1
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Stoup N, Liberelle M, Lebègue N, Van Seuningen I. Emerging paradigms and recent progress in targeting ErbB in cancers. Trends Pharmacol Sci 2024; 45:552-576. [PMID: 38797570 DOI: 10.1016/j.tips.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024]
Abstract
The epidermal growth factor receptor (EGFR) family is a class of transmembrane proteins, highly regarded as anticancer targets due to their pivotal role in various malignancies. Standard cancer treatments targeting the ErbB receptors include tyrosine kinase inhibitors (TKIs) and monoclonal antibodies (mAbs). Despite their substantial survival benefits, the achievement of curative outcomes is hindered by acquired resistance. Recent advancements in anti-ErbB approaches, such as inhibitory peptides, nanobodies, targeted-protein degradation strategies, and bispecific antibodies (BsAbs), aim to overcome such resistance. More recently, emerging insights into the cell surface interactome of the ErbB family open new avenues for modulating ErbB signaling by targeting specific domains of ErbB partners. Here, we review recent progress in ErbB targeting and elucidate emerging paradigms that underscore the significance of EGF domain-containing proteins (EDCPs) as new ErbB-targeting pathways.
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Affiliation(s)
- Nicolas Stoup
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Maxime Liberelle
- University of Lille, Inserm, CHU Lille, UMR-S 1172 - LiNC -Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Nicolas Lebègue
- University of Lille, Inserm, CHU Lille, UMR-S 1172 - LiNC -Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Isabelle Van Seuningen
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France.
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2
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Toussaint K, Appert-Collin A, Vanalderwiert L, Bour C, Terryn C, Spenlé C, Van Der Heyden M, Roumieux M, Maurice P, Romier-Crouzet B, Sartelet H, Duca L, Blaise S, Bennasroune A. Inhibition of neuraminidase-1 sialidase activity by interfering peptides impairs insulin receptor activity in vitro and glucose homeostasis in vivo. J Biol Chem 2024; 300:107316. [PMID: 38663826 PMCID: PMC11167521 DOI: 10.1016/j.jbc.2024.107316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 03/18/2024] [Accepted: 04/09/2024] [Indexed: 06/02/2024] Open
Abstract
Neuraminidases (NEUs) also called sialidases are glycosidases which catalyze the removal of terminal sialic acid residues from glycoproteins, glycolipids, and oligosaccharides. Mammalian NEU-1 participates in regulation of cell surface receptors such as insulin receptor (IR), epithelial growth factor receptor, low-density lipoprotein receptor, and toll-like receptor 4. At the plasma membrane, NEU-1 can be associated with the elastin-binding protein and the carboxypeptidase protective protein/cathepsin A to constitute the elastin receptor complex. In this complex, NEU-1 is essential for elastogenesis, signal transduction through this receptor and for biological effects of the elastin-derived peptides on atherosclerosis, thrombosis, insulin resistance, nonalcoholic steatohepatitis, and cancers. This is why research teams are developing inhibitors targeting this sialidase. Previously, we developed interfering peptides to inhibit the dimerization and the activation of NEU-1. In this study, we investigated the effects of these peptides on IR activation in vitro and in vivo. Using cellular overexpression and endogenous expression models of NEU-1 and IR (COS-7 and HepG2 cells, respectively), we have shown that interfering peptides inhibit NEU-1 dimerization and sialidase activity which results in a reduction of IR phosphorylation. These results demonstrated that NEU-1 positively regulates IR phosphorylation and activation in our conditions. In vivo, biodistribution study showed that interfering peptides are well distributed in mice. Treatment of C57Bl/6 mice during 8 weeks with interfering peptides induces a hyperglycemic effect in our experimental conditions. Altogether, we report here that inhibition of NEU-1 sialidase activity by interfering peptides decreases IR activity in vitro and glucose homeostasis in vivo.
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Affiliation(s)
- Kevin Toussaint
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France
| | | | | | - Camille Bour
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France
| | | | - Caroline Spenlé
- UMR7242 Biotechnology and Cell Signalling, Centre National de la Recherche Scientifique, Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, Illkirch-Graffenstaden, France
| | | | | | - Pascal Maurice
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France
| | | | - Hervé Sartelet
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France
| | - Laurent Duca
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France
| | - Sébastien Blaise
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France.
| | - Amar Bennasroune
- Université de Reims Champagne-Ardenne, CNRS, MEDyC, Reims, France.
