1
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Ding X, Chen X, Sullivan EE, Shay TF, Gradinaru V. Fast, accurate ranking of engineered proteins by target-binding propensity using structure modeling. Mol Ther 2024:S1525-0016(24)00219-3. [PMID: 38582966 DOI: 10.1016/j.ymthe.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/08/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
Deep-learning-based methods for protein structure prediction have achieved unprecedented accuracy, yet their utility in the engineering of protein-based binders remains constrained due to a gap between the ability to predict the structures of candidate proteins and the ability toprioritize proteins by their potential to bind to a target. To bridge this gap, we introduce Automated Pairwise Peptide-Receptor Analysis for Screening Engineered proteins (APPRAISE), a method for predicting the target-binding propensity of engineered proteins. After generating structural models of engineered proteins competing for binding to a target using an established structure prediction tool such as AlphaFold-Multimer or ESMFold, APPRAISE performs a rapid (under 1 CPU second per model) scoring analysis that takes into account biophysical and geometrical constraints. As proof-of-concept cases, we demonstrate that APPRAISE can accurately classify receptor-dependent vs. receptor-independent adeno-associated viral vectors and diverse classes of engineered proteins such as miniproteins targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike, nanobodies targeting a G-protein-coupled receptor, and peptides that specifically bind to transferrin receptor or programmed death-ligand 1 (PD-L1). APPRAISE is accessible through a web-based notebook interface using Google Colaboratory (https://tiny.cc/APPRAISE). With its accuracy, interpretability, and generalizability, APPRAISE promises to expand the utility of protein structure prediction and accelerate protein engineering for biomedical applications.
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Affiliation(s)
- Xiaozhe Ding
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA.
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA
| | - Erin E Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA
| | - Timothy F Shay
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California, Boulevard, Pasadena, CA 91125, USA.
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2
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Beyer H, Sommerfeld M, Grandien K, Faust C, Tillmann B, Leuschner WD, Régnier-Vigouroux A, Weil S, Rao E, Langer T. Functional studies with IgM and IgA immunoglobulins: binding to pIgR, FcαμR, FcμR, and CDC activities. APMIS 2024; 132:277-288. [PMID: 38232051 DOI: 10.1111/apm.13377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
IgMs are the first antibodies produced by the immune system upon encounter of a possible pathogen and are one of five antibody subclasses in humans. For IgG, the most intensively studied antibody class, the N-linked glycosylation site located in the Fc-domain is directly involved in high affinity binding to the respective receptors and initiation of corresponding immune response. IgM molecules have five N-glycosylation sites and one N-glycosylation site in the J-chain, which can be incorporated in IgM or IgA molecules. There is only limited knowledge available concerning the function of these N-glycosylations in IgMs. To address this question, we produced IgM molecules lacking a particular N-glycosylation site and tested these variants as well as IgA molecules for binding to the known receptors: the polymeric immunoglobulin receptor (pIgR), the dual receptor for IgA and IgM, FcαμR, and the specific receptor for IgM, FcμR. The single glycosylation sites did not show an impact on expression and multimerization, except for variant N402Q, which could not be expressed. In SPR measurements, no major impact on the binding to the receptors by particular glycosylation sites could be detected. In cellular assays, deglycosylated variants showed some alterations in induction of CDC activity. Most strikingly, we observed also binding of IgA to the FcμR in the same affinity range as IgM, suggesting that this might have a physiological role. To further substantiate the binding of IgA to FcμR we used IgA from different origins and were able to confirm binding of IgA preparations to the FcμR.
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Affiliation(s)
- Hanna Beyer
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
- Institute for Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| | - Mark Sommerfeld
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Kaj Grandien
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Christine Faust
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Bodo Tillmann
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Wulf Dirk Leuschner
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Anne Régnier-Vigouroux
- Institute for Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| | - Sandra Weil
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Ercole Rao
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
| | - Thomas Langer
- Sanofi-Aventis Deutschland GmbH, R&D Large Molecules Research, Frankfurt am Main, Germany
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3
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Roy A, Dodd-O JB, Robang AS, He D, West O, Siddiqui Z, Aguas ED, Goldberg H, Griffith A, Heffernan C, Hu Y, Paravastu AK, Kumar VA. Self-Assembling Peptides with Insulin-Like Growth Factor Mimicry. ACS Appl Mater Interfaces 2024; 16:364-375. [PMID: 38145951 DOI: 10.1021/acsami.3c15660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Growth factor (GF) mimicry involves recapitulating the signaling of larger molecules or cells. Although GF mimicry holds considerable promise in tissue engineering and drug design applications, difficulties in targeting the signaling molecule to the site of delivery and dissociation of mimicking peptides from their target receptors continue to limit its clinical application. To address these challenges, we utilized a self-assembling peptide (SAP) platform to generate synthetic insulin-like growth factor (IGF)-signaling, self-assembling GFs. Our peptide hydrogels are biocompatible and bind target IGF receptors in a dose-dependent fashion, activate proangiogenic signaling, and facilitate formation of angiogenic microtubules in vitro. Furthermore, infiltrated hydrogels are stable for weeks to months. We conclude that the enhanced targeting and long-term stability of our SAP/GF mimicry implants may improve the efficacy and safety of future GF mimic therapeutics.
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Affiliation(s)
- Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph B Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dongjing He
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Owen West
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Erika Davidoff Aguas
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey 08544, United States
| | - Hannah Goldberg
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Alexandra Griffith
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Yuhang Hu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, New Jersey 07103, United States
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4
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Serafin P, Szeleszczuk Ł, Zhukov I, Szűcs E, Gombos D, Stefanucci A, Mollica A, Pisklak DM, Kleczkowska P. Opioid/Dopamine Receptor Binding Studies, NMR and Molecular Dynamics Simulation of LENART01 Chimera, an Opioid-Bombesin-like Peptide. Molecules 2024; 29:272. [PMID: 38202853 PMCID: PMC10780910 DOI: 10.3390/molecules29010272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
The design and development of hybrid compounds as a new class of drug candidates remains an excellent opportunity to improve the pharmacological properties of drugs (including enzymatic stability, efficacy and pharmacokinetic and pharmacodynamic profiles). In addition, considering various complex diseases and/or disorders, the conjugate chemistry approach is highly acceptable and justified. Opioids have long been recognized as the most potent analgesics and serve as the basic pharmacophore for potent hybrid compounds that may be useful in pain management. However, a risk of tolerance and physical dependence exists. Since dopamine receptors have been implicated in the aforementioned adverse effects of opioids, the construction of a hybrid with dual action at opioid and dopamine receptors is of interest. Herein, we present nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulation results for LENART01, an opioid-ranatensin hybrid peptide. Apart from molecular docking, protein-ligand interactions were also assessed in vitro using a receptor binding assay, which proved LENART01 to be bound to mu-opioid and dopamine receptors, respectively.
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Affiliation(s)
- Pawel Serafin
- Department of Military Health Service, Ministry of National Defence of the Republic of Poland, Niepodleglosci 211 Street, 00-911 Warsaw, Poland;
| | - Łukasz Szeleszczuk
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland; (Ł.S.); (D.M.P.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a Street, 02-106 Warsaw, Poland;
| | - Edina Szűcs
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Temesvári krt. 62, H-6726 Szeged, Hungary; (E.S.); (D.G.)
| | - Dávid Gombos
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Temesvári krt. 62, H-6726 Szeged, Hungary; (E.S.); (D.G.)
- Doctoral School of Theoretical Medicine, Faculty of Medicine, University of Szeged, Dugonics Square 13, H-6720 Szeged, Hungary
| | - Azzurra Stefanucci
- Department of Pharmacy, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (A.S.); (A.M.)
| | - Adriano Mollica
- Department of Pharmacy, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (A.S.); (A.M.)
| | - Dariusz Maciej Pisklak
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Street, 02-093 Warsaw, Poland; (Ł.S.); (D.M.P.)
| | - Patrycja Kleczkowska
- Maria Sklodowska-Curie Medical Academy in Warsaw, Solidarnosci 12 Street, 03-411 Warsaw, Poland
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5
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Chang P, Yang J, Karunarathna TK, Qureshi M, Sadeyen JR, Iqbal M. Characterization of the haemagglutinin properties of the H5N1 avian influenza virus that caused human infections in Cambodia. Emerg Microbes Infect 2023; 12:2244091. [PMID: 37526446 PMCID: PMC10461499 DOI: 10.1080/22221751.2023.2244091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/04/2023] [Accepted: 07/30/2023] [Indexed: 08/02/2023]
Abstract
High pathogenicity avian influenza (HPAI) H5N1 is a subtype of the influenza A virus primarily found in birds. The subtype emerged in China in 1996 and has spread globally, causing significant morbidity and mortality in birds and humans. In Cambodia, a lethal case was reported in February 2023 involving an 11-year-old girl, marking the first human HPAI H5N1 infection in the country since 2014. This research examined the zoonotic potential of the human H5N1 isolate, A/Cambodia/NPH230032/2023 (KHM/23), by assessing its receptor binding, fusion pH, HA thermal stability, and antigenicity. Results showed that KHM/23 exhibits similar receptor binding and antigenicity as the early clade 2.3.2.1c HPAI H5N1 strain, and it does not bind to human-like receptors. Despite showing limited zoonotic risk, the increased thermal stability and reduced pH of fusion in KHM/23 indicate a potential threat to poultry, emphasizing the need for vigilant monitoring.
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Affiliation(s)
| | - Jiayun Yang
- The Pirbright Institute, Pirbright, Woking, GU24 0NF, UK
| | - Thusitha K. Karunarathna
- The Pirbright Institute, Pirbright, Woking, GU24 0NF, UK
- Royal Veterinary College, Hawkshead Lane North Mymms, Hertfordshire, AL9 7TA, UK
| | - Mehnaz Qureshi
- The Pirbright Institute, Pirbright, Woking, GU24 0NF, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK
| | | | - Munir Iqbal
- The Pirbright Institute, Pirbright, Woking, GU24 0NF, UK
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6
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Niazi SK. Support for Removing Pharmacodynamic and Clinical Efficacy Testing of Biosimilars: A Critical Analysis. Clin Pharmacol Drug Dev 2023; 12:1134-1141. [PMID: 37963837 DOI: 10.1002/cpdd.1349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023]
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7
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Niazi SK. A Critical Analysis of the FDA's Omics-Driven Pharmacodynamic Biomarkers to Establish Biosimilarity. Pharmaceuticals (Basel) 2023; 16:1556. [PMID: 38004421 PMCID: PMC10675618 DOI: 10.3390/ph16111556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Demonstrating biosimilarity entails comprehensive analytical assessment, clinical pharmacology profiling, and efficacy testing in patients for at least one medical indication, as required by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The efficacy testing can be waived if the drug has known pharmacodynamic (PD) markers, leaving most therapeutic proteins out of this concession. To overcome this, the FDA suggests that biosimilar developers discover PD biomarkers using omics technologies such as proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. This approach is redundant since the mode-action-action biomarkers of approved therapeutic proteins are already available, as compiled in this paper for the first time. Other potential biomarkers are receptor binding and pharmacokinetic profiling, which can be made more relevant to ensure biosimilarity without requiring biosimilar developers to conduct extensive research, for which they are rarely qualified.
