution-phase glycans to immobilized viruses, we confirmed that the glycan-HA affinity constant is in the range of 10 mM and the reaction is enthalpy-driven.
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Affiliation(s)
- Yiyan Fei
- Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Fudan University, 220 Handan Road, Shanghai 200433, China.
- Department of Physics, University of California, Davis, CA 95616, USA.
| | - Yung-Shin Sun
- Department of Physics, University of California, Davis, CA 95616, USA.
- Department of Physics, Fu-Jen Catholic University, New Taipei City 24205, Taiwan.
| | - Yanhong Li
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - Kam Lau
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - James P Landry
- Department of Physics, University of California, Davis, CA 95616, USA.
| | - Zeng Luo
- Center for Comparative Medicine, University of California, Davis, CA 95616, USA.
| | - Nicole Baumgarth
- Center for Comparative Medicine, University of California, Davis, CA 95616, USA.
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - Xiangdong Zhu
- Department of Physics, University of California, Davis, CA 95616, USA.
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Landry JP, Malovichko G, Zhu XD. High-Throughput Dose–Response Measurement Using a Label-Free Microarray-in-Microplate Assay Platform. Anal Chem 2015; 87:5640-8. [DOI: 10.1021/acs.analchem.5b00720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. P. Landry
- Department
of Physics, University of California at Davis, Davis, California 95616, United States
| | - G. Malovichko
- Department
of Physics, University of California at Davis, Davis, California 95616, United States
| | - X. D. Zhu
- Department
of Physics, University of California at Davis, Davis, California 95616, United States
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Landry JP, Ke Y, Yu GL, Zhu XD. Measuring affinity constants of 1450 monoclonal antibodies to peptide targets with a microarray-based label-free assay platform. J Immunol Methods 2015; 417:86-96. [PMID: 25536073 PMCID: PMC4339518 DOI: 10.1016/j.jim.2014.12.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
Monoclonal antibodies (mAbs) are major reagents for research and clinical diagnosis. For their inherently high specificities to intended antigen targets and thus low toxicity in general, they are pursued as one of the major classes of new drugs. Yet binding properties of most monoclonal antibodies are not well characterized in terms of affinity constants and how they vary with presentations and/or conformational isomers of antigens, buffer compositions, and temperature. We here report a microarray-based label-free assay platform for high-throughput measurements of monoclonal antibody affinity constants to antigens immobilized on solid surfaces. Using this platform we measured affinity constants of over 1410 rabbit monoclonal antibodies and 46 mouse monoclonal antibodies to peptide targets that are immobilized through a terminal cysteine residue to a glass surface. The experimentally measured affinity constants vary from 10 pM to 200 pM with the median value at 66 pM. We compare the results obtained from the microarray-based platform with those from a benchmarking surface-plasmon-resonance-based (SPR) sensor (Biacore 3000).
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Affiliation(s)
- J P Landry
- Department of Physics, University of California, Davis, CA, 95616, USA
| | | | | | - X D Zhu
- Department of Physics, University of California, Davis, CA, 95616, USA.
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48
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Tang L, Yin Q, Xu Y, Zhou Q, Cai K, Yen J, Dobrucki LW, Cheng J. Bioorthogonal Oxime Ligation Mediated In Vivo Cancer Targeting. Chem Sci 2015; 6:2182-2186. [PMID: 26146536 PMCID: PMC4486360 DOI: 10.1039/c5sc00063g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Here, we report an in vivo cancer targeting strategy mediated by bioorthogonal oxime ligation.
Current cancer targeting relying on specific biological interaction between the cell surface antigen and respective antibody or its analogue has proven to be effective in the treatment of different cancers; however, this strategy has its own limitations, such as the heterogeneity of cancer cells and immunogenicity of the biomacromolecule binding ligands. Bioorthogonal chemical conjugation has emerged as an attractive alternative to biological interaction for in vivo cancer targeting. Here, we report an in vivo cancer targeting strategy mediated by bioorthogonal oxime ligation. An oxyamine group, the artificial target, is introduced onto 4T1 murine breast cancer cells through liposome delivery and fusion. Poly(ethylene glycol)-polylactide (PEG-PLA) nanoparticles (NPs) are surface-functionalized with aldehyde groups as targeting ligands. The improved in vivo cancer targeting of PEG-PLA NPs is achieved through specific and efficient chemical reaction between the oxyamine and aldehyde groups.
