151
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Sebastian J, Raghav D, Rathinasamy K. MD simulation-based screening approach identified tolvaptan as a potential inhibitor of Eg5. Mol Divers 2022:10.1007/s11030-022-10482-w. [DOI: 10.1007/s11030-022-10482-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
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152
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Augustynek B, Gyimesi G, Dernič J, Sallinger M, Albano G, Klesse GJ, Kandasamy P, Grabmayr H, Frischauf I, Fuster DG, Peinelt C, Hediger MA, Bhardwaj R. Discovery of novel gating checkpoints in the Orai1 calcium channel by systematic analysis of constitutively active mutants of its paralogs and orthologs. Cell Calcium 2022; 105:102616. [PMID: 35792401 DOI: 10.1016/j.ceca.2022.102616] [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: 05/05/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/24/2022]
Abstract
In humans, there are three paralogs of the Orai Ca2+ channel that form the core of the store-operated calcium entry (SOCE) machinery. While the STIM-mediated gating mechanism of Orai channels is still under active investigation, several artificial and natural variants are known to cause constitutive activity of the human Orai1 channel. Surprisingly, little is known about the conservation of the gating checkpoints among the different human Orai paralogs and orthologs in other species. In our work, we show that the mutation corresponding to the activating mutation H134A in transmembrane helix 2 (TM2) of human Orai1 also activates Orai2 and Orai3, likely via a similar mechanism. However, this cross-paralog conservation does not apply to the "ANSGA" nexus mutations in TM4 of human Orai1, which is reported to mimic the STIM1-activated state of the channel. In investigating the mechanistic background of these differences, we identified two positions, H171 and F246 in human Orai1, that are not conserved among paralogs and that seem to be crucial for the channel activation triggered by the "ANSGA" mutations in Orai1. However, mutations of the same residues still allow gating of Orai1 by STIM1, suggesting that the ANSGA mutant of Orai1 may not be a surrogate for the STIM1-activated state of the Orai1 channel. Our results shed new light on these important gating checkpoints and show that the gating mechanism of Orai channels is affected by multiple factors that are not necessarily conserved among orai homologs, such as the TM4-TM3 coupling.
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Affiliation(s)
- Bartłomiej Augustynek
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Gergely Gyimesi
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Jan Dernič
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Matthias Sallinger
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Giuseppe Albano
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Gabriel J Klesse
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Palanivel Kandasamy
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Herwig Grabmayr
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Irene Frischauf
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, A-4020 Linz, Austria
| | - Daniel G Fuster
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Christine Peinelt
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Matthias A Hediger
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland.
| | - Rajesh Bhardwaj
- Membrane Transport Discovery Lab, Department of Nephrology and Hypertension and Department of Biomedical Research, Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland; Current address: Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, 111 TW Alexander Drive, NC 27709, USA.
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153
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Pitsillou E, Liang J, Hung A, Karagiannis TC. The SARS-CoV-2 helicase as a target for antiviral therapy: Identification of potential small molecule inhibitors by in silico modelling. J Mol Graph Model 2022; 114:108193. [PMID: 35462185 PMCID: PMC9014761 DOI: 10.1016/j.jmgm.2022.108193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/18/2022]
Abstract
Although vaccines that provide protection against severe illness from coronavirus disease (COVID-19) have been made available, emerging variant strains of severe acute respiratory syndrome 2 coronavirus 2 (SARS-CoV-2) are of concern. A different research direction involves investigation of antiviral therapeutics. In addition to structural proteins, the SARS-CoV-2 non-structural proteins are of interest and this includes the helicase (nsp13). In this study, an initial screen of 300 ligands was performed to identify potential inhibitors of the SARS-CoV-2 nsp13 examining the nucleoside triphosphatase site (NTPase activity) as the target region. The antiviral activity of polyphenols has been previously reported in the literature and as a result, the phenolic compounds and fatty acids from the OliveNet™ library were utilised. Synthetic compounds with antimicrobial and anti-inflammatory properties were also selected. The structures of the SARS-CoV and MERS-CoV helicases, as well as the human RECQ-like DNA helicase, DHX9 helicase, PcrA helicase, hepatitis C NS3 helicase, and mouse Dna2 nuclease-helicase were used for comparison. As expected, sequence and structural homology between the various species was evident. A number of broad-spectrum and well-known inhibitors interacted with the NTPase active site highlighting the need to potentially identify more specific inhibitors for SARS-CoV-2. Acetylcysteine, clavulanic acid and homovanillic acid were identified as potential lead compounds for the SARS-CoV-2 helicase. Molecular dynamics simulations were performed with the leads bound to the SARS-CoV-2 helicase for 200 ns in triplicate, with favourable binding free energies to the NTPase site. Given their availability, further exploration of their potential inhibitory activity could be considered.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3052, Australia.
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154
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Gallardo A, Bogart BM, Dutagaci B. Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:3079-3089. [PMID: 35686985 DOI: 10.1021/acs.jcim.2c00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA polymerase II (Pol II) forms a complex with elongation factors to proceed to the elongation stage of the transcription process. In this work, we studied the elongation factor SPT5 and explored the protein-nucleic acid interactions for the isolated systems of KOW1 and KOW4 domains of SPT5 with DNA and RNA, respectively. We performed molecular dynamics (MD) simulations using three commonly used force fields that are CHARMM c36m, AMBER ff14sb, and ff19sb. Simulations showed strong protein-nucleic acid interactions and low electrostatic binding free energies for all force fields used. RNA was found to be highly dynamic with all force fields, while DNA had relatively more stable conformations with the AMBER force fields compared to that with CHARMM. Furthermore, we performed MD simulations of the complete elongation complex using CHARMM c36m and AMBER ff19sb force fields to compare the dynamics and interactions with the isolated systems. Similarly, strong KOW1 and DNA interactions were observed in the complete elongation complex simulations and DNA was further stabilized by a network of interactions involving SPT5-KOW1, SPT4, and rpb2 of Pol II. Overall, our study showed that the differences between CHARMM and AMBER force fields strongly affect the dynamics of the nucleic acids. CHARMM provides highly flexible DNA, while AMBER largely stabilizes the DNA structure. Although the presence of the entire interaction network stabilized the DNA and decreased the differences in the results from the two force fields, the discrepancies of the force fields for smaller systems may reflect their problems in generating accurate dynamics of nucleic acids.