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Affiliation(s)
- Sarfaraz K Niazi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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8
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Bonnavion R, Liu S, Kawase H, Roquid KA, Offermanns S. Large chemokine binding spectrum of human and mouse atypical chemokine receptor GPR182 (ACKR5). Front Pharmacol 2023; 14:1297596. [PMID: 38026988 PMCID: PMC10646305 DOI: 10.3389/fphar.2023.1297596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Atypical chemokine receptors (ACKRs) play pivotal roles in immune regulation by binding chemokines and regulating their spatial distribution without inducing G-protein activation. Recently, GPR182, provisionally named ACKR5, was identified as a novel ACKR expressed in microvascular and lymphatic endothelial cells, with functions in hematopoietic stem cell homeostasis. Here, we comprehensively investigated the chemokine binding profile of human and mouse GPR182. Competitive binding assays using flow cytometry revealed that besides CXCL10, CXCL12 and CXCL13, also human and mouse CXCL11, CXCL14 and CCL25, as well as human CCL1, CCL11, CCL19, CCL26, XCL1 and mouse CCL22, CCL24, CCL27 and CCL28 bind with an affinity of less than 100 nM to GPR182. In line with the binding affinity observed in vitro, elevated serum levels of CCL22, CCL24, CCL25, and CCL27 were observed in GPR182-deficient mice, underscoring the role of GPR182 in chemokine scavenging. These data show a broader chemokine binding repertoire of GPR182 than previously reported and they will be important for future work exploring the physiological and pathophysiological roles of GPR182, which we propose to be renamed atypical chemokine receptor 5 (ACKR5).
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Affiliation(s)
- Remy Bonnavion
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardiopulmonary Institute, Bad Nauheim, Germany
| | - Shangmin Liu
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Haruya Kawase
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Kenneth Anthony Roquid
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Offermanns
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardiopulmonary Institute, Bad Nauheim, Germany
- Center for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
- German Center for Cardiovascular Research, Partner Site Frankfurt, Bad Nauheim, Germany
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9
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Niazi SK. The FDA's New Guideline "Generally Accepted Scientific Knowledge" (GASK): An Opportunity to Expedite the Approval of Biosimilars. Pharmaceuticals (Basel) 2023; 16:1517. [PMID: 38004383 PMCID: PMC10674418 DOI: 10.3390/ph16111517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The US FDA's new guideline suggests using "Generally Accepted Science Knowledge" (GASK) to develop nonclinical testing protocols for developing drugs and biologicals to remove unnecessary testing. Interpreting acceptable scientific knowledge as a rational approach has motivated the author to suggest substantial changes to the development of biosimilars, as demonstrated in this paper. The FDA can accept these suggestions without requiring any legislative change to the Act that defines such requirements. Suggested here is the waiving of clinical efficacy testing due to its lower sensitivity compared to analytical and functional testing and pharmacokinetic profiling. Also questioned is the need to test pharmacodynamic markers that do not correlate with clinical response and find new biomarkers requiring extensive testing to validate their use. Should the FDA accept these scientifically rational suggestions, it will significantly reduce the time and cost of approving biosimilars without safety or efficacy risk, as justified based on acceptable scientific knowledge and rationality.
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Affiliation(s)
- Sarfaraz K Niazi
- College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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10
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Chen J, Zheng Y, Wang L, Pang X, Gao F, Xiao H, Huo N. Expression, purification, and biological characterization of recombinant human interleukin-31 protein. Biotechnol Appl Biochem 2023; 70:1731-1740. [PMID: 37096330 DOI: 10.1002/bab.2470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Interleukin-31 (IL-31), belonging to the IL-6 cytokine family, is involved in skin inflammation and pruritus, as well as some tumors' progression. Here, we reported the expression and purification of recombinant human IL-31 (rhIL-31) using a prokaryotic system. This recombinant protein was expressed in the form of inclusion bodies, refolded and purified by size-exclusion chromatography. Circular dichroism analysis revealed that the secondary structure of rhIL-31 was mainly composed of alpha-helix, which is in consistence with the 3D model structure built by AlphaFold server. In vitro studies showed that rhIL-31 exhibited a good binding ability to the recombinant hIL-31 receptor alpha fused with human Fc fragment (rhIL-31RA-hFc) with EC50 value of 16.36 µg/mL in ELISA assay. Meanwhile, flow cytometry demonstrated that rhIL-31 was able to bind to hIL-31RA or hOSMRβ expressed on the cell surface, independently. Furthermore, rhIL-31 could induce the phosphorylation of STAT3 in A549 cells. In conclusion, the prepared rhIL-31 in this study possesses the binding ability to its receptors, and can activate the signal pathway of JAK/STAT. Thus, it can be applied in further studies, including investigation of hIL-31-related diseases, structural analysis, and development of therapeutic drugs, and monoclonal antibodies targeting hIL-31.
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Affiliation(s)
- Jing Chen
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yuxin Zheng
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lixian Wang
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xuefei Pang
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Feng Gao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haixia Xiao
- Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Nairui Huo
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
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11
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Santos EJ, Nassehi N, Bow EW, Chambers DR, Gutman ES, Jacobson AE, Lutz JA, Marsh SA, Rice KC, Sulima A, Selley DE, Negus SS. Role of efficacy as a determinant of locomotor activation by mu-opioid receptor (MOR) ligands in female and male mice. II. Effects of novel MOR-selective phenylmorphans with high-to-low MOR efficacy. Pharmacol Res Perspect 2023; 11:e01111. [PMID: 37381112 DOI: 10.1002/prp2.1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Abstract
Low-efficacy mu-opioid receptor (MOR) agonists represent promising therapeutics, but existing compounds (e.g., buprenorphine, nalbuphine) span a limited range of low MOR efficacies and have poor MOR selectivity. Accordingly, new and selective low-efficacy MOR agonists are of interest. A novel set of chiral C9-substituted phenylmorphans has been reported to display improved MOR selectivity and a range of high-to-low MOR efficacies under other conditions; however, a full opioid receptor binding profile for these drugs has not been described. Additionally, studies in mice will be useful for preclinical characterization of these novel compounds, but the pharmacology of these drugs in mice has also not been examined. Accordingly, the present study characterized the binding selectivity and in vitro efficacy of these compounds using assays of opioid receptor binding and ligand-stimulated [35 S]GTPɣS binding. Additionally, locomotor effects were evaluated as a first step for in vivo behavioral assessment in mice. The high-efficacy MOR agonist and clinically effective antidepressant tianeptine was included as a comparator. In binding studies, all phenylmorphans showed improved MOR selectivity relative to existing lower-efficacy MOR agonists. In the ligand-stimulated [35 S]GTPɣS binding assay, seven phenylmorphans had graded levels of sub-buprenorphine MOR efficacy. In locomotor studies, the compounds again showed graded efficacy with a rapid onset and ≥1 h duration of effects, evidence for MOR mediation, and minor sex differences. Tianeptine functioned as a high-efficacy MOR agonist. Overall, these in vitro and in vivo studies support the characterization of these compounds as MOR-selective ligands with graded MOR efficacy and utility for further behavioral studies in mice.
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Affiliation(s)
- Edna J Santos
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Nima Nassehi
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Eric W Bow
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Dana R Chambers
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Eugene S Gutman
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Arthur E Jacobson
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Joshua A Lutz
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Samuel A Marsh
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Kenner C Rice
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Agnieszka Sulima
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, NIDA and NIAAA, Bethesda, Maryland, USA
| | - Dana E Selley
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - S Stevens Negus
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
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Vishnivetskiy SA, Weinstein LD, Zheng C, Gurevich EV, Gurevich VV. Functional Role of Arrestin-1 Residues Interacting with Unphosphorylated Rhodopsin Elements. Int J Mol Sci 2023; 24:ijms24108903. [PMID: 37240250 DOI: 10.3390/ijms24108903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Arrestin-1, or visual arrestin, exhibits an exquisite selectivity for light-activated phosphorylated rhodopsin (P-Rh*) over its other functional forms. That selectivity is believed to be mediated by two well-established structural elements in the arrestin-1 molecule, the activation sensor detecting the active conformation of rhodopsin and the phosphorylation sensor responsive to the rhodopsin phosphorylation, which only active phosphorylated rhodopsin can engage simultaneously. However, in the crystal structure of the arrestin-1-rhodopsin complex there are arrestin-1 residues located close to rhodopsin, which do not belong to either sensor. Here we tested by site-directed mutagenesis the functional role of these residues in wild type arrestin-1 using a direct binding assay to P-Rh* and light-activated unphosphorylated rhodopsin (Rh*). We found that many mutations either enhanced the binding only to Rh* or increased the binding to Rh* much more than to P-Rh*. The data suggest that the native residues in these positions act as binding suppressors, specifically inhibiting the arrestin-1 binding to Rh* and thereby increasing arrestin-1 selectivity for P-Rh*. This calls for the modification of a widely accepted model of the arrestin-receptor interactions.
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Affiliation(s)
| | - Liana D Weinstein
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Chen Zheng
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
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13
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Kremling V, Loll B, Pach S, Dahmani I, Weise C, Wolber G, Chiantia S, Wahl MC, Osterrieder N, Azab W. Crystal structures of glycoprotein D of equine alphaherpesviruses reveal potential binding sites to the entry receptor MHC-I. Front Microbiol 2023; 14:1197120. [PMID: 37250020 PMCID: PMC10213783 DOI: 10.3389/fmicb.2023.1197120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Cell entry of most alphaherpesviruses is mediated by the binding of glycoprotein D (gD) to different cell surface receptors. Equine herpesvirus type 1 (EHV-1) and EHV-4 gDs interact with equine major histocompatibility complex I (MHC-I) to initiate entry into equine cells. We have characterized the gD-MHC-I interaction by solving the crystal structures of EHV-1 and EHV-4 gDs (gD1, gD4), performing protein-protein docking simulations, surface plasmon resonance (SPR) analysis, and biological assays. The structures of gD1 and gD4 revealed the existence of a common V-set immunoglobulin-like (IgV-like) core comparable to those of other gD homologs. Molecular modeling yielded plausible binding hypotheses and identified key residues (F213 and D261) that are important for virus binding. Altering the key residues resulted in impaired virus growth in cells, which highlights the important role of these residues in the gD-MHC-I interaction. Taken together, our results add to our understanding of the initial herpesvirus-cell interactions and will contribute to the targeted design of antiviral drugs and vaccine development.
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Affiliation(s)
- Viviane Kremling
- Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Berlin, Germany
| | - Bernhard Loll
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Szymon Pach
- Institute of Pharmacy (Pharmaceutical Chemistry), Freie Universität Berlin, Berlin, Germany
| | - Ismail Dahmani
- Universität Potsdam, Institut für Biochemie und Biologie, Potsdam, Brandenburg, Germany
| | - Christoph Weise
- BioSupraMol Core Facility, Bio-Mass Spectrometry, Freie Universität Berlin, Berlin, Germany
| | - Gerhard Wolber
- Institute of Pharmacy (Pharmaceutical Chemistry), Freie Universität Berlin, Berlin, Germany
| | - Salvatore Chiantia
- Universität Potsdam, Institut für Biochemie und Biologie, Potsdam, Brandenburg, Germany
| | - Markus C. Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Nikolaus Osterrieder
- Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Berlin, Germany
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Walid Azab
- Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Berlin, Germany
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Glatfelter GC, Naeem M, Pham DNK, Golen JA, Chadeayne AR, Manke DR, Baumann MH. Receptor Binding Profiles for Tryptamine Psychedelics and Effects of 4-Propionoxy- N,N-dimethyltryptamine in Mice. ACS Pharmacol Transl Sci 2023; 6:567-577. [PMID: 37082754 PMCID: PMC10111620 DOI: 10.1021/acsptsci.2c00222] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Indexed: 03/12/2023]
Abstract
Analogues of 4-phosphoryloxy-N,N-dimethyltryptamine (psilocybin) are being sold on recreational drug markets and developed as potential medications for psychedelic-assisted therapies. Many of these tryptamine-based psilocybin analogues produce psychedelic-like effects in rodents and humans primarily by agonist activity at serotonin 2A receptors (5-HT2A). However, the comprehensive pharmacological target profiles for these compounds compared to psilocybin and its active metabolite 4-hydroxy-N,N-dimethyltryptamine (psilocin) are unknown. The present study determined the receptor binding profiles of various tryptamine-based psychedelics structurally related to psilocybin across a broad range of potential targets. Specifically, we examined tryptamine psychedelics with different 4-position (hydroxy, acetoxy, propionoxy) and N,N-dialkyl (dimethyl, methyl-ethyl, diethyl, methyl-propyl, ethyl-propyl, diisopropyl, methyl-allyl, diallyl) substitutions. Further, the psilocybin analogue 4-propionoxy-N,N-dimethyltryptamine (4-PrO-DMT) was administered to mice in experiments measuring head twitch response (HTR), locomotor activity, and body temperature. Overall, the present pharmacological profile screening data show that the tryptamine psychedelics target multiple serotonin receptors, including serotonin 1A receptors (5-HT1A). 4-Acetoxy and 4-propionoxy analogues of 4-hydroxy compounds displayed somewhat weaker binding affinities but similar target profiles across 5-HT receptors and other identified targets. Additionally, differential binding screen profiles were observed with N,N-dialkyl position variations across several non-5-HT receptor targets (i.e., alpha receptors, dopamine receptors, histamine receptors, and serotonin transporters), which could impact in vivo pharmacological effects of the compounds. In mouse experiments, 4-PrO-DMT displayed dose-related psilocybin-like effects to produce 5-HT2A-mediated HTR (0.3-3 mg/kg s.c.) as well as 5-HT1A-mediated hypothermia and hypolocomotion (3-30 mg/kg s.c.). Lastly, our data support a growing body of evidence that the 5-HT2A-mediated HTR induced by tryptamine psychedelics is attenuated by 5-HT1A receptor agonist activity at high doses in mice.