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Affiliation(s)
- Li Tang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, USA. ; Tel: +1 217-244-3924
| | - Qian Yin
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, USA. ; Tel: +1 217-244-3924
| | - Yunxiang Xu
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, USA. ; Tel: +1 217-244-3924
| | - Qin Zhou
- Department of Pharmaceutical Science, Guangdong Pharmaceutical University, Guangzhou, Guangdong, 510006, China
| | - Kaimin Cai
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, USA. ; Tel: +1 217-244-3924
| | - Jonathan Yen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, USA. ; Tel: +1 217-244-3924
| | - Lawrence W Dobrucki
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 West Green Street, Urbana, IL 61801, USA. ; Tel: +1 217-244-3924 ; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Sun YS, Fei Y, Luo J, Dixon S, Landry JP, Lam KS, Zhu X. Generating Encoded Compound Libraries for Fabricating Microarrays as a High-Throughput Protein Ligand Discovery Platform. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.840728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yung-Shin Sun
- a Department of Physics , Fu-Jen Catholic University , New Taipei City , Taiwan
| | - Yiyan Fei
- b Department of Optical Science and Engineering , Fudan University , Shanghai , China
- c Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Department of Optical Science and Engineering, Shanghai Ultra-Precision Optical Manufacturing Engineering Center , Fudan University , Shanghai , China
| | - Juntao Luo
- d Department of Pharmacology , Upstate Cancer Research Institute, State University of New York Upstate Medical University , Syracuse , New York , USA
| | - Seth Dixon
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - James P. Landry
- f Department of Physics , University of California at Davis , Davis , California , USA
| | - Kit S. Lam
- e Division of Hematology and Oncology, Department of Internal Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
- g Department of Biochemistry and Molecular Medicine , School of Medicine, University of California at Davis , Sacramento , California , USA
| | - Xiangdong Zhu
- f Department of Physics , University of California at Davis , Davis , California , USA
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Landry JP, Fei Y, Zhu X, Ke Y, Yu G, Lee P. Discovering small molecule ligands of vascular endothelial growth factor that block VEGF-KDR binding using label-free microarray-based assays. Assay Drug Dev Technol 2014; 11:326-32. [PMID: 23772553 DOI: 10.1089/adt.2012.485] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We present here a label-free microarray-based assay platform that we used to identify inhibitors of vascular endothelial growth factor (VEGF)-kinase-insertion domain receptor (KDR) binding. Supported by a combination of special ellipsometry-based optical detection and small molecule microarrays (SMM), this platform consists of three assays: (1) the first assay detects binding of a target protein with SMM and identifies ligands to the protein as inhibitor candidates; (2) the second assay detects binding of a receptor protein with identical SMM and subsequent binding of the target protein (a sandwich assay) to identify the ligands to the receptor protein that do not interfere with the target-receptor binding; (3) the third assay detects binding of the target protein to the receptor protein in the presence of the ligands of the target protein identified from the first assay, with the receptor protein immobilized to a solid surface through the ligands identified in the second assay, to yield dose-response curves. Using this platform, we screened 7,961 compounds from the National Cancer Institute and found 12 inhibitors to VEGF-KDR (VEGFR2) interactions with IC₅₀ ranging from 0.3 to 60 μM. The inhibitory potency of these inhibitors found in the microarray-based assay was confirmed by their inhibition of VEGF-induced VEGFR2 phosphorylation in a cell-based assay.
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Affiliation(s)
- James P Landry
- Department of Physics, University of California at Davis, Davis, CA 95616, USA
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