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Affiliation(s)
- Adan Gallardo
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
| | - Brandon M Bogart
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
| | - Bercem Dutagaci
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
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155
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Park S, Seok C. GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. J Chem Inf Model 2022; 62:3157-3168. [PMID: 35749367 DOI: 10.1021/acs.jcim.2c00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins interact with numerous water molecules to perform their physiological functions in biological organisms. Most water molecules act as solvent media; hence, their roles may be considered implicitly in theoretical treatments of protein structure and function. However, some water molecules interact intimately with proteins and require explicit treatment to understand their effects. Most physics-based computational methods are limited in their ability to accurately locate water molecules on protein surfaces because of inaccurate energy functions. Instead of relying on an energy function, this study attempts to learn the locations of water molecules from structural data. GalaxyWater-convolutional neural network (CNN) predicts water positions on protein chains, protein-protein interfaces, and protein-compound binding sites using a 3D-CNN model that is trained to generate a water score map on a given protein structure. The training data are compiled from high-resolution protein crystal structures resolved together with water molecules. GalaxyWater-CNN shows improved water prediction performance both in the coverage of crystal water molecules and in the accuracy of the predicted water positions when compared with previous energy-based methods. This method shows a superior performance in predicting water molecules that form hydrogen-bond networks precisely. The web service and the source code of this water prediction method are freely available at https://galaxy.seoklab.org/gwcnn and https://github.com/seoklab/GalaxyWater-CNN, respectively.
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Affiliation(s)
- Sangwoo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.,Galux Inc., Gwanak-gu, Seoul 08738, Republic of Korea
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156
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Hurwitz N, Zaidman D, Wolfson HJ. Pep–Whisperer: Inhibitory peptide design. Proteins 2022; 90:1886-1895. [DOI: 10.1002/prot.26384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Naama Hurwitz
- Blavatnik School of Computer Science Tel Aviv University Tel Aviv Israel
| | - Daniel Zaidman
- Department of Organic Chemistry Weizmann Institute of Science Rehovot Israel
| | - Haim J. Wolfson
- Blavatnik School of Computer Science Tel Aviv University Tel Aviv Israel
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157
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Biswas H, Zhao SJ, Makinwa Y, Bassett JS, Musich PR, Liu JY, Zou Y. Prolyl Isomerization-Mediated Conformational Changes Define ATR Subcellular Compartment-Specific Functions. Front Cell Dev Biol 2022; 10:826576. [PMID: 35721505 PMCID: PMC9204103 DOI: 10.3389/fcell.2022.826576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
ATR is a PI3K-like kinase protein, regulating checkpoint responses to DNA damage and replication stress. Apart from its checkpoint function in the nucleus, ATR actively engages in an antiapoptotic role at mitochondria following DNA damage. The different functions of ATR in the nucleus and cytoplasm are carried out by two prolyl isomeric forms of ATR: trans- and cis-ATR, respectively. The isomerization occurs at the Pin1 Ser428-Pro429 motif of ATR. Here, we investigated the structural basis of the subcellular location-specific functions of human ATR. Using a mass spectrometry-based footprinting approach, the surface accessibility of ATR lysine residues to sulfo-NHS-LC-biotin modification was monitored and compared between the cis- and the trans-isomers. We have identified two biotin-modified lysine residues, K459 and K469, within the BH3-like domain of cis-ATR that were not accessible in trans-ATR, indicating a conformational change around the BH3 domain between cis- and trans-ATR. The conformational alteration also involved the N-terminal domain and the middle HEAT domain. Moreover, experimental results from an array of complementary assays show that cis-ATR with the accessible BH3 domain was able to bind to tBid while trans-ATR could not. In addition, both cis- and trans-ATR can directly form homodimers via their C-terminal domains without ATRIP, while nuclear (trans-ATR) in the presence of ATRIP forms dimer-dimer complexes involving both N- and C-termini of ATR and ATRIP after UV. Structural characteristics around the Ser428-Pro429 motif and the BH3 domain region are also analyzed by molecular modeling and dynamics simulation. In support, cis conformation was found to be significantly more energetically favorable than trans at the Ser428-Pro429 bond in a 20-aa wild-type ATR peptide. Taken together, our results suggest that the isomerization-induced structural changes of ATR define both its subcellular location and compartment-specific functions and play an essential role in promoting cell survival and DNA damage responses.
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Affiliation(s)
- Himadri Biswas
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Shu-Jun Zhao
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH, United States
| | - Yetunde Makinwa
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - James S. Bassett
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Phillip R. Musich
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Jing-Yuan Liu
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
- Department of Bioengineering, University of Toledo College of Engineering, Toledo, OH, United States
| | - Yue Zou
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
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158
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Romero-Molina S, Ruiz-Blanco YB, Mieres-Perez J, Harms M, Münch J, Ehrmann M, Sanchez-Garcia E. PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity. J Proteome Res 2022; 21:1829-1841. [PMID: 35654412 PMCID: PMC9361347 DOI: 10.1021/acs.jproteome.2c00020] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Virtual screening
of protein–protein and protein–peptide
interactions is a challenging task that directly impacts the processes
of hit identification and hit-to-lead optimization in drug design
projects involving peptide-based pharmaceuticals. Although several
screening tools designed to predict the binding affinity of protein–protein
complexes have been proposed, methods specifically developed to predict
protein–peptide binding affinity are comparatively scarce.
Frequently, predictors trained to score the affinity of small molecules
are used for peptides indistinctively, despite the larger complexity
and heterogeneity of interactions rendered by peptide binders. To
address this issue, we introduce PPI-Affinity, a tool that leverages
support vector machine (SVM) predictors of binding affinity to screen
datasets of protein–protein and protein–peptide complexes,
as well as to generate and rank mutants of a given structure. The
performance of the SVM models was assessed on four benchmark datasets,
which include protein–protein and protein–peptide binding
affinity data. In addition, we evaluated our model on a set of mutants
of EPI-X4, an endogenous peptide inhibitor of the chemokine receptor
CXCR4, and on complexes of the serine proteases HTRA1 and HTRA3 with
peptides. PPI-Affinity is freely accessible at https://protdcal.zmb.uni-due.de/PPIAffinity.
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Affiliation(s)
- Sandra Romero-Molina
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Michael Ehrmann
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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159
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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160
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Rajendran M, Ferran MC, Babbitt GA. Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics. BIOPHYSICAL REPORTS 2022; 2:100056. [PMID: 35403093 PMCID: PMC8978532 DOI: 10.1016/j.bpr.2022.100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 01/08/2023]
Abstract
The identification of viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a molecular dynamics (MD)-based approach that goes beyond contact mapping, scales well to a desktop computer with a modern graphics processor, and enables the user to identify functional protein sites that are prone to vaccine escape in a viral antigen. We first implement our MD pipeline to employ site-wise calculation of Kullback-Leibler divergence in atom fluctuation over replicate sets of short-term MD production runs thus enabling a statistical comparison of the rapid motion of influenza hemagglutinin (HA) in both the presence and absence of three well-known neutralizing antibodies. Using this simple comparative method applied to motions of viral proteins, we successfully identified in silico all previously empirically confirmed sites of escape in influenza HA, predetermined via selection experiments and neutralization assays. Upon the validation of our computational approach, we then surveyed potential hotspot residues in the receptor binding domain of the SARS-CoV-2 virus in the presence of COVOX-222 and S2H97 antibodies. We identified many single sites in the antigen-antibody interface that are similarly prone to potential antibody escape and that match many of the known sites of mutations arising in the SARS-CoV-2 variants of concern. In the Omicron variant, we find only minimal adaptive evolutionary shifts in the functional binding profiles of both antibodies. In summary, we provide an inexpensive and accurate computational method to monitor hotspots of functional evolution in antibody binding footprints.