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Affiliation(s)
- Grant C. Glatfelter
- Designer
Drug Research Unit, National Institute on
Drug Abuse, Intramural Research Program, Baltimore, Maryland 21224 United States
| | - Marilyn Naeem
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | - Duyen N. K. Pham
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | - James A. Golen
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | | | - David R. Manke
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | - Michael H. Baumann
- Designer
Drug Research Unit, National Institute on
Drug Abuse, Intramural Research Program, Baltimore, Maryland 21224 United States
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15
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Santillo MF, Sprando RL. Picamilon, a γ-aminobutyric acid (GABA) analogue and marketed nootropic, is inactive against 50 biological targets. Basic Clin Pharmacol Toxicol 2023; 132:355-358. [PMID: 36668678 DOI: 10.1111/bcpt.13836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Picamilon is an analogue of the neurotransmitter γ-aminobutyric acid (GABA), which is marketed as a nootropic claiming to enhance cognition. There is a lack of in silico, in vitro and in vivo data on the safety of picamilon. Therefore, to ascertain potential physiological effects of picamilon, it was screened against 50 safety-related biological targets (receptors, ion channels, enzymes and transporters) by in silico and in vitro methods. Using two in silico tools, picamilon was not predicted to bind to the targets. Similarly, picamilon exhibited weak or no binding to the targets when measured in vitro at 10 μM. Overall, this data shows that picamilon, although structurally similar to other GABA analogues, has a different biological target binding profile. Picamilon's lack of binding to the 50 targets fills important data gaps among GABA analogues, a group of structurally related substances found in drugs and other consumer products.
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Affiliation(s)
- Michael F Santillo
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration (FDA), Laurel, Maryland, USA
| | - Robert L Sprando
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration (FDA), Laurel, Maryland, USA
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Chang P, Lukosaityte D, Sealy JE, Rijal P, Sadeyen JR, Bhat S, Crossley S, Daines R, Huang KA, Townsend AR, Iqbal M. Antigenic Characterization of Human Monoclonal Antibodies for Therapeutic Use against H7N9 Avian Influenza Virus. J Virol 2023; 97:e0143122. [PMID: 36541801 DOI: 10.1128/jvi.01431-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Since 2013, H7N9 avian influenza viruses (AIVs) have caused more than 1,500 human infections and the culling of millions of poultry. Despite large-scale poultry vaccination, H7N9 AIVs continue to circulate among poultry in China and pose a threat to human health. Previously, we isolated and generated four monoclonal antibodies (mAbs) derived from humans naturally infected with H7N9 AIV. Here, we investigated the hemagglutinin (HA) epitopes of H7N9 AIV targeted by these mAbs (L3A-44, K9B-122, L4A-14, and L4B-18) using immune escape studies. Our results revealed four key antigenic epitopes at HA amino acid positions 125, 133, 149, and 217. The mutant H7N9 viruses representing escape mutations containing an alanine-to-threonine substitution at residue 125 (A125T), a glycine-to-glutamic acid substitution at residue 133 (G133E), an asparagine-to-aspartic acid substitution at residue 149 (N149D), or a leucine-to-glutamine substitution at residue 217 (L217Q) showed reduced or completely abolished cross-reactivity with the mAbs, as measured by a hemagglutination inhibition (HI) assay. We further assessed the potential risk of these mutants to humans should they emerge following mAb treatment by measuring the impact of these HA mutations on virus fitness and evasion of host adaptive immunity. Here, we showed that the L4A-14 mAb had broad neutralizing capabilities, and its escape mutant N149D had reduced viral stability and human receptor binding and could be neutralized by both postinfection and antigen-induced sera. Therefore, the L4A-14 mAb could be a therapeutic candidate for H7N9 AIV infection in humans and warrants further investigation for therapeutic applications. IMPORTANCE Avian influenza virus (AIV) H7N9 continues to circulate and evolve in birds, posing a credible threat to humans. Antiviral drugs have proven useful for the treatment of severe influenza infections in humans; however, concerns have been raised as antiviral-resistant mutants have emerged. Monoclonal antibodies (mAbs) have been studied for both prophylactic and therapeutic applications in infectious disease control and have demonstrated great potential. For example, mAb treatment has significantly reduced the risk of people developing severe disease with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In addition to the protection efficiency, we should also consider the potential risk of the escape mutants generated by mAb treatment to public health by assessing their viral fitness and potential to compromise host adaptive immunity. Considering these parameters, we assessed four human mAbs derived from humans naturally infected with H7N9 AIV and showed that the mAb L4A-14 displayed potential as a therapeutic candidate.
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Cook TW, Wilstermann AM, Mitchell JT, Arnold NE, Rajasekaran S, Bupp CP, Prokop JW. Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics. Biomolecules 2023; 13:257. [PMID: 36830626 PMCID: PMC9953665 DOI: 10.3390/biom13020257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Insulin is amongst the human genome's most well-studied genes/proteins due to its connection to metabolic health. Within this article, we review literature and data to build a knowledge base of Insulin (INS) genetics that influence transcription, transcript processing, translation, hormone maturation, secretion, receptor binding, and metabolism while highlighting the future needs of insulin research. The INS gene region has 2076 unique variants from population genetics. Several variants are found near the transcriptional start site, enhancers, and following the INS transcripts that might influence the readthrough fusion transcript INS-IGF2. This INS-IGF2 transcript splice site was confirmed within hundreds of pancreatic RNAseq samples, lacks drift based on human genome sequencing, and has possible elevated expression due to viral regulation within the liver. Moreover, a rare, poorly characterized African population-enriched variant of INS-IGF2 results in a loss of the stop codon. INS transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3'UTR alternatively spliced INS transcript. Finally, by combining literature, evolutionary profiling, and structural biology, we map rare missense variants that influence preproinsulin translation, proinsulin processing, dimer/hexamer secretory storage, receptor activation, and C-peptide detection for quasi-insulin blood measurements.
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Affiliation(s)
- Taylor W. Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jackson T. Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Nicholas E. Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Corewell Health, Grand Rapids, MI 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
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Thammasittirong A, Thammasittirong SN. Aromatic Residues on the Side Surface of Cry4Ba-Domain II of Bacillus thuringiensis subsp. israelensis Function in Binding to Their Counterpart Residues on the Aedes aegypti Alkaline Phosphatase Receptor. Toxins (Basel) 2023; 15. [PMID: 36828427 DOI: 10.3390/toxins15020114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Receptor binding is a prerequisite process to exert the mosquitocidal activity of the Cry4Ba toxin of Bacillus thuringiensis subsp. israelensis. The beta-sheet prism (domain II) and beta-sheet sandwich (domain III) of the Cry4Ba toxin have been implicated in receptor binding, albeit the precise binding mechanisms of these remain unclear. In this work, alanine scanning was used to determine the contribution to receptor binding of some aromatic and hydrophobic residues on the surface of domains II and III that are predicted to be responsible for binding to the Aedes aegypti membrane-bound alkaline phosphatase (Aa-mALP) receptor. Larvicidal activity assays against A. aegypti larvae revealed that aromatic residues (Trp327 on the β2 strand, Tyr347 on the β3-β4 loop, and Tyr359 on the β4 strand) of domain II were important to the toxicity of the Cry4Ba toxin. Quantitative binding assays using enzyme-linked immunosorbent assay (ELISA) showed similar decreasing trends in binding to the Aa-mALP receptor and in toxicity of the Cry4Ba mutants Trp327Ala, Tyr347Ala, and Tyr359Ala, suggesting that a possible function of these surface-exposed aromatic residues is receptor binding. In addition, binding assays of the Cry4Ba toxin to the mutants of the binding residues Gly513, Ser490, and Phe497 of the Aa-mALP receptor supported the binding function of Trp327, Tyr347, and Tyr359 of the Cry4Ba toxin, respectively. Altogether, our results showed for the first time that aromatic residues on a side surface of the Cry4Ba domain II function in receptor binding. This finding provides greater insight into the possible molecular mechanisms of the Cry4Ba toxin.
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Zheng L, Wang K, Chen M, Qin F, Yan C, Zhang XE. Characterization and Function of Glycans on the Spike Proteins of SARS-CoV-2 Variants of Concern. Microbiol Spectr 2022; 10:e0312022. [PMID: 36318020 DOI: 10.1128/spectrum.03120-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) pose a great challenge to viral prevention and treatment owing to spike (S) protein mutations, which enhance their infectivity and capacity for immune evasion. However, whether these S protein mutations affect glycosylation patterns and thereby influence infectivity and immunogenicity remains unclear. In this study, four VOC S proteins-S-Alpha, S-Beta, S-Delta, and S-Omicron-were expressed and purified. Lectin microarrays were performed to characterize their glycosylation patterns. Several glycans were differentially expressed among the four VOC S proteins. Furthermore, the functional examination of glycans differentially expressed on S-Omicron revealed a higher expression of fucose-containing glycans, which modestly increased the binding of S-Omicron to angiotensin converting enzyme 2 (ACE2). A higher abundance of sialic acid and galactose-containing glycan was observed on S-Omicron, which significantly reduced its sensitivity against broad S protein-neutralizing antibodies. These findings contribute to the further understanding of SARS-CoV-2 infection mechanisms and provide novel glycan targets for emerging and future variants of SARS-CoV-2. IMPORTANCE Though glycosylation sites of SARS-CoV-2 S protein remain highly conserved, we confirmed that mutations in the Spike gene affect the S protein glycan expression pattern in different variants. More importantly, we found that glycans were differentially expressed on the S protein of the Omicron variant, enabling different forms of receptor binding and neutralization resistance. This study improves our understanding of SARS-CoV-2 glycomics and glycobiology and provides novel therapeutic and preventive strategies for SARS-CoV-2 VOCs.