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3
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Guillot A, Toussaint K, Ebersold L, ElBtaouri H, Thiebault E, Issad T, Peiretti F, Maurice P, Sartelet H, Bennasroune A, Martiny L, Dauchez M, Duca L, Durlach V, Romier B, Baud S, Blaise S. Sialic acids cleavage induced by elastin-derived peptides impairs the interaction between insulin and its receptor in adipocytes 3T3-L1. J Physiol Biochem 2024; 80:363-379. [PMID: 38393636 DOI: 10.1007/s13105-024-01010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
Abstract
The insulin receptor (IR) plays an important role in insulin signal transduction, the defect of which is believed to be the root cause of type 2 diabetes. In 3T3-L1 adipocytes as in other cell types, the mature IR is a heterotetrameric cell surface glycoprotein composed of two α subunits and two β subunits. Our objective in our study, is to understand how the desialylation of N-glycan chains, induced by elastin-derived peptides, plays a major role in the function of the IR. Using the 3T3-L1 adipocyte line, we show that removal of the sialic acid from N-glycan chains (N893 and N908), induced by the elastin receptor complex (ERC) and elastin derived-peptides (EDPs), leads to a decrease in the autophosphorylation activity of the insulin receptor. We demonstrate by molecular dynamics approaches that the absence of sialic acids on one of these two sites is sufficient to generate local and general modifications of the structure of the IR. Biochemical approaches highlight a decrease in the interaction between insulin and its receptor when ERC sialidase activity is induced by EDPs. Therefore, desialylation by EDPs is synonymous with a decrease of IR sensitivity in adipocytes and could thus be a potential source of insulin resistance associated with diabetic conditions.
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Affiliation(s)
- Alexandre Guillot
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Kevin Toussaint
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Lucrece Ebersold
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Hassan ElBtaouri
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Emilie Thiebault
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Tarik Issad
- Université Paris Cité, Institut Cochin, CNRS, INSERM, 24 Rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Franck Peiretti
- INSERM, INRAE, C2VN, Aix Marseille University, 27 Bd Jean Moulin, 13385, Marseille, France
| | - Pascal Maurice
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Hervé Sartelet
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Amar Bennasroune
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Laurent Martiny
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Manuel Dauchez
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
- P3M, Multi-Scale Molecular Modeling Platform, Université de Reims Champagne Ardenne, 51100, Reims, France
| | - Laurent Duca
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Vincent Durlach
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
- Cardiovascular and Thoracic Division, University Hospital of Reims, 51100, Reims, France
| | - Béatrice Romier
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
| | - Stéphanie Baud
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France
- P3M, Multi-Scale Molecular Modeling Platform, Université de Reims Champagne Ardenne, 51100, Reims, France
| | - Sébastien Blaise
- UMR CNRS 7369 MEDyC, University of Reims Champagne-Ardenne, UFR SEN, chemin des Rouliers, 51100, Reims, France.
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4
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Johnson TS, Bourdine AA, Deber CM. Hydrophobic moment drives penetration of bacterial membranes by transmembrane peptides. J Biol Chem 2023; 299:105266. [PMID: 37734555 PMCID: PMC10585379 DOI: 10.1016/j.jbc.2023.105266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
With antimicrobial resistance (AMR) remaining a persistent and growing threat to human health worldwide, membrane-active peptides are gaining traction as an alternative strategy to overcome the issue. Membrane-embedded multi-drug resistant (MDR) efflux pumps are a prime target for membrane-active peptides, as they are a well-established contributor to clinically relevant AMR infections. Here, we describe a series of transmembrane peptides (TMs) to target the oligomerization motif of the AcrB component of the AcrAB-TolC MDR efflux pump from Escherichia coli. These peptides contain an N-terminal acetyl-A-(Sar)3 (sarcosine; N-methylglycine) tag and a C-terminal lysine tag-a design strategy our lab has utilized to improve the solubility and specificity of targeting for TMs previously. While these peptides have proven useful in preventing AcrB-mediated substrate efflux, the mechanisms by which these peptides associate with and penetrate the bacterial membrane remained unknown. In this study, we have shown peptide hydrophobic moment (μH)-the measure of concentrated hydrophobicity on one face of a lipopathic α-helix-drives bacterial membrane permeabilization and depolarization, likely through lateral-phase separation of negatively-charged POPG lipids and the disruption of lipid packing. Our results show peptide μH is an important consideration when designing membrane-active peptides and may be the determining factor in whether a TM will function in a permeabilizing or non-permeabilizing manner when embedded in the bacterial membrane.