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161
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Frampton DJA, Choudhury K, Nikesjö J, Delemotte L, Liin SI. Subtype-specific responses of hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids reveal an unconventional modulatory site and mechanism. eLife 2022; 11:77672. [PMID: 35642964 PMCID: PMC9159753 DOI: 10.7554/elife.77672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
The KV7.4 and KV7.5 subtypes of voltage-gated potassium channels play a role in important physiological processes such as sound amplification in the cochlea and adjusting vascular smooth muscle tone. Therefore, the mechanisms that regulate KV7.4 and KV7.5 channel function are of interest. Here, we study the effect of polyunsaturated fatty acids (PUFAs) on human KV7.4 and KV7.5 channels expressed in Xenopus oocytes. We report that PUFAs facilitate activation of hKV7.5 by shifting the V50 of the conductance versus voltage (G(V)) curve toward more negative voltages. This response depends on the head group charge, as an uncharged PUFA analogue has no effect and a positively charged PUFA analogue induces positive V50 shifts. In contrast, PUFAs inhibit activation of hKV7.4 by shifting V50 toward more positive voltages. No effect on V50 of hKV7.4 is observed by an uncharged or a positively charged PUFA analogue. Thus, the hKV7.5 channel's response to PUFAs is analogous to the one previously observed in hKV7.1-7.3 channels, whereas the hKV7.4 channel response is opposite, revealing subtype-specific responses to PUFAs. We identify a unique inner PUFA interaction site in the voltage-sensing domain of hKV7.4 underlying the PUFA response, revealing an unconventional mechanism of modulation of hKV7.4 by PUFAs.
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Affiliation(s)
- Damon J A Frampton
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Koushik Choudhury
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Johan Nikesjö
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Sara I Liin
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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162
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Hulce KR, Jaishankar P, Lee GM, Bohn MF, Connelly EJ, Wucherer K, Ongpipattanakul C, Volk RF, Chuo SW, Arkin MR, Renslo AR, Craik CS. Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine. Cell Chem Biol 2022; 29:785-798.e19. [PMID: 35364007 PMCID: PMC9133232 DOI: 10.1016/j.chembiol.2022.03.007] [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: 07/07/2021] [Revised: 01/07/2022] [Accepted: 03/10/2022] [Indexed: 11/03/2022]
Abstract
Viruses are responsible for some of the most deadly human diseases, yet available vaccines and antivirals address only a fraction of the potential viral human pathogens. Here, we provide a methodology for managing human herpesvirus (HHV) infection by covalently inactivating the HHV maturational protease via a conserved, non-catalytic cysteine (C161). Using human cytomegalovirus protease (HCMV Pr) as a model, we screened a library of disulfides to identify molecules that tether to C161 and inhibit proteolysis, then elaborated hits into irreversible HCMV Pr inhibitors that exhibit broad-spectrum inhibition of other HHV Pr homologs. We further developed an optimized tool compound targeted toward HCMV Pr and used an integrative structural biology and biochemical approach to demonstrate inhibitor stabilization of HCMV Pr homodimerization, exploiting a conformational equilibrium to block proteolysis. Irreversible HCMV Pr inhibition disrupts HCMV infectivity in cells, providing proof of principle for targeting proteolysis via a non-catalytic cysteine to manage viral infection.
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Affiliation(s)
- Kaitlin R Hulce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Emily J Connelly
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Kristin Wucherer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Chayanid Ongpipattanakul
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Regan F Volk
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Shih-Wei Chuo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA.
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163
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Kim S, Chung J, Arlt H, Pak AJ, Farese RV, Walther TC, Voth GA. Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane. eLife 2022; 11:75808. [PMID: 35583926 PMCID: PMC9122495 DOI: 10.7554/elife.75808] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Lipid droplets (LDs) are organelles formed in the endoplasmic reticulum (ER) to store triacylglycerol (TG) and sterol esters. The ER protein seipin is key for LD biogenesis. Seipin forms a cage-like structure, with each seipin monomer containing a conserved hydrophobic helix and two transmembrane (TM) segments. How the different parts of seipin function in TG nucleation and LD budding is poorly understood. Here, we utilized molecular dynamics simulations of human seipin, along with cell-based experiments, to study seipin’s functions in protein–lipid interactions, lipid diffusion, and LD maturation. An all-atom simulation indicates that seipin TM segment residues and hydrophobic helices residues located in the phospholipid tail region of the bilayer attract TG. Simulating larger, growing LDs with coarse-grained models, we find that the seipin TM segments form a constricted neck structure to facilitate conversion of a flat oil lens into a budding LD. Using cell experiments and simulations, we also show that conserved, positively charged residues at the end of seipin’s TM segments affect LD maturation. We propose a model in which seipin TM segments critically function in TG nucleation and LD growth.
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Affiliation(s)
- Siyoung Kim
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, United States
| | - Jeeyun Chung
- Department of Molecular Metabolism, Harvard T H Chan School of Public Health, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Henning Arlt
- Department of Molecular Metabolism, Harvard T H Chan School of Public Health, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard T H Chan School of Public Health, Boston, United States
| | - Alexander J Pak
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, United States
| | - Robert V Farese
- Department of Molecular Metabolism, Harvard T H Chan School of Public Health, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Tobias C Walther
- Department of Molecular Metabolism, Harvard T H Chan School of Public Health, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard T H Chan School of Public Health, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
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164
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Wang YP, Wang YD, Liu YP, Cao JX, Yang ML, Wang YF, Khan A, Zhao TR, Cheng GG. 6'- O-Caffeoylarbutin from Que Zui tea ameliorates acetaminophen-induced liver injury via enhancing antioxidant ability and regulating the PI3K signaling pathway. Food Funct 2022; 13:5299-5316. [PMID: 35441652 DOI: 10.1039/d2fo00507g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Que Zui tea (QT), a traditional herbal tea in China, has a significant hepatoprotective effect. 6'-O-Caffeoylarbutin (CA) is the most abundant chemical compound in the QT. However, the hepatoprotective effect of CA has not been investigated. This study is aimed to evaluate the protective effect of CA on acetaminophen (APAP) induced hepatotoxicity in vivo and in vitro and its possible underlying mechanism. In APAP-induced HepG-2 cells, CA inhibited intracellular ROS accumulation and cell apoptosis, and improved the expression of antioxidants including SOD, CAT and GSH. In APAP-administrated mice, CA pretreatment remarkably ameliorated the histopathological damage and inflammatory response, and antioxidant enzyme activity in the serum and liver tissues. Moreover, the immunohistochemistry and immunofluorescence assay results revealed that the CA markedly reduced ROS production and apoptosis, and activated antioxidant transcription factor Nrf2 in the liver. Meanwhile, molecular docking results showed that the strong binding force of CA and PI3K was due to the higher number of hydrogen- and π-bonds with active site residues. Notably, CA pretreatment significantly regulated the expression of PI3K, Akt, Nrf2, NQO1, HO-1, Bcl-2, Bax, caspase-3, and caspase-9 proteins in APAP-treated liver tissues. These data demonstrated that CA had a protective effect against APAP-induced hepatotoxicity via regulating the PI3K/Akt and Nrf2 signaling pathway.