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Hinuma S, Fujita K, Kuroda S. Specific Binding and Endocytosis of Liposomes to HEK293T Cells via Myrisoylated Pre-S1 Peptide Bound to Sodium Taurocholate Cotransporting Polypeptide. Vaccines (Basel) 2022; 10. [PMID: 36560460 DOI: 10.3390/vaccines10122050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
(1) Background: Sodium taurocholate cotransporting polypeptide (NTCP) functions as a key receptor for the hepatitis B virus (HBV) infection. Analyzing HBV and NTCP interaction is an important issue not only for basic research but also for the development of anti-HBV therapeutics. We developed here a novel model system to analyze the interaction of NTCP with liposomes instead of HBV. (2) Methods: Liposomal binding and endocytosis through NTCP in HEK293T cells were achieved by serial treatments of HEL293T cells transiently expressing NTCP-green fluorescence protein (GFP) fusion protein with a synthetic biotinylated pre-S1 peptide (Myr47-Bio) and streptavidin (SA) complex (i.e., Myr47-Bio+SA) followed by biotinylated liposomes. By this procedure, binding of [biotinylated liposomes]-[Myr47-Bio+SA]-[NTCP-GFP] was formed. (3) Results: Using this model system, we found that liposomal binding to NTCP on the cell surface via Myr47-Bio+SA was far more efficient than that to scavenger receptor class B type 1 (SR-B1). Furthermore, liposomes bound to cell surface NTCP via Myr47-Bio+SA were endocytosed into cells after cells were cultured at 37 °C. However, this endocytosis was suppressed by 4 °C or cytochalasin B treatment. (4) Conclusions: This model system will be useful for not only analyzing HBV entry mechanisms but also screening substances to prevent HBV infection.
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Wan Z, Gong J, Sang J, Jiang W, Zhao Z, Lian M, Tang T, Li Y, Kan Q, Xie Q, Li T, Shao H, Gao W, Qin A, Ye J. Mouse adaptation of H6 avian influenza viruses and their molecular characteristics. Front Microbiol 2022; 13:1049979. [PMID: 36466692 PMCID: PMC9713515 DOI: 10.3389/fmicb.2022.1049979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/24/2022] [Indexed: 10/27/2023] Open
Abstract
H6 avian influenza viruses (AIVs) not only continue to circulate in both domestic poultry and wild waterfowl, but also have occasionally caused spillovers infections in pigs and humans, posing a potential threat to public health. However, the molecular mechanism of H6 AIV adaptation to mammals remains largely unknown. In this study, two mouse-adapted (MA) H6 AIV strains, named as MA E-Teal/417 and MA GWF-Goose/740, were generated through blind passages in BALB/c mice. The two MA H6 strains replicated more efficiently and showed higher virulence than the corresponding wild type (WT) H6 strains in mice. Genome sequencing revealed that MA E-Teal/417 and MA GWF-Goose/740 carried six amino acid mutations (PB2-T224A/E627K, HA-G124R, NA-F167L/Y356H and M1-M92R), and four amino acid mutations (PB1-K577E, PA-T97I/D514E and HA-T276K), respectively, when compared to the corresponding WT virus. Receptor binding assay showed MA E-Teal/417 had stronger binding activity to α-2,3 SA than WT E-Teal/417. Moreover, the polymerase activity analysis found the RNP polymerase activity of both MA H6 viruses was significantly higher than that of the corresponding WT virus in 293T cells. All these demonstrate that H6 AIV can acquire limit amino acid substitutions to adapt to mammals and increase virulence, highlighting the significance of monitoring such mutations of H6 AIV in the field for alarming the potential of its cross-transmission and pathogenesis in mammals.
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Affiliation(s)
- Zhimin Wan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jianxi Gong
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jianjun Sang
- Sinopharm Yangzhou VAC Biological Engineering Co. Ltd, Yangzhou, Jiangsu, China
| | - Wenjie Jiang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhehong Zhao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mingjun Lian
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ting Tang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yafeng Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiuqi Kan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Quan Xie
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tuofan Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Hongxia Shao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Wei Gao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Aijian Qin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, College of Veterinary Medicine, Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, China
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22
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Vishnivetskiy SA, Huh EK, Karnam PC, Oviedo S, Gurevich EV, Gurevich VV. The Role of Arrestin-1 Middle Loop in Rhodopsin Binding. Int J Mol Sci 2022; 23. [PMID: 36430370 DOI: 10.3390/ijms232213887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Arrestins preferentially bind active phosphorylated G protein-coupled receptors (GPCRs). The middle loop, highly conserved in all arrestin subtypes, is localized in the central crest on the GPCR-binding side. Upon receptor binding, it directly interacts with bound GPCR and demonstrates the largest movement of any arrestin element in the structures of the complexes. Comprehensive mutagenesis of the middle loop of rhodopsin-specific arrestin-1 suggests that it primarily serves as a suppressor of binding to non-preferred forms of the receptor. Several mutations in the middle loop increase the binding to unphosphorylated light-activated rhodopsin severalfold, which makes them candidates for improving enhanced phosphorylation-independent arrestins. The data also suggest that enhanced forms of arrestin do not bind GPCRs exactly like the wild-type protein. Thus, the structures of the arrestin-receptor complexes, in all of which different enhanced arrestin mutants and reengineered receptors were used, must be interpreted with caution.
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23
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Guo Y, Ding P, Li Y, Zhang Y, Zheng Y, Yu M, Suzuki Y, Zhang H, Ping J. Genetic and biological properties of H10N3 avian influenza viruses: A potential pandemic candidate? Transbound Emerg Dis 2022; 69:e3171-e3182. [PMID: 35067005 DOI: 10.1111/tbed.14458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/16/2022] [Accepted: 01/16/2022] [Indexed: 11/26/2022]
Abstract
The continued emergence of human illness caused by avian influenza viruses (AIVs) demonstrates the threat of strains such as H5N1, H7N9, H10N8, and now H10N3. The genetic and biological properties of H10N3 viruses are not fully understood. In this study, three H10N3 strains isolated from live poultry markets (LPMs) were systematically studied. Genome sequencing showed that the poultry-origin viruses are highly homologous to the human H10N3 isolate. The three avian strains were A/chicken/Jiangsu/0146/2021(abbreviated as JS146, H10N3), A/chicken/Jiangsu/0169/2021 (JS169, H10N3), and A/chicken/Jiangsu/0189/2021(JS189, H10N3). Animal studies indicated that all three viruses are highly pathogenic to mice and that all could replicate efficiently in mouse nasal turbinate and lungs despite maintaining their avian receptor binding affinity. We also found that these viruses replicated efficiently in A549 cells and chicken embryos. The strain JS146 had sensitivity to the neuraminidase-targeting drugs oseltamivir and zanamivir, whereas JS169 and JS189 were more resistant; genetic comparison implied that a substitution at NA position 368 conferred drug resistance. Importantly, several key molecular markers associated with mammalian adaptation had been detected in both avian and human-isolated H10N3 influenza viruses in the HA (G228S), PB2 (I292V and A588V), PB1 (M317V and I368V), and PA (A343S, K356R and S409N) protein. The above work contributes new insight into the biology of this potentially zoonotic subtype and provides evidence supporting the continued epidemiological monitoring of human infections caused by AIV subtype H10N3.
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Affiliation(s)
- Yanna Guo
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pingyun Ding
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yinjing Li
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yaping Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute in CAAS, Harbin, China
| | - Yiqing Zheng
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mengqi Yu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yasuo Suzuki
- College of Life and Health Sciences, Chubu University, Aichi, Japan
| | - Haitao Zhang
- Lihua Nanjing Industrial Research Institute Co., Ltd, Nanjing, China
| | - Jihui Ping
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety & Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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24
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Goldsmith JA, DiVenere AM, Maynard JA, McLellan JS. Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin. Cell Rep 2022; 40:111196. [PMID: 35977491 PMCID: PMC9416875 DOI: 10.1016/j.celrep.2022.111196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β2 integrins on phagocytes. The Bordetella adenylate cyclase toxin (ACT) uses the αMβ2 integrin as a receptor, but the structural basis for integrin binding and neutralization by antibodies is poorly understood. Here, we use cryoelectron microscopy to determine a 2.7 Å resolution structure of an ACT fragment bound to αMβ2. This structure reveals that ACT interacts with the headpiece and calf-2 of the αM subunit in a non-canonical manner specific to bent, inactive αMβ2. Neutralizing antibody epitopes map to ACT residues involved in αM binding, providing the basis for antibody-mediated attachment inhibition. Furthermore, binding to αMβ2 positions the essential ACT acylation sites, which are conserved among toxins exported by type I secretion systems, at the cell membrane. These findings reveal a structural mechanism for integrin-mediated attachment and explain antibody-mediated neutralization of ACT intoxication.
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Affiliation(s)
- Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrea M DiVenere
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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25
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Patrick C, Upadhyay V, Lucas A, Mallela KM. Biophysical Fitness Landscape of the SARS-CoV-2 Delta Variant Receptor Binding Domain. J Mol Biol 2022; 434:167622. [PMID: 35533762 PMCID: PMC9076029 DOI: 10.1016/j.jmb.2022.167622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/21/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022]
Abstract
Among the five known SARS-CoV-2 variants of concern, Delta is the most virulent leading to severe symptoms and increased mortality among infected people. Our study seeks to examine how the biophysical parameters of the Delta variant correlate to the clinical observations. Receptor binding domain (RBD) is the first point of contact with the human host cells and is the immunodominant form of the spike protein. Delta variant RBD contains two novel mutations L452R and T478K. We examined the effect of single as well as the double mutations on RBD expression in human Expi293 cells, RBD stability using urea and thermal denaturation, and RBD binding to angiotensin converting enzyme 2 (ACE2) receptor and to neutralizing antibodies using isothermal titration calorimetry. Delta variant RBD showed significantly higher expression compared to the wild-type RBD, and the increased expression is due to L452R mutation. Despite their non-conservative nature, none of the mutations significantly affected RBD structure and stability. All mutants showed similar binding affinity to ACE2 and to Class 1 antibodies (CC12.1 and LY-CoV016) as that of the wild-type. Delta double mutant L452R/T478K showed no binding to Class 2 antibodies (P2B-2F6 and LY-CoV555) and a hundred-fold weaker binding to a Class 3 antibody (REGN10987), and the decreased antibody binding is determined by the L452R mutation. These results indicate that the immune escape from neutralizing antibodies, rather than increased receptor binding, is the main biophysical parameter that determined the fitness landscape of the Delta variant RBD.
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Affiliation(s)
| | | | | | - Krishna M.G. Mallela
- Corresponding author at: Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd, MS C238-V20, Aurora, CO 80045, USA
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26
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Li Z, Liu L, Unione L, Lang Y, de Groot RJ, Boons GJ. Synthetic O-Acetyl- N-glycolylneuraminic Acid Oligosaccharides Reveal Host-Associated Binding Patterns of Coronaviral Glycoproteins. ACS Infect Dis 2022; 8:1041-1050. [PMID: 35416033 DOI: 10.1021/acsinfecdis.2c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A panel of O-acetylated N-glycolylneuraminic acid oligosaccharides has been prepared by diversification of common synthetic precursors by regioselective de-O-acetylation by coronaviral hemagglutinin-esterase (HE) combined with C7-to-C9 acetyl ester migration. The resulting compound library was printed on streptavidin-coated glass slides to give a microarray to investigate receptor binding specificities of viral envelope glycoproteins, including spike proteins and HEs from animal and human coronaviruses. It was found that the binding patterns of the viral proteins for N-glycolylated sialosides differ considerable from those of the previously synthesized N-acetylated counterparts. Generally, the spike proteins tolerate N-glycolyl modification, but selectivities differ among viruses targeting different hosts. On the other hand, the lectin domain of the corresponding HEs showed a substantial decrease or loss of binding of N-glycolylated sialosides. MD simulations indicate that glycolyl recognition by HE is mediated by polar residues in a loop region (109-119) that interacts with the 5-N-glycolyl moiety. Collectively, the results indicate that coronaviruses have adjusted their receptor fine specificities to adapt to the sialoglycome of their host species.