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Affiliation(s)
- Tyler S Johnson
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Aleksandra A Bourdine
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Charles M Deber
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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5
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Polyansky AA, Efremov RG. On a mechanistic impact of transmembrane tetramerization in the pathological activation of RTKs. Comput Struct Biotechnol J 2023; 21:2837-2844. [PMID: 37216019 PMCID: PMC10192832 DOI: 10.1016/j.csbj.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Constitutive activation of receptor tyrosine kinases (RTKs) via different mutations has a strong impact on the development of severe human disorders, including cancer. Here we propose a putative activation scenario of RTKs, whereby transmembrane (TM) mutations can also promote higher-order oligomerization of the receptors that leads to the subsequent ligand-free activation. We illustrate this scenario using a computational modelling framework comprising sequence-based structure prediction and all-atom 1 µs molecular dynamics (MD) simulations in a lipid membrane for a previously characterised oncogenic TM mutation V536E in platelet-derived growth factor receptor alpha (PDGFRA). We show that in the course of MD simulations the mutant TM tetramer retains stable and compact configuration strengthened by tight protein-protein interactions, while the wild type TM tetramer demonstrates looser packing and a tendency to dissociate. Moreover, the mutation affects the characteristic motions of mutated TM helical segments by introducing additional non-covalent crosslinks in the middle of the TM tetramer, which operate as mechanical hinges. This leads to dynamic decoupling of the C-termini from the rigidified N-terminal parts and facilitates more pronounced possible displacement between the C-termini of the mutant TM helical regions that can provide more freedom for mutual rearrangement of the kinase domains located downstream. Our results for the V536E mutation in the context of PDGFRA TM tetramer allow for the possibility that the effect of oncogenic TM mutations can go beyond alternating the structure and dynamics of TM dimeric states and might also promote the formation of higher-order oligomers directly contributing to ligand-independent signalling effectuated by PDGFRA and other RTKs.
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Affiliation(s)
- Anton A. Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, A-1030 Vienna, Austria
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 20 Myasnitskaya St., Moscow 101000, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141701, Russia
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6
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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7
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Mitchell CJ, Johnson TS, Deber CM. Transmembrane peptide effects on bacterial membrane integrity and organization. Biophys J 2022; 121:3253-3262. [PMID: 35923102 PMCID: PMC9463641 DOI: 10.1016/j.bpj.2022.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/10/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022] Open
Abstract
As the bacterial multidrug resistance crisis continues, membrane-active antimicrobial peptides are being explored as an alternate treatment to conventional antibiotics. In contrast to antimicrobial peptides, which function by a nonspecific membrane disruption mechanism, here we describe a series of transmembrane (TM) peptides that are designed to act as drug efflux inhibitors by aligning with and out-competing a conserved TM4-TM4 homodimerization motif within bacterial small multidrug resistance proteins. The peptides contain two terminal tags: a C-terminal lysine tag to direct the peptides toward the negatively charged bacterial membrane, and an uncharged N-terminal sarcosine (N-methyl-glycine) tag to promote membrane insertion. While effective at inhibiting efflux activity, ostensibly through their designed mechanism of action, the impact of the peptides on the bacterial inner membrane remains undetermined. To evaluate the extant peptide-membrane interactions, we performed a series of biophysical measurements. Circular dichroism spectroscopy and Trp fluorescence showed that the peptides insert into the membrane generally in helical form. Interestingly, differential scanning calorimetry of the peptides added to bacterial-like membranes (POPE:POPG 3:1) revealed the peptides' ability to demix the POPE and POPG lipids, creating two pools, one of which is likely a peptide-POPG conglomerate, and the other a POPE-rich component where the native POPG content has been depleted. However, dye leakage assays confirmed that these events occur without causing significant membrane disruption both in vitro and in vivo, indicating that the peptides can target the small multidrug resistance TM4-TM4 motif without nonspecific membrane disruption. In related studies, DiOC2(3) fluorescence indicated moderate peptide-mediated reduction of the proton motive force for all peptides, including control peptides that did not display inhibitory activity. The overall findings suggest that peptides designed with suitable tags, sequence hydrophobicity, and charge distribution can be directed more generally to impact proteins whose function involves membrane-embedded protein-protein interactions.
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Affiliation(s)
- Chloe J Mitchell
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Tyler S Johnson
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Charles M Deber
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada.