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Affiliation(s)
- Yong-Peng Wang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yu-Dan Wang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China. .,National and Local Joint Engineering Research Center for Green Preparation Technology of Biobased Materials, Yunnan Minzu University, Kunming, 650500, China
| | - Ya-Ping Liu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Jian-Xin Cao
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Mei-Lian Yang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yi-Fen Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Afsar Khan
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Tian-Rui Zhao
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Gui-Guang Cheng
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
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165
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Dlamini Z, Skepu A, Kim N, Mkhabele M, Khanyile R, Molefi T, Mbatha S, Setlai B, Mulaudzi T, Mabongo M, Bida M, Kgoebane-Maseko M, Mathabe K, Lockhat Z, Kgokolo M, Chauke-Malinga N, Ramagaga S, Hull R. AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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166
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Kumari R, Rathi R, Pathak SR, Dalal V. Structural-based virtual screening and identification of novel potent antimicrobial compounds against YsxC of Staphylococcus aureus. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132476] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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167
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García-Cebollada H, López A, Sancho J. Protposer: the web server that readily proposes protein stabilizing mutations with high PPV. Comput Struct Biotechnol J 2022; 20:2415-2433. [PMID: 35664235 PMCID: PMC9133766 DOI: 10.1016/j.csbj.2022.05.008] [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: 03/16/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mutations. Unfortunately, even the best currently used predictors fail to compute the stability of protein variants with sufficient accuracy and their usefulness as tools to guide the rational stabilisation of proteins is limited. We present here Protposer, a protein stabilising tool based on a different approach. Instead of quantifying changes in stability, Protposer uses structure- and sequence-based screening modules to nominate candidate mutations for subsequent evaluation by a logistic regression model, carefully trained to avoid overfitting. Thus, Protposer analyses PDB files in search for stabilization opportunities and provides a ranked list of promising mutations with their estimated success rates (eSR), their probabilities of being stabilising by at least 0.5 kcal/mol. The agreement between eSRs and actual positive predictive values (PPV) on external datasets of mutations is excellent. When Protposer is used with its Optimal kappa selection threshold, its PPV is above 0.7. Even with less stringent thresholds, Protposer largely outperforms FoldX, Rosetta and PoPMusiC. Indicating the PDB file of the protein suffices to obtain a ranked list of mutations, their eSRs and hints on the likely source of the stabilization expected. Protposer is a distinct, straightforward and highly successful tool to design protein stabilising mutations, and it is freely available for academic use at http://webapps.bifi.es/the-protposer.
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168
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Yu J, Li X, Huang J, Yu M, Wu Z, Cao S. Molecular dynamics simulation of α‐gliadin in ethanol/aqueous organic solvents. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie‐Ting Yu
- School of Food Science and Engineering Foshan University Foshan528000China
- Guangdong Key Laboratory of Food Intelligent Manufacturing Foshan University Foshan528000China
| | - Xin‐Yao Li
- School of Food Science and Engineering Foshan University Foshan528000China
- Guangdong Key Laboratory of Food Intelligent Manufacturing Foshan University Foshan528000China
| | - Jia‐Hui Huang
- School of Food College South China Agricultural University Guangzhou510642China
| | - Ming‐Yi Yu
- School of Food Science and Engineering Foshan University Foshan528000China
| | - Zi‐Yi Wu
- School of Food College South China Agricultural University Guangzhou510642China
| | - Shi‐Lin Cao
- School of Food Science and Engineering Foshan University Foshan528000China
- Guangdong Key Laboratory of Food Intelligent Manufacturing Foshan University Foshan528000China
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169
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Papakyriakou A, Mpakali A, Stratikos E. Can ERAP1 and ERAP2 Form Functional Heterodimers? A Structural Dynamics Investigation. Front Immunol 2022; 13:863529. [PMID: 35514997 PMCID: PMC9065437 DOI: 10.3389/fimmu.2022.863529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) play important roles in the generation of antigenic peptides presented by Major Histocompatibility Class I (MHCI) molecules and indirectly regulate adaptive immune responses. Although the discrete function of these enzymes has been extensively characterized, recent reports have suggested that they can also form heterodimers with functional consequences. However, lack of structural characterization of a putative ERAP1/ERAP2 dimer has limited our understanding of its biological role and significance. To address this, we employed computational molecular dynamics calculations to explore the topology of interactions between these two, based on experimentally determined homo-dimerization interfaces observed in crystal structures of ERAP2 or homologous enzymes. Our analysis of 8 possible dimerization models, suggested that the most likely ERAP1/ERAP2 heterodimerization topology involves the exon 10 loop, a non-conserved loop previously implicated in interactions between ERAP1 and the disulfide-bond shuffling chaperone ERp44. This dimerization topology allows access to the active site of both enzymes and is consistent with a previously reported construct in which ERAP1 and ERAP2 were linked by Fos/Jun zipper tags. The proposed model constitutes a tentative structural template to help understand the physiological role and significance of ERAP1/ERAP2 molecular interactions.
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Affiliation(s)
- Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Anastasia Mpakali
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Efstratios Stratikos
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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170
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Mehmood A, Pan F, Ai X, Tang X, Cai S, Soliman MM, Albogami S, Usman M, Murtaza MA, Nie Y, Zhao L. Novel angiotensin-converting enzyme (ACE) inhibitory mechanism of peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2). J Food Biochem 2022; 46:e14168. [PMID: 35393673 DOI: 10.1111/jfbc.14168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 01/10/2023]
Abstract
This work aimed to identify novel angiotensin-converting-enzyme (ACE) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2). The MiAMP2 protein was hydrolyzed through in silico digestion, and the generated peptides were screened for ACE inhibitory activity. The in silico enzyme digestion results revealed that 18 unreported peptides were obtained using AHTPDB and BIOPEP-UWM, and none were thought to be toxic based on absorption, distribution, metabolism, and excretion (ADMET) prediction. PGPR, RPLY, MNPQR, and AAPR were predicted to exhibit good biological activity. The molecular docking results revealed that the four peptides tightly bound to the active pocket of ACE via hydrogen bonds and hydrophobic interactions, among which RPLY and MNPQR bound to ACE more strongly. The in vitro assay results confirmed that RPLY and MNPQR peptides inhibited ACE via competitive manner. These results provide theoretical guidance for the development of novel foodborne antihypertensive peptides from Macadamia nut proteins. PRACTICAL APPLICATIONS: This study provides new insight on the inhibitory potential of Macadamia nut peptides against ACE, which may be further applied to the development of antihypertensive peptides in the medical industry.