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Affiliation(s)
- Zeshi Li
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Yifei Lang
- Virology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Raoul J. de Groot
- Virology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CHUtrecht, The Netherlands
- Chemistry Department, University of Georgia, Athens, Georgia 30602, United States
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27
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Gorman D, Li XX, Payne CD, Cui CS, Lee JD, Rosengren KJ, Woodruff TM, Clark RJ. Development of Synthetic Human and Mouse C5a: Application to Binding and Functional Assays In Vitro and In Vivo. ACS Pharmacol Transl Sci 2021; 4:1808-1817. [PMID: 34927012 PMCID: PMC8669711 DOI: 10.1021/acsptsci.1c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/28/2022]
Abstract
The complement activation peptide C5a is a key mediator of inflammation that is associated with numerous immune disorders. C5a binds and activates two seven-transmembrane receptors, C5aR1 and C5aR2. Experimentally, C5a is utilized to investigate C5a receptor biology and to screen for potential C5aR1/C5aR2 therapeutics. Currently, laboratory sources of C5a stem from either isolation of endogenous C5a from human serum or most predominantly via recombinant expression. An alternative approach to C5a production is chemical synthesis, which has several advantages, including the ability to introduce non-natural amino acids and site-specific modifications whilst also maintaining a lower probability of C5a being contaminated with microbial molecules or other endogenous proteins. Here, we describe the efficient synthesis of both human (hC5a) and mouse C5a (mC5a) without the need for ligation chemistry. We validate the synthetic peptides by comparing pERK1/2 signaling in CHO-hC5aR1 cells and primary human macrophages (for hC5a) and in RAW264.7 cells (for mC5a). C5aR2 activation was confirmed by measuring β-arrestin recruitment in C5aR2-transfected HEK293 cells. We also demonstrate the functionalization of synthetic C5a through the introduction of a lanthanide chelating cage to facilitate a screen for the binding of ligands to C5aR1. Finally, we verify that the synthetic ligands are functionally similar to recombinant or native C5a by assessing hC5a-induced neutrophil chemotaxis in vitro and mC5a-mediated neutrophil mobilization in vivo. We propose that the synthetic hC5a and mC5a described herein are valuable alternatives to recombinant or purified C5a for in vitro and in vivo applications and add to the growing complement reagent toolbox.
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Affiliation(s)
- Declan
M. Gorman
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Xaria X. Li
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Colton D. Payne
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Cedric S. Cui
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - John D. Lee
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - K. Johan Rosengren
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
| | - Trent M. Woodruff
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
- Queensland
Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Richard J. Clark
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, Queensland 4072, Australia
- Institute
for Molecular Bioscience, The University
of Queensland, Brisbane, Queensland 4072, Australia
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28
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Verlov NA, Dorotenko AR, Gulina LS, Kalatanova AV, Trashkov AP, Burdakov VS. [Investigation of ligand-receptor interaction and biodistribution of a drug containing cattle retinal polypeptides in various administration routes]. Vestn Oftalmol 2021; 137:94-101. [PMID: 34726863 DOI: 10.17116/oftalma202113705194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It is important to understand the features of the interaction of drug components with body receptors and obtain data on its distribution in various administration routes in recommended doses in order for its usage in clinical practice to be safe and effective. PURPOSE To investigate in vitro the interactions of a drug consisting of water-soluble polypeptide fractions produced on animal retina with a wide range of receptor targets, and to assess its biodistribution in the organs of laboratory animals. MATERIAL AND METHODS The biodistribution of the radioactively marked drug in different organs and tissues of laboratory mice in various routes of administration was studied at the National Research Centre «Kurchatov Institute». Evaluation of the ligand-receptor interaction of the drug was carried out in the laboratory at Eurofins Pharma Discovery Services by the method of competitive radioligand binding. RESULTS A significant effect of the interaction of the polypeptide drug was revealed with different subtypes of glutamate receptors: AMPA, NMDA, and mGluR1. As a result of an in vivo test, we have obtained biodistribution data of the drug for intravenous, intramuscular and parabulbar administration, and the dynamics of drug accumulation in the tissues of the brain and eyes. CONCLUSION According to the study results, the peptide drug binds to receptors associated with the loss of retinal ganglion cells. Interaction with these receptors potentially provides the test subject with neuroprotective effect. The content dynamics of the studied drug in the blood of animals depends on the route of administration and the amount of drug administered. At the time point of 0.5 hours for intravenous and intramuscular administration in the dose of 1.7 mg/kg, the studied drug has sufficiently high bioavailability in the tissues of the brain and eye. The data suggest that the main route of excretion of the studied drug is through kidneys.
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Affiliation(s)
- N A Verlov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - A R Dorotenko
- Closed Joint-Stock Company «Pharm-Holding», Saint Petersburg, Russia
| | - L S Gulina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - A V Kalatanova
- Closed Joint-Stock Company «Pharm-Holding», Saint Petersburg, Russia
| | - A P Trashkov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - V S Burdakov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
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29
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Liu K, Ding P, Pei Y, Gao R, Han W, Zheng H, Ji Z, Cai M, Gu J, Li X, Gu M, Hu J, Liu X, Hu S, Zhang P, Wang X, Wang X, Liu X. Emergence of a novel reassortant avian influenza virus (H10N3) in Eastern China with high pathogenicity and respiratory droplet transmissibility to mammals. Sci China Life Sci 2021; 65:1024-1035. [PMID: 34542812 DOI: 10.1007/s11427-020-1981-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/13/2021] [Indexed: 11/29/2022]
Abstract
Decades have passed since the first discovery of H10-subtype avian influenza virus (AIV) in chickens in 1949, and it has been detected in many species including mammals such as minks, pigs, seals and humans. Cases of human infections with H10N8 viruses identified in China in 2013 have raised widespread attention. Two novel reassortant H10N3 viruses were isolated from chickens in December 2019 in eastern China during routine surveillance for AIVs. The internal genes of these viruses were derived from genotype S (G57) H9N2 and were consistent with H5N6, H7N9 and H10N8, which cause fatal infections in humans. Their viral pathogenicity and transmissibility were further studied in different animal models. The two H10N3 isolates had low pathogenicity in chickens and were transmitted between chickens via direct contact. These viruses were highly pathogenic in mice and could be transmitted between guinea pigs via direct contact and respiratory droplets. More importantly, these viruses can bind to both human-type SAα-2,6-Gal receptors and avian-type SAα-2,3-Gal receptors. Asymptomatic shedding in chickens and good adaptability to mammals of these H10N3 isolates would make it easier to transmit to humans and pose a threat to public health.
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Affiliation(s)
- Kaituo Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Pingyun Ding
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Yuru Pei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Ruyi Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China
| | - Wenwen Han
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Huafen Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Zhuxing Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Miao Cai
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Jinyuan Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Xiuli Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Min Gu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China
| | - Jiao Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China
| | - Xiaowen Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China
| | - Shunlin Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China
| | - Pinghu Zhang
- Institute of Translational Medicine, Key Laboratory of Geriatric Disease Prevention and Control of Jiangsu Province, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Xiaobo Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoquan Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China.
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Key Laboratory of Zoonosis, Yangzhou, 225009, China.
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30
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Forni D, Cagliani R, Arrigoni F, Benvenuti M, Mozzi A, Pozzoli U, Clerici M, De Gioia L, Sironi M. Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host. Virus Evol 2021; 7:veab061. [PMID: 34527284 PMCID: PMC8344746 DOI: 10.1093/ve/veab061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics-phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) and are polymorphic. Molecular dating for the HCoV-229E spike protein indicated that RBD Classes I, II, III, and IV emerged 3-9 years apart. However, since the appearance of Class V (with much higher binding affinity), around 25 years ago, limited genetic diversity accumulated in the RBD. These different time intervals are not fully consistent with the hypothesis that HCoV-229E spike evolution was driven by antigenic drift. An alternative, not mutually exclusive possibility is that strains with higher affinity for the cellular receptor have out-competed strains with lower affinity. The evolution of the HCoV-OC43 spike protein was also suggested to undergo antigenic drift. However, we also found abundant signals of positive selection in HE. Whereas such signals might result from antigenic drift, as well, previous data showing co-evolution of the spike protein with HE suggest that optimization for human cell infection also drove the evolution of this virus. These data provide insight into the possible trajectories of SARS-CoV-2 evolution, especially in case the virus should become endemic.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Martino Benvenuti
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, via Francesco Sforza, Milan 20122, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza, Milan 20126, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, via don Luigi Monza, 23843 Bosisio Parini, Italy
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Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG. Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. J Biol Chem 2021; 297:101175. [PMID: 34499924 PMCID: PMC8421091 DOI: 10.1016/j.jbc.2021.101175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 01/22/2023] Open
Abstract
The spike protein is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the human angiotensin-converting enzyme 2 receptor, a critical step in infection, and is the preferential target for spike-neutralizing antibodies. Posttranslational modifications of the spike receptor-binding motif have been shown to modulate viral infectivity and host immune response, but these modifications are still being explored. Here we studied asparagine deamidation of the spike protein, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, which affect both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike protein. Asparagine residues 481 and 501 in the receptor-binding motif deamidate with a half-life of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed at 4 °C, indicating a strong dependence of spike protein molecular aging on environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the human angiotensin-converting enzyme 2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion illustrating how deamidation of the spike receptor-binding motif could lead to the accumulation on the virion surface of a nonnegligible chemically diverse spike population in a timescale of days. Our findings provide a potential mechanism for molecular aging of the spike protein with significant consequences for understanding virus infectivity and vaccine development.
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Affiliation(s)
- Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Lucas A Defelipe
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lucio Aliperti
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Christian Löw
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María García-Alai
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Ignacio E Sánchez
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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Huang J, Chopra P, Liu L, Nagy T, Murray J, Tripp RA, Boons GJ, Mousa JJ. Structure, Immunogenicity, and Conformation-Dependent Receptor Binding of the Postfusion Human Metapneumovirus F Protein. J Virol 2021; 95:e0059321. [PMID: 34160259 DOI: 10.1128/JVI.00593-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human metapneumovirus (hMPV) is an important cause of acute viral respiratory infection. As the only target of neutralizing antibodies, the hMPV fusion (F) protein has been a major focus for vaccine development and targeting by drugs and monoclonal antibodies (MAbs). While X-ray structures of trimeric prefusion and postfusion hMPV F proteins from genotype A, and monomeric prefusion hMPV F protein from genotype B have been determined, structural data for the postfusion conformation for genotype B is lacking. We determined the crystal structure of this protein and compared the structural differences of postfusion hMPV F between hMPV A and B genotypes. We also assessed the receptor binding properties of the hMPV F protein to heparin and heparan sulfate (HS). A library of HS oligomers was used to verify the HS binding activity of hMPV F, and several compounds showed binding to predominantly prefusion hMPV F, but had limited binding to postfusion hMPV F. Furthermore, MAbs to antigenic sites III and the 66-87 intratrimeric epitope block heparin binding. In addition, we evaluated the efficacy of postfusion hMPV B2 F protein as a vaccine candidate in BALB/c mice. Mice immunized with hMPV B2 postfusion F protein showed a balanced Th1/Th2 immune response and generated neutralizing antibodies against both subgroup A2 and B2 hMPV strains, which protected the mice from hMPV challenge. Antibody competition analysis revealed the antibodies generated by immunization target two known antigenic sites (III and IV) on the hMPV F protein. Overall, this study provides new characteristics of the hMPV F protein, which may be informative for vaccine and therapy development. IMPORTANCE Human metapneumovirus (hMPV) is an important cause of viral respiratory disease. In this paper, we report the X-ray crystal structure of the hMPV fusion (F) protein in the postfusion conformation from genotype B. We also assessed binding of the hMPV F protein to heparin and heparan sulfate, a previously reported receptor for the hMPV F protein. Furthermore, we determined the immunogenicity and protective efficacy of postfusion hMPV B2 F protein, which is the first study using a homogenous conformation of the protein. Antibodies generated in response to vaccination give a balanced Th1/Th2 response and target two previously discovered neutralizing epitopes.