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8
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Is It Possible to Find an Antimicrobial Peptide That Passes the Membrane Bilayer with Minimal Force Resistance? An Attempt at a Predictive Approach by Molecular Dynamics Simulation. Int J Mol Sci 2022; 23:ijms23115997. [PMID: 35682676 PMCID: PMC9180591 DOI: 10.3390/ijms23115997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022] Open
Abstract
There is still no answer to the mechanism of penetration of AMP peptides through the membrane bilayer. Several mechanisms for such a process have been proposed. It is necessary to understand whether it is possible, using the molecular dynamics method, to determine the ability of peptides of different compositions and lengths to pass through a membrane bilayer. To explain the passage of a peptide through a membrane bilayer, a method for preparing a membrane phospholipid bilayer was proposed, and 656 steered molecular dynamics calculations were carried out for pulling 7 amyloidogenic peptides with antimicrobial potential, and monopeptides (homo-repeats consisting of 10 residues of the same amino acid: Poly (Ala), Poly (Leu), Poly (Met), Poly (Arg), and Poly (Glu)) with various sequences through the membrane. Among the 15 studied peptides, the peptides exhibiting the least force resistance when passing through the bilayer were found, and the maximum reaction occurred at the boundary of the membrane bilayer entry. We found that the best correlation between the maximum membrane reaction force and the calculated parameters corresponds to the instability index (the correlation coefficient is above 0.9). One of the interesting results of this study is that the 10 residue amyloidogenic peptides and their extended peptides, with nine added residue cell-penetrating peptides and four residue linkers, both with established antimicrobial activity, have the same bilayer resistance force. All calculated data are summarized and posted on the server.
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9
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Marques-Pereira C, Pires MN, Gouveia RP, Pereira NN, Caniceiro AB, Rosário-Ferreira N, Moreira IS. SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. Int J Mol Sci 2022; 23:2986. [PMID: 35328409 PMCID: PMC8948900 DOI: 10.3390/ijms23062986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) is composed of four structural proteins and several accessory non-structural proteins. SARS-CoV-2's most abundant structural protein, Membrane (M) protein, has a pivotal role both during viral infection cycle and host interferon antagonism. This is a highly conserved viral protein, thus an interesting and suitable target for drug discovery. In this paper, we explain the structural nature of M protein homodimer. To do so, we developed and applied a detailed and robust in silico workflow to predict M protein dimeric structure, membrane orientation, and interface characterization. Single Nucleotide Polymorphisms (SNPs) in M protein were retrieved from over 1.2 M SARS-CoV-2 genomes and proteins from the Global Initiative on Sharing All Influenza Data (GISAID) database, 91 of which were located at the predicted dimer interface. Among those, we identified SNPs in Variants of Concern (VOC) and Variants of Interest (VOI). Binding free energy differences were evaluated for dimer interfacial SNPs to infer mutant protein stabilities. A few high-prevalent mutated residues were found to be especially relevant in VOC and VOI. This realization may be a game-changer to structure-driven formulation of new therapeutics for SARS-CoV-2.
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Affiliation(s)
- Catarina Marques-Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- IIIs—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Manuel N. Pires
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- Department of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Raquel P. Gouveia
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nádia N. Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Ana B. Caniceiro
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nícia Rosário-Ferreira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- CQC—Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-535 Coimbra, Portugal
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10
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Manipulating Macrophage/Microglia Polarization to Treat Glioblastoma or Multiple Sclerosis. Pharmaceutics 2022; 14:pharmaceutics14020344. [PMID: 35214076 PMCID: PMC8877500 DOI: 10.3390/pharmaceutics14020344] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/24/2022] Open
Abstract
Macrophages and microglia are implicated in several diseases with divergent roles in physiopathology. This discrepancy can be explained by their capacity to endorse different polarization states. Theoretical extremes of these states are called M1 and M2. M1 are pro-inflammatory, microbicidal, and cytotoxic whereas M2 are anti-inflammatory, immunoregulatory cells in favor of tumor progression. In pathological states, these polarizations are dysregulated, thus restoring phenotypes could be an interesting treatment approach against diseases. In this review, we will focus on compounds targeting macrophages and microglia polarization in two very distinctive pathologies: multiple sclerosis and glioblastoma. Multiple sclerosis is an inflammatory disease characterized by demyelination and axon degradation. In this case, macrophages and microglia endorse a M1-like phenotype inducing inflammation. Promoting the opposite M2-like polarization could be an interesting treatment strategy. Glioblastoma is a brain tumor in which macrophages and microglia facilitate tumor progression, spreading, and angiogenesis. They are part of the tumor associated macrophages displaying an anti-inflammatory phenotype, thereby inhibiting anti-tumoral immunity. Re-activating them could be a method to limit and reduce tumor progression. These two pathologies will be used to exemplify that targeting the polarization of macrophages and microglia is a promising approach with a broad spectrum of applications deserving more attention.