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Affiliation(s)
- Arshad Mehmood
- Yunnan Forestry and Grassland Technology Extension Center, Kunming City, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Fei Pan
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Xin Ai
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Xiaoning Tang
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming, China
| | - Shengbao Cai
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Mohamed Mohamed Soliman
- Clinical Laboratory Sciences Department, Turabah University College, Taif University, Taif, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Muhammad Usman
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China.,Department of Food Science and Technology, Riphah International University Faisalabad, Punjab, Pakistan
| | - Mian Anjum Murtaza
- Institute of Food Science and Nutrition, University of Sargodha, Sargodha, Pakistan
| | - Yanli Nie
- Yunnan Forestry and Grassland Technology Extension Center, Kunming City, China
| | - Lei Zhao
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
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171
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Brinkmann V, Romeo M, Larigot L, Hemmers A, Tschage L, Kleinjohann J, Schiavi A, Steinwachs S, Esser C, Menzel R, Giani Tagliabue S, Bonati L, Cox F, Ale-Agha N, Jakobs P, Altschmied J, Haendeler J, Coumoul X, Ventura N. Aryl Hydrocarbon Receptor-Dependent and -Independent Pathways Mediate Curcumin Anti-Aging Effects. Antioxidants (Basel) 2022; 11:613. [PMID: 35453298 PMCID: PMC9024831 DOI: 10.3390/antiox11040613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 02/04/2023] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor whose activity can be modulated by polyphenols, such as curcumin. AhR and curcumin have evolutionarily conserved effects on aging. Here, we investigated whether and how the AhR mediates the anti-aging effects of curcumin across species. Using a combination of in vivo, in vitro, and in silico analyses, we demonstrated that curcumin has AhR-dependent or -independent effects in a context-specific manner. We found that in Caenorhabditis elegans, AhR mediates curcumin-induced lifespan extension, most likely through a ligand-independent inhibitory mechanism related to its antioxidant activity. Curcumin also showed AhR-independent anti-aging activities, such as protection against aggregation-prone proteins and oxidative stress in C. elegans and promotion of the migratory capacity of human primary endothelial cells. These AhR-independent effects are largely mediated by the Nrf2/SKN-1 pathway.
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Affiliation(s)
- Vanessa Brinkmann
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Margherita Romeo
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Lucie Larigot
- Faculté des Sciences Fondamentales et Biomédicales, Université de Paris, 45 Rue des Saints-Pères, F-75006 Paris, France; (L.L.); (X.C.)
| | - Anne Hemmers
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Lisa Tschage
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Jennifer Kleinjohann
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Alfonso Schiavi
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Swantje Steinwachs
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Charlotte Esser
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Ralph Menzel
- Institute of Biology, Humboldt-University Berlin, Philippstr. 13, 10115 Berlin, Germany;
| | - Sara Giani Tagliabue
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (S.G.T.); (L.B.)
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy; (S.G.T.); (L.B.)
| | - Fiona Cox
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
- Institute of Clinical Pharmacology and Pharmacology, Medical Faculty, University Hospital and Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany
| | - Niloofar Ale-Agha
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
| | - Philipp Jakobs
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
| | - Joachim Altschmied
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
| | - Judith Haendeler
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
| | - Xavier Coumoul
- Faculté des Sciences Fondamentales et Biomédicales, Université de Paris, 45 Rue des Saints-Pères, F-75006 Paris, France; (L.L.); (X.C.)
| | - Natascia Ventura
- Institute of Clinical Chemistry and Laboratory Diagnostic, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr 5, 40225 Düsseldorf, Germany; (V.B.); (M.R.); (A.S.); (F.C.); (N.A.-A.); (P.J.); (J.A.); (J.H.)
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.H.); (L.T.); (J.K.); (S.S.); (C.E.)
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172
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Igaev M, Grubmüller H. Bending-torsional elasticity and energetics of the plus-end microtubule tip. Proc Natl Acad Sci U S A 2022; 119:e2115516119. [PMID: 35302883 PMCID: PMC8944587 DOI: 10.1073/pnas.2115516119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/10/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe mechanochemical basis of microtubule growth, which is essential for the normal function and division of eukaryotic cells, has remained elusive and controversial, despite extensive work. In particular, recent findings have created the paradox that the microtubule plus-end tips look very similar during both growing and shrinking phases, thereby challenging the traditional textbook picture. Our large-scale atomistic simulations resolve this paradox and explain microtubule growth and shrinkage dynamics as a process governed by energy barriers between protofilament conformations, the heights of which are in turn fine-tuned by different nucleotide states, thus implementing an information-driven Brownian ratchet.
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Affiliation(s)
- Maxim Igaev
- Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
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173
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Sepay N, Banerjee M, Islam R, Dey SP, Halder UC. Crystallography-based exploration of non-covalent interactions for the design and synthesis of coumarin for stronger protein binding. Phys Chem Chem Phys 2022; 24:6605-6615. [PMID: 35234237 DOI: 10.1039/d2cp00082b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein molecules are a good target for the inhibition or promotion of biological processes. Different methods like QSAR and molecular docking have been developed to accurately design small binder molecules for target proteins. An alternative model has been developed wherein a statistical method is used to find the propensity of different non-covalent interactions between small molecules and amino acid residues of the protein. The results give hints as to the choice of substituents required at the SM to strongly bind to a protein. In this case, 75 different types of proteins bound with coumarin derivatives have been investigated and the non-covalent interactions observed between the basic coumarin moiety and amino acids have been analyzed. Density functional theory (DFT) calculations were used to identify the electronic features of coumarin to understand the feasibility of the observed non-covalent interactions and to find appropriate groups that can modulate these interactions. The binding affinity towards a protein (β-lactoglobulin (BLG)) and the stability of the protein complex have been investigated through docking and molecular dynamics of 100 ns, respectively. The modeled compounds were synthesized and investigated with regards to their interactions with the model carrier protein. The thermodynamics of the interactions were also investigated and the binding is governed by the Le Chatelier principle.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College, Kolkata-700017, India.