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Liu Y, Choi CKK, Hong H, Xiao Y, Kwok ML, Liu H, Tian XY, Choi CHJ. Dopamine Receptor-Mediated Binding and Cellular Uptake of Polydopamine-Coated Nanoparticles. ACS Nano 2021; 15:13871-13890. [PMID: 34379407 DOI: 10.1021/acsnano.1c06081] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Polydopamine (PDA)-coated nanoparticles (NPs) are emerging carriers of therapeutic agents for nanomedicine applications due to their biocompatibility and abundant entry to various cell types, yet it remains unknown whether their cellular entry engages cell-surface receptors. As monomeric dopamine (DA) is an endogenous ligand of dopamine receptor and raw ingredient of PDA, we elucidate the interaction between polyethylene glycol-stabilized, PDA-coated gold NPs (Au@PDA@PEG NPs) and dopamine receptors, particularly D2 (D2DR). After proving the binding of Au@PDA@PEG NPs to recombinant and cellular D2DR, we employ antibody blocking, gene knockdown, and gene overexpression to establish the role of D2DR in the cellular uptake of Au@PDA@PEG NPs in vitro. By preparing a series of PEG-coated AuNPs that contain different structural analogues of DA (Au@PEG-X NPs), we demonstrate that catechol and amine groups collectively enhance the binding of NPs to D2DR and their cellular uptake. By intravenously injecting Au@PDA@PEG NPs to Balb/c mice, we reveal their in vivo binding to D2DR in the liver by competitive inhibition and immunohistochemistry together with their preferential association to D2DR-rich resident Kupffer cells by flow cytometry, a result consistent with the profuse expression of D2DR by resident Kupffer cells. Catechol and amine groups jointly contribute to the preferential association of NPs to D2DR-rich Kupffer cells. Our data highlight the importance of D2DR expression and DA-related functional groups in mediating the cell-nano interactions of PDA-based nanomedicines.
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Thammasittirong A, Thammasittirong SNR, Imtong C, Charoenjotivadhanakul S, Sakdee S, Li HC, Okonogi S, Angsuthanasombat C. Bacillus thuringiensis Cry4Ba Insecticidal ToxinExploits Leu 615 in Its C-Terminal Domain to Interact with a Target Receptor- Aedes aegypti Membrane-Bound Alkaline Phosphatase. Toxins (Basel) 2021; 13:toxins13080553. [PMID: 34437424 PMCID: PMC8402544 DOI: 10.3390/toxins13080553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
In addition to the receptor-binding domain (DII), the C-terminal domain (DIII) of three-domain Cry insecticidal δ-endotoxins from Bacillus thuringiensis has been implicated in target insect specificity, yet its precise mechanistic role remains unclear. Here, the 21 kDa high-purity isolated DIII fragment derived from the Cry4Ba mosquito-specific toxin was achieved via optimized preparative FPLC, allowing direct rendering analyses for binding characteristics toward its target receptor—Aedes aegypti membrane-bound alkaline phosphatase (Aa-mALP). Binding analysis via dotblotting revealed that the Cry4Ba-DIII truncate was capable of specific binding to nitrocellulose-bound Aa-mALP, with a binding signal comparable to its 65 kDa Cry4Ba-R203Q full-length toxin. Further determination of binding affinity via sandwich ELISA revealed that Cry4Ba-DIII exhibited a rather weak binding to Aa-mALP with a dissociation constant (Kd) of ≈1.1 × 10−7 M as compared with the full-length toxin. Intermolecular docking between the Cry4Ba-R203Q active toxin and Aa-mALP suggested that four Cry4Ba-DIII residues, i.e., Glu522, Asn552, Asn576, and Leu615, are potentially involved in such toxin–receptor interactions. Ala substitutions of each residue (E522A, N552A, N576A and L615A) revealed that only the L615A mutant displayed a drastic decrease in biotoxicity against A. aegypti larvae. Additional binding analysis revealed that the L615A-impaired toxin also exhibited a reduction in binding capability to the surface-immobilized Aa-mALP receptor, while two bio-inactive DII-mutant toxins, Y332A and F364A, which almost entirely lost their biotoxicity, apparently retained a higher degree of binding activity. Altogether, our data disclose a functional importance of the C-terminal domain of Cry4Ba for serving as a potential receptor-binding moiety in which DIII-Leu615 could conceivably be exploited for the binding to Aa-mALP, highlighting its contribution to toxin interactions with such a target receptor in mediating larval toxicity.
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Affiliation(s)
- Anon Thammasittirong
- Microbial Biotechnology Unit, Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Nakhon Pathom 73140, Thailand;
- Correspondence: (A.T.); (C.A.)
| | - Sutticha Na-Ranong Thammasittirong
- Microbial Biotechnology Unit, Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Chompounoot Imtong
- Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand;
| | - Sathapat Charoenjotivadhanakul
- Bacterial Toxin Research Innovation Cluster (BRIC), Institute of Molecular Biosciences, Salaya Campus, Mahidol University, Nakorn Pathom 73170, Thailand; (S.C.); (S.S.)
| | - Somsri Sakdee
- Bacterial Toxin Research Innovation Cluster (BRIC), Institute of Molecular Biosciences, Salaya Campus, Mahidol University, Nakorn Pathom 73170, Thailand; (S.C.); (S.S.)
| | - Hui-Chun Li
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
| | - Siriporn Okonogi
- Research Center of Pharmaceutical Nanotechnology, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Chanan Angsuthanasombat
- Bacterial Toxin Research Innovation Cluster (BRIC), Institute of Molecular Biosciences, Salaya Campus, Mahidol University, Nakorn Pathom 73170, Thailand; (S.C.); (S.S.)
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
- Laboratory of Synthetic Biophysics and Chemical Biology, Biophysics Institute for Research and Development (BIRD), Chiang Mai 50130, Thailand
- Correspondence: (A.T.); (C.A.)
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Masuyer G, Davies JR, Stenmark P. Mechanism of Ganglioside Receptor Recognition by Botulinum Neurotoxin Serotype E. Int J Mol Sci 2021; 22:8315. [PMID: 34361086 DOI: 10.3390/ijms22158315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/10/2023] Open
Abstract
The botulinum neurotoxins are potent molecules that are not only responsible for the lethal paralytic disease botulism, but have also been harnessed for therapeutic uses in the treatment of an increasing number of chronic neurological and neuromuscular disorders, in addition to cosmetic applications. The toxins act at the cholinergic nerve terminals thanks to an efficient and specific mechanism of cell recognition which is based on a dual receptor system that involves gangliosides and protein receptors. Binding to surface-anchored gangliosides is the first essential step in this process. Here, we determined the X-ray crystal structure of the binding domain of BoNT/E, a toxin of clinical interest, in complex with its GD1a oligosaccharide receptor. Beyond confirmation of the conserved ganglioside binding site, we identified key interacting residues that are unique to BoNT/E and a significant rearrangement of loop 1228–1237 upon carbohydrate binding. These observations were also supported by thermodynamic measurements of the binding reaction and assessment of ganglioside selectivity by immobilised-receptor binding assays. These results provide a structural basis to understand the specificity of BoNT/E for complex gangliosides.
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Fedotova AO, Egorova BV, Posypanova GA, Titchenko NA, Khachatryan DS, Kolotaev AV, Osipov VN, Kalmykov SN. Labeling and receptor affinity of an ultra-short somatostatin analogue Thz-Phe-D-Trp-Lys-Thr-DOTA. J Pept Sci 2021; 27:e3361. [PMID: 34291534 DOI: 10.1002/psc.3361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/06/2022]
Abstract
Somatostatin analogues play an important role in the therapy of neuroendocrine tumors by binding to somatostatin receptors on the surface of cancer cells. In this work, we analyze the receptor-binding affinity and in vitro stability of a novel ultra-short somatostatin analogue Thz-Phe-D-Trp-Lys-Thr-DOTA (DOTA-P4). This conjugate is successfully radiolabeled with 44 Sc, 90 Y, 152 Eu, and 207 Bi, characterized and validated by thin layer and high-performance liquid chromatography. The optimum conditions for M-DOTA-P4 labeling are found. In vitro stability studies are performed in saline, in the presence of serum proteins, and with biologically relevant metal cations. All complexes demonstrate no cation release in vitro within 4-24 h. The conformations of DOTA-conjugates are studied by circular dichroism spectroscopy. The circular dichroism spectra of DOTA-P4 conjugates show a negative peak at 225 nm, which may correspond to the required β-sheet conformation. The binding to somatostatin receptors of types 2 and 5 is performed with the IMR-32 cells at 4°C, with non-specific binding representing 26% of the total binding. A two-line approximation of the Scatchard plot results in the apparent dissociation constants of 0.10 and 2.25 nM. It is shown that the chelator position with respect to the amino acid sequence significantly affects the labeling conditions with cations of different ionic radii. For the first time, the binding of a linear type ultra-short peptide conjugate with DOTA to somatostatin receptors is demonstrated. The obtained results are promising for experiments with DOTA-P4 in vivo in mice with inoculated tumors.
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Affiliation(s)
| | - Bayirta V Egorova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Derenik S Khachatryan
- «Kurchatov Institute» National Research Centre, Moscow, Russia.,Institute of Chemical Reagents and High Purity Chemical Substances, «Kurchatov Institute» National Research Centre, Moscow, Russia
| | - Anton V Kolotaev
- «Kurchatov Institute» National Research Centre, Moscow, Russia.,Institute of Chemical Reagents and High Purity Chemical Substances, «Kurchatov Institute» National Research Centre, Moscow, Russia
| | - Vasiliy N Osipov
- «N.N. Blokhin National Medical Research Centre of oncology», Health Ministry of Russia, Moscow, Russia
| | - Stepan N Kalmykov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,«Kurchatov Institute» National Research Centre, Moscow, Russia
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Liu Q, Zhang P, Lusso P. Quaternary Interaction of the HIV-1 Envelope Trimer with CD4 and Neutralizing Antibodies. Viruses 2021; 13:1405. [PMID: 34372611 DOI: 10.3390/v13071405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/25/2022] Open
Abstract
The entry of HIV-1 into host cells is initiated by the interaction of the viral envelope (Env) spike with the CD4 receptor. During this process, the spike undergoes a series of conformational changes that eventually lead to the exposure of the fusion peptide located at the N-terminus of the transmembrane glycoprotein, gp41. Recent structural and functional studies have provided important insights into the interaction of Env with CD4 at various stages. However, a fine elucidation of the earliest events of CD4 contact and its immediate effect on the Env conformation remains a challenge for investigation. Here, we summarize the discovery of the quaternary nature of the CD4-binding site in the HIV-1 Env and the role of quaternary contact in the functional interaction with the CD4 receptor. We propose two models for this initial contact based on the current knowledge and discuss how a better understanding of the quaternary interaction may lead to improved immunogens and antibodies targeting the CD4-binding site.