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11
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Jiang C, Wang X, Teng B, Wang Z, Li F, Zhao Y, Guo Y, Zeng Q. Peptide-Targeted High-Density Lipoprotein Nanoparticles for Combinatorial Treatment against Metastatic Breast Cancer. ACS APPLIED MATERIALS & INTERFACES 2021; 13:35248-35265. [PMID: 34284582 DOI: 10.1021/acsami.1c02074] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The sonic hedgehog (SHH) signaling pathway exhibits aberrant activation in triple-negative breast cancer (TNBC), wherein it regulates several malignant phenotypes related to tumor metastasis. GANT61, an inhibitor of the SHH signaling pathway, may offer promise when administered in combination with conventional chemotherapy to treat metastatic TNBC. However, poor bioavailability and substantial off-target toxicity limit its clinical application. To address these limitations, we designed a peptide-functionalized dual-targeting delivery system encapsulating paclitaxel and GANT61 in tLyP-1 peptide-modified reconstituted high-density lipoprotein nanoparticle (tLyP-1-rHDL-PTX/GANT61 NP) for metastatic TNBC treatment. The apolipoprotein A-1 and tLyP-1 peptide modified on the surface of nanoparticles enable the delivery system to target tumor cells by binding to the overexpressed scavenger receptor B type I and neuropilin-1 receptor. Moreover, the tLyP-1 peptide also enables the deep tumor penetration of nanoparticles further facilitating paclitaxel and GANT61 delivery. Increased cellular uptake of the nanoparticles was observed in both MDA-MB-231, BT-549 tumor cells, and their 3D tumor spheroids. A series of in vitro experiments reveal that GANT61 was able to suppress key metastasis-related tumor cell activities including angiogenesis, migration, invasion, and stemness. Owing to more effective drug administration, the metastasis suppression efficiency of GANT61 was significantly enhanced by the dual-targeting tLyP-1-rHDL delivery system. Meanwhile, the codelivery of paclitaxel and GANT61 by dual-targeting tLyP-1-rHDL nanoparticles demonstrated superior efficiency of disrupting proliferation and inducing apoptosis in tumor cells compared with drug solutions. In a spontaneous metastasis breast cancer NCG mice model, the tLyP-1-rHDL-PTX/GANT61 nanoparticles exhibited highly tumor-specific distribution and result in significant inhibition of the primary tumor growth and dramatic reduction of lung metastasis without obvious side effects. The present work suggests that a combination of the SHH signaling pathway suppression and chemotherapy assisted by peptide-functionalized targeting tLyP-1-rHDL nanoparticles may provide a promising strategy for metastatic TNBC treatment.
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Affiliation(s)
- Chuli Jiang
- Department of Vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xingyue Wang
- Chongqing Key Laboratory of Ultrasound Molecular Imaging, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Biyun Teng
- Department of Vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhe Wang
- Department of Vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Fenghe Li
- Department of Vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yu Zhao
- Department of Vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yuan Guo
- Chongqing Key Laboratory of Ultrasound Molecular Imaging, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Qiu Zeng
- Department of Vascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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12
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Silva TFD, Vila-Viçosa D, Machuqueiro M. Improved Protocol to Tackle the pH Effects on Membrane-Inserting Peptides. J Chem Theory Comput 2021; 17:3830-3840. [PMID: 34115492 DOI: 10.1021/acs.jctc.1c00020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Many important biological pathways rely on membrane-interacting peptides or proteins, which can alter the biophysical properties of the cell membrane by simply adsorbing to its surface to undergo a full insertion process. To study these phenomena with atomistic detail, model peptides have been used to refine the current computational methodologies. Improvements have been made with force-field parameters, enhanced sampling techniques to obtain faster sampling, and the addition of chemical-physical properties, such as pH, whose influence dramatically increases at the water/membrane interface. The pH (low) insertion peptide (pHLIP) is a peptide that inserts across a membrane bilayer depending on the pH due to the presence of a key residue (Asp14) whose acidity-induced protonation triggers the whole process. The complex nature of these peptide/membrane interactions resulted in sampling limitations of the protonation and configurational space albeit using state-of-the-art methods such as the constant-pH molecular dynamics. To address this issue and circumvent those limitations, new simulations were performed with our newly developed pH-replica exchange method using wild-type (wt)-pHLIP in different 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine membrane sizes. This technique provided enhanced sampling and allowed for the calculation of more complete Asp14 pKa profiles. The conformational heterogeneity derived from strong electrostatic interactions between Asp14 and the lipid phosphate groups was identified as the source of most pKa variability. In spite of these persistent and harder-to-equilibrate phosphate interactions, the pKa values at deeper regions (6.0-6.2) still predicted the experimental pK of insertion (6.0) since the electrostatic perturbation decays as the residue inserts further into the membrane. We also observed that reducing the system size leads to membrane deformations where it increasingly loses the ability to accommodate the pHLIP-induced perturbations. This indicates that large membrane patches, such as 256 or even 352 lipids, are needed to obtain stable and more realistic pHLIP/membrane systems. These results strengthen our method pKa predictive and analytical capabilities to study the intricate play of electrostatic effects of the peptide/membrane interface, granting confidence for future applications in similar systems.