| | - Manami Banerjee
- Department of Chemistry, Diamond Harbour Women's University, Sarisha-743368, India
| | - Rajibul Islam
- Department of Chemistry, Jadavpur University, Kolkata-700032, India
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174
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Scott H, Huang W, Andra K, Mamillapalli S, Gonti S, Day A, Zhang K, Mehzabeen N, Battaile KP, Raju A, Lovell S, Bann JG, Taylor DJ. Structure of the anthrax protective antigen D425A dominant negative mutant reveals a stalled intermediate state of pore maturation. J Mol Biol 2022; 434:167548. [PMID: 35304125 DOI: 10.1016/j.jmb.2022.167548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The tripartite protein complex produced by anthrax bacteria (Bacillus anthracis) is a member of the AB family of β-barrel pore-forming toxins. The protective antigen (PA) component forms an oligomeric prepore that assembles on the host cell surface and serves as a scaffold for binding of lethal and edema factors. Following endocytosis, the acidic environment of the late endosome triggers a pH-induced conformational rearrangement to promote maturation of the PA prepore to a functional, membrane spanning pore that facilitates delivery of lethal and edema factors to the cytosol of the infected host. Here, we show that the dominant-negative D425A mutant of PA stalls anthrax pore maturation in an intermediate state at acidic pH. Our 2.7 Å cryo-EM structure of the intermediate state reveals structural rearrangements that involve constriction of the oligomeric pore combined with an intramolecular dissociation of the pore-forming module. In addition to defining the early stages of anthrax pore maturation, the structure identifies asymmetric conformational changes in the oligomeric pore that are influenced by the precise configuration of adjacent protomers.
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Affiliation(s)
- Harry Scott
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kiran Andra
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | | | - Srinivas Gonti
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Alexander Day
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kaiming Zhang
- Stanford Linear Accelerator Center and the Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, APS, Argonne National Laboratory, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439, USA
| | - Anjali Raju
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, KS 66047, USA
| | - James G Bann
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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175
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Qu C, Yang ZK, Wang S, Zhao HP, Li FQ, Yang XL, Luo C. Binding Affinity Characterization of Four Antennae-Enriched Odorant-Binding Proteins From Harmonia axyridis (Coleoptera: Coccinellidae). Front Physiol 2022; 13:829766. [PMID: 35350682 PMCID: PMC8957989 DOI: 10.3389/fphys.2022.829766] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
Harmonia axyridis is an important natural enemy that consumes many agricultural and forestry pests. It relies on a sensitive olfactory system to find prey and mates. Odorant-binding proteins (OBPs) as the first-step of recognizing volatiles, transport odors through sensillum lymph to odorant receptors (ORs). However, little is known about the molecular mechanisms of H. axyridis olfaction. In this study, four H. axyridis antenna specific OBP genes, HaxyOBP3, 5, 12, and 15, were bacterially expressed and the binding features of the four recombinant proteins to 40 substances were investigated using fluorescence competitive binding assays. Three-dimensional structure modeling and molecular docking analysis predicted the binding sites between HaxyOBPs and candidate volatiles. Developmental expression analyses showed that the four HaxyOBP genes displayed a variety of expression patterns at different development stages. The expression levels of HaxyOBP3 and HaxyOBP15 were higher in the adult stage than in the other developmental stages, and HaxyOBP15 was significantly transcriptionally enriched in adult stage. Ligand-binding analysis demonstrated that HaxyOBP3 and HaxyOBP12 only combined with two compounds, β-ionone and p-anisaldehyde. HaxyOBP5 protein displayed binding affinities with methyl salicylate, β-ionone, and p-anisaldehyde (Ki = 18.15, 11.71, and 13.45 μM). HaxyOBP15 protein had a broad binding profile with (E)-β-farnesene, β-ionone, α-ionone, geranyl acetate, nonyl aldehyde, dihydro-β-ionone, and linalyl acetate (Ki = 4.33-31.01 μM), and hydrophobic interactions played a key role in the binding of HaxyOBP15 to these substances according to molecular docking. Taken together, HaxyOBP15 exhibited a broader ligand-binding spectrum and a higher expression in adult stage than HaxyOBP3, 5, and 12, indicating HaxyOBP15 may play a greater role in binding volatiles than other three HaxyOBPs. The results will increase our understanding of the molecular mechanism of H. axyridis olfaction and may also result in new management strategies (attractants/repellents) that increase the biological control efficacy of H. axyridis.
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Affiliation(s)
- Cheng Qu
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhao-kai Yang
- Department of Applied Chemistry, Innovation Center of Pesticide Research, China Agricultural University, Beijing, China
| | - Su Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hai-peng Zhao
- College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Feng-qi Li
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xin-ling Yang
- Department of Applied Chemistry, Innovation Center of Pesticide Research, China Agricultural University, Beijing, China
| | - Chen Luo
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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176
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An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale. Proc Natl Acad Sci U S A 2022; 119:2105819119. [PMID: 35217601 PMCID: PMC8892348 DOI: 10.1073/pnas.2105819119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Synthetic auxin herbicides intersect basic plant developmental biology and applied weed management. We investigated resistance to 2,4-D in the Australian weed Sisymbrium orientale (Indian hedge mustard). We identified a mechanism involving an in-frame 27-bp deletion in the degron tail of auxin coreceptor IAA2, one member of the gene family of Aux/IAA auxin co-receptors. We show that this deletion in IAA2 is a gain-of-function mutation that confers synthetic auxin resistance. This field-evolved mechanism of resistance to synthetic auxin herbicides confirms previous biochemical studies showing the role of the Aux/IAA degron tail in regulating Aux/IAA protein degradation upon auxin perception. The deletion mutation could be generated in crops using gene-editing approaches for cross-resistance to multiple synthetic auxin herbicides. The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic-signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing nine amino acids in the degron tail (DT) of the auxin coreceptor Aux/IAA2 (SoIAA2). The deletion allele cosegregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D-resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This mechanism of synthetic auxin herbicide resistance assigns an in planta function to the DT region of this Aux/IAA coreceptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin-resistant crops using gene-editing.