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Zhang Y, Yi X, Huang K, Sun Q, Kong R, Chen S, Liang C, Li M, Letcher RJ, Liu C. Tris(1,3-dichloro-2-propyl)phosphate Reduces Growth Hormone Expression via Binding to Growth Hormone Releasing Hormone Receptors and Inhibits the Growth of Crucian Carp. Environ Sci Technol 2021; 55:8108-8118. [PMID: 34062063 DOI: 10.1021/acs.est.0c07708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) has commonly been used as an additive flame retardant and frequently detected in the aquatic environment and in biological samples worldwide. Recently, it was found that exposure to TDCIPP inhibited the growth of zebrafish, but the relevant molecular mechanisms remained unclear. In this study, 5 day-old crucian carp (Carassius auratus) larvae were treated with 0.5, 5, or 50 μg/L TDCIPP for 90 days; the effect on growth was evaluated; and related molecular mechanisms were explored. Results demonstrated that 5 or 50 μg/L TDCIPP treatment significantly inhibited the growth of crucian carp and downregulated the expression of growth hormones (ghs), growth hormone receptor (ghr), and insulin-like growth factor 1 (igf1). Molecular docking, dual-luciferase reporter gene assay, and in vitro experiments demonstrated that TDCIPP could bind to the growth hormone releasing hormone receptor protein of crucian carp and disturb the stimulation of growth hormone releasing hormone to the expression of ghs, resulting in the decrease of the mRNA level of gh1 and gh2 in pituitary cells. Our findings provide new perceptions into the molecular mechanisms of developmental toxicity of TDCIPP in fish.
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Affiliation(s)
- Yongkang Zhang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun'e Yi
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai Huang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Sun
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ren Kong
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng Chen
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengqian Liang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Li
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert J Letcher
- Departments of Chemistry and Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Chunsheng Liu
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
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Hoare SRJ. The Problems of Applying Classical Pharmacology Analysis to Modern In Vitro Drug Discovery Assays: Slow Binding Kinetics and High Target Concentration. SLAS Discov 2021; 26:835-850. [PMID: 34112012 DOI: 10.1177/24725552211019653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The analysis framework used to quantify drug potency in vitro (e.g., Kd or Ki) was initially developed for classical pharmacology bioassays, for example, organ bath experiments testing moderate-affinity natural products. Modern drug discovery can infringe the assumptions of the classical pharmacology analysis equations, owing to the reduction of assay volume in miniaturization, target overexpression, and the increase of compound-target affinity in medicinal chemistry. These assumptions are that (1) the compound concentration greatly exceeds the target concentration (i.e., minimal ligand depletion), and (2) the compound is at equilibrium with the receptor (i.e., rapid ligand binding kinetics). Unappreciated infringement of these assumptions can lead to substantial underestimation of compound affinity, which negatively impacts the drug discovery process, from early-stage lead optimization to prediction of human dosing. This study evaluates the real-world impact of these factors on the target interaction assays used in drug discovery using literature examples, database searches, and simulations. The ranges of compound affinity and the assay types that are prone to depletion and equilibration artifacts are identified. Importantly, the highest-affinity compounds, usually the highest value chemical matter in drug discovery, are the most affected. Methods and simulation tools are provided to enable investigators to evaluate, manage, and minimize depletion or equilibration artifacts. This study enables the correct application of pharmacological data analysis to accurately quantify affinity using modern drug discovery assay technology.
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Martinez WE, Arenas JE, Mok L, Wong NY, Lozano MM, Lin WC, Gutierrez MG, Sierra Chavera R, McGivern JG. Bioelectronic Measurement of Target Engagement to a Membrane-Bound Transporter. SLAS Discov 2021; 26:1004-1013. [PMID: 33980065 DOI: 10.1177/24725552211013067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect and characterize drug binding to a target protein is of high priority in drug discovery research. However, there are inherent challenges when the target of interest is an integral membrane protein (IMP). Assuming successful purification of the IMP, traditional approaches for measuring binding such as surface plasmon resonance (SPR) and fluorescence resonance energy transfer (FRET) have been proven valuable. However, the mass dependence of SPR signals may preclude the detection of binding events when the ligand has a significantly smaller mass than the target protein. In FRET-based experiments, protein labeling through modification may inadvertently alter protein dynamics. Graphene Bio-Electronic Sensing Technology (GBEST) aims to overcome these challenges. Label-free characterization takes place in a microfluidic chamber wherein a fluid lipid membrane is reconstituted directly above the GBEST sensor surface. By leveraging the high conductivity, sensitivity, and electrical properties of monolayer graphene, minute changes in electrostatic charges arising from the binding and unbinding of a ligand to a native IMP target can be detected in real time and in a mass-independent manner. Using crude membrane fractions prepared from cells overexpressing monocarboxylate transporter 1 (MCT1), we demonstrate the ability to (1) form a fluid lipid bilayer enriched with MCT1 directly on top of the GBEST sensor and (2) obtain kinetic binding data for an anti-MCT1 antibody. Further development of this novel technology will enable characterization of target engagement by both low- and high-molecular-weight drug candidates to native IMP targets in a physiologically relevant membrane environment.
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Affiliation(s)
- William E Martinez
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Avalor Therapeutics, Seattle, WA, USA
| | - Jaime E Arenas
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA
| | - Leo Mok
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA
| | - Ngo Yin Wong
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Ximedica, LLC, San Francisco, CA, USA
| | - Monica M Lozano
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Profusa, Inc., Emeryville, CA, USA
| | - Wan-Chen Lin
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Imgenix Corp., Paoli, PA, USA
| | - M Gertrude Gutierrez
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Pharmaceutical Science & Technology, AstraZeneca, South San Francisco, CA, USA
| | - Rodrigo Sierra Chavera
- Research and Development, Nanotech Biomachines, Inc., Richmond, CA, USA.,Sierra Intelligence, Bahrain
| | - Joseph G McGivern
- Discovery Technologies, Amgen Research, South San Francisco, CA, USA.,Denali Therapeutics, South San Francisco, CA, USA
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Socher E, Conrad M, Heger L, Paulsen F, Sticht H, Zunke F, Arnold P. Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Biomedicines 2021; 9:525. [PMID: 34066729 PMCID: PMC8151884 DOI: 10.3390/biomedicines9050525] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023] Open
Abstract
The B.1.1.7 variant of the SARS-CoV-2 virus shows enhanced infectiousness over the wild type virus, leading to increasing patient numbers in affected areas. Amino acid exchanges within the SARS-CoV-2 spike protein variant of B.1.1.7 affect inter-monomeric contact sites within the trimer (A570D and D614G) as well as the ACE2-receptor interface region (N501Y), which comprises the receptor-binding domain (RBD) of the spike protein. However, the molecular consequences of mutations within B.1.1.7 on spike protein dynamics and stability or ACE2 binding are largely unknown. Here, molecular dynamics simulations comparing SARS-CoV-2 wild type with the B.1.1.7 variant revealed inter-trimeric contact rearrangements, altering the structural flexibility within the spike protein trimer. Furthermore, we found increased flexibility in direct spatial proximity of the fusion peptide due to salt bridge rearrangements induced by the D614G mutation in B.1.1.7. This study also implies a reduced binding affinity for B.1.1.7 with ACE2, as the N501Y mutation restructures the RBD-ACE2 interface, significantly decreasing the linear interaction energy between the RBD and ACE2. Our results demonstrate how mutations found within B.1.1.7 enlarge the flexibility around the fusion peptide and change the RBD-ACE2 interface. We anticipate our findings to be starting points for in depth biochemical and cell biological analyses of B.1.1.7.
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Affiliation(s)
- Eileen Socher
- Institute of Anatomy, Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, 91054 Erlangen, Germany
| | - Marcus Conrad
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (H.S.)
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, 91052 Erlangen, Germany;
| | - Friedrich Paulsen
- Institute of Anatomy, Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
- Department of Operative Surgery and Topographic Anatomy, Sechenov University, 119992 Moscow, Russia
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (H.S.)
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Friederike Zunke
- Department of Molecular Neurology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), University Hospital Erlangen, 91054 Erlangen, Germany;
| | - Philipp Arnold
- Institute of Anatomy, Functional and Clinical Anatomy, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
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Abstract
Several subtypes of avian influenza (AI) viruses have caused human infections in recent years; however, there is a severe knowledge gap regarding the capacity of wild bird viruses to infect mammals. To assess the risk of mammalian infection by AI viruses from their natural reservoirs, a panel of isolates from 34 wild birds was examined in animal models. All selected AI virus subtypes were found to predominantly possess Eurasian lineage, although reassortment with North American lineage AI viruses was also noted in some isolates. When used to infect chickens, 20 AI isolates could be recovered from oropharyngeal swabs at 5 days post-infection (dpi) without causing significant morbidity. Similarly, mild to no observable disease was observed in mice infected with these viruses although the majority replicated efficiently in murine lungs. As expected, wild bird AI isolates were found to recognize avian-like receptors, while a few strains also exhibited detectable human-like receptor binding. Selected strains were further tested in ferrets, and 15 out of 20 were found to shed the virus in the upper respiratory tract until 5 dpi. Overall, we demonstrate that a diversity of low-pathogenic AI viruses carried by wild migratory birds have the capacity to infect land-based poultry and mammalian hosts while causing minimal signs of clinical disease. This study reiterates that there is a significant capacity for interspecies transmission of AI viruses harboured by wild aquatic birds. Thus, these viruses pose a significant threat to human health underscoring the need for continued surveillance.
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Affiliation(s)
- Eun-Ha Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Korea
| | - Young-Ll Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Korea
| | - Se Mi Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Korea
| | - Kwang-Min Yu
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Korea
| | - Mark Anthony B Casel
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Korea
| | - Seung-Gyu Jang
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Philippe Noriel Q Pascua
- Virology Division, Department. of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard J Webby
- Virology Division, Department. of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Young Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea.,Zoonotic Infectious Diseases Research Center, Chungbuk National University, Cheongju, Korea
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Gonzalez-Garcia M, Fusco G, De Simone A. Membrane Interactions and Toxicity by Misfolded Protein Oligomers. Front Cell Dev Biol 2021; 9:642623. [PMID: 33791300 PMCID: PMC8006268 DOI: 10.3389/fcell.2021.642623] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 01/13/2023] Open
Abstract
The conversion of otherwise soluble proteins into insoluble amyloid aggregates is associated with a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases, as well as non-neuropathic conditions such as type II diabetes and systemic amyloidoses. It is increasingly evident that the most pernicious species among those forming during protein aggregation are small prefibrillar oligomers. In this review, we describe the recent progress in the characterization of the cellular and molecular interactions by toxic misfolded protein oligomers. A fundamental interaction by these aggregates involves biological membranes, resulting in two major model mechanisms at the onset of the cellular toxicity. These include the membrane disruption model, resulting in calcium imbalance, mitochondrial dysfunction and intracellular reactive oxygen species, and the direct interaction with membrane proteins, leading to the alteration of their native function. A key challenge remains in the characterization of transient interactions involving heterogeneous protein aggregates. Solving this task is crucial in the quest of identifying suitable therapeutic approaches to suppress the cellular toxicity in protein misfolding diseases.
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Affiliation(s)
- Mario Gonzalez-Garcia
- Department of Life Sciences, Imperial College London, South Kensington, United Kingdom
| | - Giuliana Fusco
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, United Kingdom.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
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Li J, Li J, Chen S, Yuan Q, Zhang J, Wu J, Jiang Q, Wang Q, Xia NS, Zhang J, Tong S. Naturally occurring 5' preS1 deletions markedly enhance replication and infectivity of HBV genotype B and genotype C. Gut 2021; 70:575-584. [PMID: 32571971 DOI: 10.1136/gutjnl-2019-320096] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 05/08/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Deletion of 15-nucleotide or 18-nucleotide (nt) covering preS1 ATG frequently arises during chronic infection with HBV genotypes B and C. Since the second ATG is 33nt downstream, they truncate large (L) envelope protein by 11 residues like wild-type genotype D. This study characterised their functional consequences. METHODS HBV genomes with or without deletion were amplified from a patient with advanced liver fibrosis and assembled into replication competent 1.1mer construct. Deletion, insertion or point mutation was introduced to additional clones of different genotypes. Viral particles concentrated from transfected HepG2 cells were inoculated to sodium taurocholate cotransporting polypeptide (NTCP)-reconstituted HepG2 (HepG2/NTCP) cells or differentiated HepaRG cells, and HBV RNA, DNA, proteins were monitored. RESULTS From transfected HepG2 cells, the 15-nt and 18-nt deletions increased HBV RNA, replicative DNA and extracellular virions. When same number of viral particles was inoculated to HepG2/NTCP cells, the deletion mutants showed higher infectivity. Conversely, HBV infectivity was diminished by putting back the 18nt into naturally occurring genotype C deletion mutants and by adding 33nt to genotype D. Infectivity of full-length genotype C clones was also enhanced by mutating the first ATG codon of the preS1 region but diminished by mutating the second in-frame ATG. Removing N-terminal 11 residues from preS1 peptide 2-59 of genotype C potentiated inhibition of HBV infection and enhanced binding to HepG2/NTCP cells. CONCLUSIONS The 15-nt and 18-nt deletions somehow increase HBV RNA, replicative DNA and virion production. Shortened L protein is more efficient at mediating HBV infection.