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Affiliation(s)
- Tomás F D Silva
- Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal.,Kinetikos, Coimbra, Portugal
| | - Miguel Machuqueiro
- Departamento de Química e Bioquímica, Faculdade de Ciências, BioISI: Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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13
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Perez-Miller S, Patek M, Moutal A, de Haro PD, Cabel CR, Thorne CA, Campos SK, Khanna R. Novel Compounds Targeting Neuropilin Receptor 1 with Potential To Interfere with SARS-CoV-2 Virus Entry. ACS Chem Neurosci 2021; 12:1299-1312. [PMID: 33787218 PMCID: PMC8029449 DOI: 10.1021/acschemneuro.0c00619] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
Neuropilin-1 (NRP-1) is a multifunctional transmembrane receptor for ligands that affect developmental axonal growth and angiogenesis. In addition to a role in cancer, NRP-1 is a reported entry point for several viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19). The furin cleavage product of SARS-CoV-2 Spike protein takes advantage of the vascular endothelial growth factor A (VEGF-A) binding site on NRP-1 which accommodates a polybasic stretch ending in a C-terminal arginine. This site has long been a focus of drug discovery efforts for cancer therapeutics. We recently showed that interruption of the VEGF-A/NRP-1 signaling pathway ameliorates neuropathic pain and hypothesize that interference of this pathway by SARS-CoV-2 Spike protein interferes with pain signaling. Here, we report confirmed hits from a small molecule and natural product screen of nearly 0.5 million compounds targeting the VEGF-A binding site on NRP-1. We identified nine chemical series with lead- or drug-like physicochemical properties. Using ELISA, we demonstrate that six compounds disrupt VEGF-A-NRP-1 binding more effectively than EG00229, a known NRP-1 inhibitor. Secondary validation in cells revealed that all tested compounds inhibited VEGF-A triggered VEGFR2 phosphorylation. Further, two compounds displayed robust inhibition of a recombinant vesicular stomatitis virus protein that utilizes the SARS-CoV-2 Spike for entry and fusion. These compounds represent a first step in a renewed effort to develop small molecule inhibitors of the VEGF-A/NRP-1 signaling for the treatment of neuropathic pain and cancer with the added potential of inhibiting SARS-CoV-2 virus entry.
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Affiliation(s)
- Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Marcel Patek
- Bright Rock Path Consulting, LLC, Tucson, Arizona
| | - Aubin Moutal
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Paz Duran de Haro
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Carly R. Cabel
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
| | - Curtis A. Thorne
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
| | - Samuel K. Campos
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
- Department of Immunobiology, College of Medicine, University of Arizona
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona, USA
- Regulonix LLC, Tucson, AZ, USA
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14
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Albrecht C, Akissi ZLE, Yao-Kouassi PA, Alabdul Magid A, Maurice P, Duca L, Voutquenne-Nazabadioko L, Bennasroune A. Identification and Evaluation of New Potential Inhibitors of Human Neuraminidase 1 Extracted from Olyra latifolia L.: A Preliminary Study. Biomedicines 2021; 9:biomedicines9040411. [PMID: 33920466 PMCID: PMC8070403 DOI: 10.3390/biomedicines9040411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/02/2022] Open
Abstract
Sialidases, also called neuraminidases, are involved in several human pathologies such as neurodegenerative disorders, cancers, as well as infectious and cardiovascular diseases. Several studies have shown that neuraminidases, such as neuraminidase 1 (NEU-1), may be promising pharmacological targets. Therefore, the discovery of new selective inhibitors of NEU-1 are necessary to better understand the biological functions of this sialidase. In the present study, we describe the isolation and characterization of nine known compounds from Olyra latifolia L. leaves. This plant, known to have several therapeutic properties, belongs to the family of Poaceae and is found in the neotropics and in tropical Africa and Madagascar. Among the purified compounds, feddeiketone B, 2,3-dihydroxy-1-(4-hydroxy-3,5-diméthoxyphényl)-l-propanone, and syringylglycerol were shown to present structural analogy with DANA, and their effects on membrane NEU-1 sialidase activity were evaluated. Our results show that they possess inhibitory effects against NEU-1-mediated sialidase activity at the plasma membrane. In conclusion, we identified new natural bioactive molecules extracted from Olyra latifolia as inhibitors of human NEU-1 of strong interest to elucidate the biological functions of this sialidase and to target this protein involved in several pathophysiological contexts.