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177
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Makamte S, Thureau A, Jabrani A, Paquelin A, Plessis A, Sanial M, Rudenko O, Oteri F, Baaden M, Biou V. A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study. J Struct Biol 2022; 214:107853. [DOI: 10.1016/j.jsb.2022.107853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/10/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
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178
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Jomhori M, Mosaddeghi H. Molecular modeling of natural and synthesized inhibitors against SARS-CoV-2 spike glycoprotein. RESEARCH ON BIOMEDICAL ENGINEERING 2022. [PMCID: PMC7779244 DOI: 10.1007/s42600-020-00122-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Purpose Viral diseases increasingly endanger the world public health because of the transient efficacy of antiviral therapies. The novel coronavirus disease 2019 (COVID-19) has been recently identified as caused by a new type of coronaviruses. This type of coronavirus binds to the human receptor through the Spike glycoprotein (S) Receptor Binding Domain (RBD). The spike protein is found in inaccessible (closed) or accessible (open) conformations in which the accessible conformation causes severe infection. Thus, this receptor is a significant target for antiviral drug design. Methods An attempt was made to recognize 111 natural and synthesized compounds in order to utilize them against SARS-CoV-2 spike glycoprotein to inhibit Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using simulation methods, such as molecular docking. The FAF-Drugs3, Pan-Assay Interference Compounds (PAINS), ADME (absorption, distribution, metabolism, excretion) databases along with Lipinski’s rules were used to evaluate the drug-like properties of the identified ligands. In order to analyze and identify the residues critical in the docking process of the spike glycoprotein, the interactions of proposed ligands with both conformations of the spike glycoprotein was simulated. Results The results showed that among the available ligands, seven ligands had significant interactions with the binding site of the spike glycoprotein, in which angiotensin-converting enzyme 2 (ACE2) is bounded. Out of seven candidate molecules, six ligands exhibited drug-like characteristics. The results also demonstrated that fluorophenyl and propane groups of ligands had optimal interactions with the binding site of the spike glycoprotein. Conclusion According to the results, our findings indicated the ability of six ligands to prevent the binding of the SARS-CoV-2 spike glycoprotein to its cognate receptor, providing novel compounds for the treatment of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s42600-020-00122-3.
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Affiliation(s)
| | - Hamid Mosaddeghi
- Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111 Iran
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179
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Chandran C, Tham HY, Abdul Rahim R, Lim SHE, Yusoff K, Song AAL. Lactococcus lactis secreting phage lysins as a potential antimicrobial against multi-drug resistant Staphylococcus aureus. PeerJ 2022; 10:e12648. [PMID: 35251775 PMCID: PMC8896023 DOI: 10.7717/peerj.12648] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/26/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Staphylococcus aureus is an opportunistic Gram-positive bacterium that can form biofilm and become resistant to many types of antibiotics. The treatment of multi-drug resistant Staphylococcus aureus (MDRSA) infection is difficult since it possesses multiple antibiotic-resistant mechanisms. Endolysin and virion-associated peptidoglycan hydrolases (VAPGH) enzymes from bacteriophage have been identified as potential alternative antimicrobial agents. This study aimed to assess the ability of Lactococcus lactis NZ9000 secreting endolysin and VAPGH from S. aureus bacteriophage 88 to inhibit the growth of S. aureus PS 88, a MDRSA. METHOD Endolysin and VAPGH genes were cloned and expressed in L. lactis NZ9000 after fusion with the SPK1 signal peptide for secretion. The recombinant proteins were expressed and purified, then analyzed for antimicrobial activity using plate assay and turbidity reduction assay. In addition, the spent media of the recombinant lactococcal culture was analyzed for its ability to inhibit the growth of the S. aureus PS 88. RESULTS Extracellular recombinant endolysin (Endo88) and VAPGH (VAH88) was successfully expressed and secreted from L. lactis which was able to inhibit S. aureus PS 88, as shown by halozone formation on plate assays as well as inhibition of growth in the turbidity reduction assay. Moreover, it was observed that the spent media from L. lactis NZ9000 expressing Endo88 and VAH88 reduced the viability of PS 88 by up to 3.5-log reduction with Endo88 being more efficacious than VAH88. In addition, Endo88 was able to lyse all MRSA strains tested and Staphylococcus epidermidis but not the other bacteria while VAH88 could only lyse S. aureus PS 88. CONCLUSION Recombinant L. lactisNZ9000 expressing phage 88 endolysin may be potentially developed into a new antimicrobial agent for the treatment of MDRSA infection.
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Affiliation(s)
- Carumathy Chandran
- Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hong Yun Tham
- Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Swee Hua Erin Lim
- Health Science Division, Abu Dhabi Women’s College, Abu Dhabi, United Arab Emirates
| | - Khatijah Yusoff
- Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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180
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Anand S, Muthu Kumar S, Mukherjee K, Padmanabhan P. Insight into fermentable sugar recovery process from sugarcane bagasse: in silico elucidation of enzymatic hydrolysis and techno-economic assessment. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2022. [DOI: 10.1080/16583655.2022.2040243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shreya Anand
- Department of Bioengineering & Biotechnology, Birla Institute of Technology, Ranchi, India
| | - Sampath Muthu Kumar
- Department of Bioengineering & Biotechnology, Birla Institute of Technology, Ranchi, India
| | - Koel Mukherjee
- Department of Bioengineering & Biotechnology, Birla Institute of Technology, Ranchi, India
| | - Padmini Padmanabhan
- Department of Bioengineering & Biotechnology, Birla Institute of Technology, Ranchi, India
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181
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Santos TM, Lisboa ABP, Rodrigues W, Gomes H, Abrahão J, Del-Bem LE. Human variation in the protein receptor ACE2 affects its binding affinity to SARS-CoV-2 in a variant-dependent manner. J Biomol Struct Dyn 2022; 41:2947-2955. [PMID: 35196964 DOI: 10.1080/07391102.2022.2042387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
SARS-CoV-2 infection depend on the binding of the viral Spike glycoprotein (S) to the human receptor Angiotensin Converting Enzyme 2 (ACE2) to induce virus-cell membrane fusion. S protein evolved diverse amino acid changes that are possibly linked to more efficient binding to human ACE2, which might explain part of the increase in frequency of SARS-CoV-2 Variants Of Concern (VOCs). In this work, we investigated the role of ACE2 protein variations that are naturally found in human populations and its binding affinity with S protein from SARS-CoV-2 representative genotypes, based on a series of in silico approaches involving molecular modelling, docking and molecular dynamics simulations. Our results indicate that SARS-CoV-2 VOCs bind more efficiently to the human receptor ACE2 than the ancestral Wuhan genotype. Additionally, variations in the ACE2 protein can affect SARS-CoV-2 binding and protein-protein stability, mostly making the interaction weaker and unstable in some cases. We show that some VOCs, such as B.1.1.7 and P.1 are much less sensitive to ACE2 variants, while others like B.1.351 appear to be specifically optimized to bind to the widespread wild-type ACE2 protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thiago M Santos
- Department of Botany, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ayrton B P Lisboa
- Department of Botany, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Wenderson Rodrigues
- Department of Botany, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Helena Gomes
- Department of Botany, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Jônatas Abrahão
- Department of Microbiology, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luiz-Eduardo Del-Bem
- Department of Botany, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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182
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Karim RM, Yang L, Chen L, Bikowitz MJ, Lu J, Grassie D, Shultz ZP, Lopchuk JM, Chen J, Schönbrunn E. Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain. J Med Chem 2022; 65:4182-4200. [PMID: 35191694 DOI: 10.1021/acs.jmedchem.1c01999] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bromodomains regulate chromatin remodeling and gene transcription through recognition of acetylated lysines on histones and other proteins. Bromodomain-containing protein TAF1, a subunit of general transcription factor TFIID, initiates preinitiation complex formation and cellular transcription. TAF1 serves as a cofactor for certain oncogenic transcription factors and is implicated in regulating the p53 tumor suppressor. Therefore, TAF1 is a potential target to develop small molecule therapeutics for diseases arising from dysregulated transcription, such as cancer. Here, we report the ATR kinase inhibitor AZD6738 (Ceralasertib) and analogues thereof as bona fide inhibitors of TAF1. Crystallographic and small-angle X-ray scattering studies established that newly identified and previously reported inhibitors stabilize distinct structural states of the TAF1 tandem bromodomain through "open-closed" transitions and dimerization. Combined with functional studies on p53 signaling in cancer cell lines, the data provide new insights into the feasibility and challenges of TAF1 inhibitors as chemical probes and therapeutics.