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Affiliation(s)
- Jing Li
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Jisu Li
- Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Shiqi Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Quan Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Publich Health, Xiamen University, Xiamen, China
| | - Jing Zhang
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jingwen Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qirong Jiang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qianru Wang
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ning-Shao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Publich Health, Xiamen University, Xiamen, China
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shuping Tong
- Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA .,Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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Peacock TP, Sealy JE, Harvey WT, Benton DJ, Reeve R, Iqbal M. Genetic determinants of receptor-binding preference and zoonotic potential of H9N2 avian influenza viruses. J Virol 2021; 95:JVI. [PMID: 33268517 DOI: 10.1128/JVI.01651-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Receptor recognition and binding is the first step of viral infection and a key determinant of host specificity. The inability of avian influenza viruses to effectively bind human-like sialylated receptors is a major impediment to their efficient transmission in humans and pandemic capacity. Influenza H9N2 viruses are endemic in poultry across Asia and parts of Africa where they occasionally infect humans and are therefore considered viruses with zoonotic potential. We previously described H9N2 viruses, including several isolated from human zoonotic cases, showing a preference for human-like receptors. Here we take a mutagenesis approach, making viruses with single or multiple substitutions in H9 haemagglutinin and test binding to avian and human receptor analogues using biolayer interferometry. We determine the genetic basis of preferences for alternative avian receptors and for human-like receptors, describing amino acid motifs at positions 190, 226 and 227 that play a major role in determining receptor specificity, and several other residues such as 159, 188, 193, 196, 198 and 225 that play a smaller role. Furthermore, we show changes at residues 135, 137, 147, 157, 158, 184, 188, and 192 can also modulate virus receptor avidity and that substitutions that increased or decreased the net positive charge around the haemagglutinin receptor-binding site show increases and decreases in avidity, respectively. The motifs we identify as increasing preference for the human-receptor will help guide future H9N2 surveillance efforts and facilitate our understanding of the emergence of influenza viruses with increased zoonotic potential.IMPORTANCE As of 2020, over 60 infections of humans by H9N2 influenza viruses have been recorded in countries where the virus is endemic. Avian-like cellular receptors are the primary target for these viruses. However, given that human infections have been detected on an almost monthly basis since 2015, there may be a capacity for H9N2 viruses to evolve and gain the ability to target human-like cellular receptors. Here we identify molecular signatures that can cause viruses to bind human-like receptors, and we identify the molecular basis for the distinctive preference for sulphated receptors displayed by the majority of recent H9N2 viruses. This work will help guide future surveillance by providing markers that signify the emergence of viruses with enhanced zoonotic potential as well as improving understanding of the basis of influenza virus receptor-binding.
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46
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Hulswit RJG, Paesen GC, Bowden TA, Shi X. Recent Advances in Bunyavirus Glycoprotein Research: Precursor Processing, Receptor Binding and Structure. Viruses 2021; 13:353. [PMID: 33672327 PMCID: PMC7926653 DOI: 10.3390/v13020353] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
The Bunyavirales order accommodates related viruses (bunyaviruses) with segmented, linear, single-stranded, negative- or ambi-sense RNA genomes. Their glycoproteins form capsomeric projections or spikes on the virion surface and play a crucial role in virus entry, assembly, morphogenesis. Bunyavirus glycoproteins are encoded by a single RNA segment as a polyprotein precursor that is co- and post-translationally cleaved by host cell enzymes to yield two mature glycoproteins, Gn and Gc (or GP1 and GP2 in arenaviruses). These glycoproteins undergo extensive N-linked glycosylation and despite their cleavage, remain associated to the virion to form an integral transmembrane glycoprotein complex. This review summarizes recent advances in our understanding of the molecular biology of bunyavirus glycoproteins, including their processing, structure, and known interactions with host factors that facilitate cell entry.
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Affiliation(s)
- Ruben J. G. Hulswit
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (R.J.G.H.); (G.C.P.)
| | - Guido C. Paesen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (R.J.G.H.); (G.C.P.)
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (R.J.G.H.); (G.C.P.)
| | - Xiaohong Shi
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G61 1QH, UK
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47
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Vizarraga D, Torres-Puig S, Aparicio D, Pich OQ. The Sialoglycan Binding Adhesins of Mycoplasma genitalium and Mycoplasma pneumoniae. Trends Microbiol 2021; 29:477-481. [PMID: 33593698 DOI: 10.1016/j.tim.2021.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 01/20/2023]
Abstract
Mycoplasma genitalium (Mge) and Mycoplasma pneumoniae (Mpn) are two human pathogens associated with urogenital and respiratory tract infections, respectively. The recent elucidation of the tridimensional structure of their major cytoadhesins by X-ray crystallography and cryo-electron microscopy/tomography, has provided important insights regarding the mechanics of infection and evasion of immune surveillance.
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Affiliation(s)
- David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Sergi Torres-Puig
- Research Unit of Molecular Microbiology (RUMM), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain.
| | - Oscar Q Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208 Sabadell, Spain; Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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48
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Martínez VR, Aguirre MV, Todaro JS, Lima AM, Stergiopulos N, Ferrer EG, Williams PA. Zinc complexation improves angiotensin II receptor type 1 blockade and in vivo antihypertensive activity of telmisartan. Future Med Chem 2021; 13:13-23. [PMID: 33243020 DOI: 10.4155/fmc-2020-0093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background: Angiotensin II receptor blockers were designed as therapeutic agents to block the binding site of the angiotensin II receptor type 1 (AT1R). Methodology: The structure of telmisartan was modified by coordination to the biometal Zn(II), resulting in the compound ZnTelm. Its antihypertensive activity and cellular mechanisms in comparison to telmisartan were studied. Results: Compared with telmisartan, ZnTelm displayed stronger binding to AT1R (binding studies on AT1R-transfected human embryonic kidney cells) and a greater reduction of reactive oxygen species and cytosolic calcium concentration induced by angiotensin II. The antihypertensive activity of the complex (assessed in an N(G)-Nitro-L-arginine methyl ester-induced hypertension model) was significantly higher. ZnTelm also reduced hypertrophy in aortic artery rings and tubular collagen deposition. Conclusion: ZnTelm enhances the AT1R blockade and consequently its antihypertensive effect.
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Affiliation(s)
- Valeria R Martínez
- Centro de Química Inorgánica (CEQUINOR-CONICET-CICPBA-UNLP), 120 no. 1465, La Plata, Argentina
| | - María V Aguirre
- Laboratorio de Investigaciones Bioquímicas, Facultad de Medicina, UNNE, Moreno 1240, Corrientes, Argentina
| | - Juan S Todaro
- Laboratorio de Investigaciones Bioquímicas, Facultad de Medicina, UNNE, Moreno 1240, Corrientes, Argentina
| | - Augusto Martins Lima
- Laboratory of Hemodynamics & Cardiovascular Technology (LHTC), Institute of Bioengineering (Bâtiment MED), Station 9, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Nikolaos Stergiopulos
- Laboratory of Hemodynamics & Cardiovascular Technology (LHTC), Institute of Bioengineering (Bâtiment MED), Station 9, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evelina G Ferrer
- Centro de Química Inorgánica (CEQUINOR-CONICET-CICPBA-UNLP), 120 no. 1465, La Plata, Argentina
| | - Patricia Am Williams
- Centro de Química Inorgánica (CEQUINOR-CONICET-CICPBA-UNLP), 120 no. 1465, La Plata, Argentina
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Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional compounds that recruit the E3 ubiquitin ligase machinery to proteins of interest, resulting in their ubiquitination and subsequent proteasomal degradation. Targeted protein degradation has generated considerable interest in drug discovery because inhibition of one particular function of a protein often does not deliver the therapeutic efficacy that results from whole-protein depletion. However, the physicochemistry and intrinsically complex pharmacology of PROTACs present challenges, particularly for the development of orally bioavailable drugs. Here we describe the application of a translational pharmacology framework (called the four pillars) to expedite PROTAC development by informing pharmacokinetic-pharmacodynamic (PKPD) understanding and helping elucidate structure-activity relationships. Experimental methods are reviewed that help illuminate exposure of the drug or probe at the site of action (pillar 1) and engagement of its target(s) (pillar 2) that drive functional pharmacological effects (pillar 3) resulting in modulation of a relevant phenotype (pillar 4). We hope the guidance will be useful to those developing targeted protein degraders and help establish PROTAC molecules as robust target validation chemical probes.
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Affiliation(s)
- Radosław P Nowak
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, USA
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50
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Sayed ARM, Shah NR, Basso KB, Kamat M, Jiao Y, Moya B, Sutaria DS, Lang Y, Tao X, Liu W, Shin E, Zhou J, Werkman C, Louie A, Drusano GL, Bulitta JB. First Penicillin-Binding Protein Occupancy Patterns for 15 β-Lactams and β-Lactamase Inhibitors in Mycobacterium abscessus. Antimicrob Agents Chemother 2020; 65:e01956-20. [PMID: 33106266 DOI: 10.1128/AAC.01956-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium abscessus causes serious infections that often require over 18 months of antibiotic combination therapy. There is no standard regimen for the treatment of M. abscessus infections, and the multitude of combinations that have been used clinically have had low success rates and high rates of toxicities. With β-lactam antibiotics being safe, double β-lactam and β-lactam/β-lactamase inhibitor combinations are of interest for improving the treatment of M. abscessus infections and minimizing toxicity. However, a mechanistic approach for building these combinations is lacking since little is known about which penicillin-binding protein (PBP) target receptors are inactivated by different β-lactams in M. abscessus We determined the preferred PBP targets of 13 β-lactams and 2 β-lactamase inhibitors in two M. abscessus strains and identified PBP sequences by proteomics. The Bocillin FL binding assay was used to determine the β-lactam concentrations that half-maximally inhibited Bocillin binding (50% inhibitory concentrations [IC50s]). Principal component analysis identified four clusters of PBP occupancy patterns. Carbapenems inactivated all PBPs at low concentrations (0.016 to 0.5 mg/liter) (cluster 1). Cephalosporins (cluster 2) inactivated PonA2, PonA1, and PbpA at low (0.031 to 1 mg/liter) (ceftriaxone and cefotaxime) or intermediate (0.35 to 16 mg/liter) (ceftazidime and cefoxitin) concentrations. Sulbactam, aztreonam, carumonam, mecillinam, and avibactam (cluster 3) inactivated the same PBPs as cephalosporins but required higher concentrations. Other penicillins (cluster 4) specifically targeted PbpA at 2 to 16 mg/liter. Carbapenems, ceftriaxone, and cefotaxime were the most promising β-lactams since they inactivated most or all PBPs at clinically relevant concentrations. These first PBP occupancy patterns in M. abscessus provide a mechanistic foundation for selecting and optimizing safe and effective combination therapies with β-lactams.
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