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Affiliation(s)
- Camille Albrecht
- UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (C.A.); (P.M.); (L.D.)
| | - Zachée Louis Evariste Akissi
- UMR 7312, Institut de Chimie Moléculaire de Reims (ICMR), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (Z.L.E.A.); (A.A.M.)
- Laboratoire de Constitution et Réaction de la Matière, UFR Sciences des Structures de la Matière et de Technologie, Université Félix Houphouët-Boigny, 22 BP 582 Abidjan, Cote D’Ivoire;
| | - Philomène Akoua Yao-Kouassi
- Laboratoire de Constitution et Réaction de la Matière, UFR Sciences des Structures de la Matière et de Technologie, Université Félix Houphouët-Boigny, 22 BP 582 Abidjan, Cote D’Ivoire;
| | - Abdulmagid Alabdul Magid
- UMR 7312, Institut de Chimie Moléculaire de Reims (ICMR), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (Z.L.E.A.); (A.A.M.)
| | - Pascal Maurice
- UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (C.A.); (P.M.); (L.D.)
| | - Laurent Duca
- UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (C.A.); (P.M.); (L.D.)
| | - Laurence Voutquenne-Nazabadioko
- UMR 7312, Institut de Chimie Moléculaire de Reims (ICMR), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (Z.L.E.A.); (A.A.M.)
- Correspondence: (L.V.-N.); (A.B.)
| | - Amar Bennasroune
- UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UFR Sciences Exactes et Naturelles, CNRS, Université de Reims Champagne-Ardenne, 51097 Reims, France; (C.A.); (P.M.); (L.D.)
- Correspondence: (L.V.-N.); (A.B.)
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15
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Cao S, Wang Y, Li J, Ling X, Zhang Y, Zhou Y, Zhong H. Prognostic Implication of the Expression Level of PECAM-1 in Non-small Cell Lung Cancer. Front Oncol 2021; 11:587744. [PMID: 33828969 PMCID: PMC8019905 DOI: 10.3389/fonc.2021.587744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/08/2021] [Indexed: 01/14/2023] Open
Abstract
Background: Lung cancer is a malignant disease that threatens human health. Hence, it is crucial to identify effective prognostic factors and treatment targets. Single-cell RNA sequencing can quantify the expression profiles of transcripts in individual cells. Methods: GSE117570 profiles were downloaded from the Gene Expression Omnibus database. Key ligand-receptor genes in the tumor and the normal groups were screened to identify integrated differentially expressed genes (DEGs) from the GSE118370 and The Cancer Genome Atlas Lung Adenocarcinoma databases. DEGs associated with more ligand-receptor pairs were selected as candidate DEGs for Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and survival analysis. In addition, we conducted validation immunohistochemical experiments on postoperative specimens of 30 patients with lung cancer. Results: A total of 18 candidate DEGs were identified from the tumor and the normal groups. The analysis of the GO biological process revealed that these DEGs were mainly enriched in wound healing, in response to wounding, cell migration, cell motility, and regulation of cell motility, while the KEGG pathway analysis found that these DEGs were mainly enriched in proteoglycans in cancer, bladder cancer, malaria, tyrosine kinase inhibitor resistance in Epidermal Growth Factor Receptor (EGFR), and the ERBB signaling pathway. Survival analysis showed that a high, rather than a low, expression of platelet endothelial cell adhesion molecule-1 (PECAM-1) was associated with improved survival. Similarly, in postoperative patients with lung cancer, we found that the overall survival of the PECAM-1 high-expression group shows a better trend than the PECAM-1 low-expression group (p = 0.172). Conclusions: The candidate DEGs identified in this study may play some important roles in the occurrence and development of lung cancer, especially PECAM-1, which may present potential prognostic biomarkers for the outcome.
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Affiliation(s)
| | | | | | | | | | - Yan Zhou
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Hua Zhong
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
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16
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Albrecht C, Kuznetsov AS, Appert-Collin A, Dhaideh Z, Callewaert M, Bershatsky YV, Urban AS, Bocharov EV, Bagnard D, Baud S, Blaise S, Romier-Crouzet B, Efremov RG, Dauchez M, Duca L, Gueroult M, Maurice P, Bennasroune A. Transmembrane Peptides as a New Strategy to Inhibit Neuraminidase-1 Activation. Front Cell Dev Biol 2020; 8:611121. [PMID: 33392200 PMCID: PMC7772355 DOI: 10.3389/fcell.2020.611121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/27/2020] [Indexed: 12/31/2022] Open
Abstract
Sialidases, or neuraminidases, are involved in several human disorders such as neurodegenerative, infectious and cardiovascular diseases, and cancers. Accumulative data have shown that inhibition of neuraminidases, such as NEU1 sialidase, may be a promising pharmacological target, and selective inhibitors of NEU1 are therefore needed to better understand the biological functions of this sialidase. In the present study, we designed interfering peptides (IntPep) that target a transmembrane dimerization interface previously identified in human NEU1 that controls its membrane dimerization and sialidase activity. Two complementary strategies were used to deliver the IntPep into cells, either flanked to a TAT sequence or non-tagged for solubilization in detergent micelles. Combined with molecular dynamics simulations and heteronuclear nuclear magnetic resonance (NMR) studies in membrane-mimicking environments, our results show that these IntPep are able to interact with the dimerization interface of human NEU1, to disrupt membrane NEU1 dimerization and to strongly decrease its sialidase activity at the plasma membrane. In conclusion, we report here new selective inhibitors of human NEU1 of strong interest to elucidate the biological functions of this sialidase.
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Affiliation(s)
- Camille Albrecht
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Higher School of Economics, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Aline Appert-Collin
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Zineb Dhaideh
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Maïté Callewaert
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7312, Institut de Chimie Moléculaire de Reims, Reims, France
| | - Yaroslav V Bershatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Anatoly S Urban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Dominique Bagnard
- Université de Strasbourg, Strasbourg, France.,INSERM U1119 Biopathologie de la Myéline, Neuroprotection et Stratégies Thérapeutiques, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Sébastien Blaise
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Béatrice Romier-Crouzet
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Higher School of Economics, Moscow, Russia.,Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
| | - Manuel Dauchez
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France.,Plateau de Modélisation Moléculaire Multi-échelle, Reims, France
| | - Laurent Duca
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Marc Gueroult
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Pascal Maurice
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
| | - Amar Bennasroune
- Université de Reims Champagne-Ardenne, Reims, France.,CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims, France
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17
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Perez-Miller S, Patek M, Moutal A, Cabel CR, Thorne CA, Campos SK, Khanna R. In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.22.308783. [PMID: 32995772 PMCID: PMC7523098 DOI: 10.1101/2020.09.22.308783] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Neuropilin-1 (NRP-1) is a multifunctional transmembrane receptor for ligands that affect developmental axonal growth and angiogenesis. In addition to a role in cancer, NRP-1 is a reported entry point for several viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19). The furin cleavage product of SARS-CoV-2 Spike protein takes advantage of the vascular endothelial growth factor A (VEGF-A) binding site on NRP-1 which accommodates a polybasic stretch ending in a C-terminal arginine. This site has long been a focus of drug discovery efforts for cancer therapeutics. We recently showed that interruption of the VEGF-A/NRP-1 signaling pathway ameliorates neuropathic pain and hypothesize that interference of this pathway by SARS-CoV-2 spike protein interferes with pain signaling. Here, we report hits from a small molecule and natural product screen of nearly 0.5 million compounds targeting the VEGF-A binding site on NRP-1. We identified nine chemical series with lead- or drug-like physico-chemical properties. Using an ELISA, we demonstrate that six compounds disrupt VEGF-A-NRP-1 binding more effectively than EG00229, a known NRP-1 inhibitor. Secondary validation in cells revealed that almost all tested compounds inhibited VEGF-A triggered VEGFR2 phosphorylation. Two compounds displayed robust inhibition of a recombinant vesicular stomatitis virus protein that utilizes the SARS-CoV-2 Spike for entry and fusion. These compounds represent a first step in a renewed effort to develop small molecule inhibitors of the VEGF-A/NRP-1 signaling for the treatment of neuropathic pain and cancer with the added potential of inhibiting SARS-CoV-2 virus entry.
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Affiliation(s)
- Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona 85724, USA
| | - Marcel Patek
- Bright Rock Path Consulting, LLC, Tucson, Arizona
| | - Aubin Moutal
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Carly R. Cabel
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
| | - Curtis A. Thorne
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
| | - Samuel K. Campos
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
- Department of Immunobiology, College of Medicine, University of Arizona
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona 85724, USA
- Regulonix LLC, 1555 E. Entrada Segunda, Tucson, AZ 85718, USA
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18
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Lazim R, Suh D, Choi S. Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems. Int J Mol Sci 2020; 21:E6339. [PMID: 32882859 PMCID: PMC7504087 DOI: 10.3390/ijms21176339] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.
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Affiliation(s)
- Raudah Lazim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Donghyuk Suh
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
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