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Affiliation(s)
- Rezaul Md Karim
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Leixiang Yang
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Lihong Chen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Melissa J Bikowitz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Junhao Lu
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Dylan Grassie
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Zachary P Shultz
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Justin M Lopchuk
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Jiandong Chen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
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183
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Chen J, Nelson DC, Shukla D. Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants. J Chem Inf Model 2022; 62:1712-1722. [PMID: 35192364 DOI: 10.1021/acs.jcim.1c01258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Parasitic weeds such as Striga have led to significant losses in agricultural productivity worldwide. These weeds use the plant hormone strigolactone as a germination stimulant. Strigolactone signaling involves substrate hydrolysis followed by a conformational change of the receptor to a "closed" or "active" state that associates with a signaling partner, MAX2/D3. Crystal structures of active and inactive AtD14 receptors have helped elucidate the structural changes involved in activation. However, the mechanism by which the receptor activates remains unknown. The ligand dependence of AtD14 activation has been disputed by mutagenesis studies showing that enzymatically inactive receptors are able to associate with MAX2 proteins. Furthermore, activation differences between strigolactone receptor in Striga, ShHTL7, and AtD14 could contribute to the high sensitivity to strigolactones exhibited by parasitic plants. Using molecular dynamics simulations, we demonstrate that both AtD14 and ShHTL7 could adopt an active conformation in the absence of ligand. However, ShHTL7 exhibits a higher population in the inactive apo state as compared to the AtD14 receptor. We demonstrate that this difference in inactive state population is caused by sequence differences between their D-loops and interactions with the catalytic histidine that prevent full binding pocket closure in ShHTL7. These results indicate that ligand hydrolysis would enhance the active state population by destabilizing the inactive state in ShHTL7 as compared to AtD14. We also show that the mechanism of activation is more concerted in AtD14 than in ShHTL7 and that the main barrier to activation in ShHTL7 is closing of the binding pocket.
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Affiliation(s)
- Jiming Chen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California 92521, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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184
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Uriu K, Cárdenas P, Muñoz E, Barragan V, Kosugi Y, Shirakawa K, Takaori-Kondo A, Sato K. Characterization of the immune resistance of SARS-CoV-2 Mu variant and the robust immunity induced by Mu infection. J Infect Dis 2022; 226:1200-1203. [PMID: 35176774 PMCID: PMC8903444 DOI: 10.1093/infdis/jiac053] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/15/2022] [Indexed: 11/14/2022] Open
Abstract
We have recently revealed that the SARS-CoV-2 Mu variant shows a pronounced resistance to antibodies elicited by natural SARS-CoV-2 infection and vaccination. However, it remains unclear which mutations determine the resistance of SARS-CoV-2 Mu to antiviral sera. Also, it is unclear how SARS-CoV-2 Mu infection induces antiviral immunity. Here we reveal that the two mutations in the SARS-CoV-2 Mu spike protein, YY144-145TSN and E484K, are responsible for the resistance to COVID-19 convalescent sera during early 2020 and vaccine sera. Notably, the convalescent sera of SARS-CoV-2 Mu-infected individuals are broadly antiviral against Mu as well as other SARS-CoV-2 variants of concern/interest.
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Affiliation(s)
- Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Paúl Cárdenas
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Erika Muñoz
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Veronica Barragan
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan
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185
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The Full Model of the pMHC-TCR-CD3 Complex: A Structural and Dynamical Characterization of Bound and Unbound States. Cells 2022; 11:cells11040668. [PMID: 35203317 PMCID: PMC8869815 DOI: 10.3390/cells11040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/31/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The machinery involved in cytotoxic T-cell activation requires three main characters: the major histocompatibility complex class I (MHC I) bound to the peptide (p), the T-cell receptor (TCR), and the CD3 complex, a multidimer interfaced with the intracellular side. The pMHC:TCR interaction has been largely studied by means of both experimental and computational models, giving a contribution in understanding the complexity of the TCR triggering. Nevertheless, a detailed study of the structural and dynamical characterization of the full complex (pMHC:TCR:CD3 complex) is still missing due to a lack of structural information of the CD3-chains arrangement around the TCR. Very recently, the determination of the TCR:CD3 complex structure by means of Cryo-EM technique has given a chance to build the entire system essential in the activation of T-cells, a fundamental mechanism in the adaptive immune response. Here, we present the first complete model of the pMHC interacting with the TCR:CD3 complex, built in a lipid environment. To describe the conformational behavior associated with the unbound and the bound states, all-atom Molecular Dynamics simulations were performed for the TCR:CD3 complex and for two pMHC:TCR:CD3 complex systems, bound to two different peptides. Our data point out that a conformational change affecting the TCR Constant β (Cβ) region occurs after the binding to the pMHC, revealing a key role of this region in the propagation of the signal. Moreover, we found that TCR reduces the flexibility of the MHC I binding groove, confirming our previous results.
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186
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In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Life (Basel) 2022; 12:life12020231. [PMID: 35207518 PMCID: PMC8876804 DOI: 10.3390/life12020231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
The 2019 coronavirus disease (COVID-19) pandemic continues to challenge health care systems worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the cause of global pandemic. Type 2 transmembrane serine protease (TMPRSS2) is important in the cell entry and spread of SARS-CoV-2 and plays a crucial role in the proteolytic cleavage of SARS-CoV-2 spike (S) glycoprotein. Here, using reported structural data, we analyzed the molecular complex of TMPRSS2 and the S glycoprotein and further examined intermolecular interactions of natural TMPRSS2 polymorphic variants. We identified several TMPRSS2 variants that could possibly alter host susceptibility to the SARS-CoV-2 infection. Molecular docking analysis revealed that G462D/G462S variants were predicted to be protective variants, whereas Q438E and S339F variants were predicted to increase susceptibility. In addition, we examined intermolecular interactions between TMPRSS2 and its two potential serine protease inhibitors, camostat mesylate and nafamostat. Further, we investigated the effect of TMPRSS2 variants on these interactions. Our structural analysis revealed that G462D, C297S and S460R variants had possibly altered the interactions with the protease inhibitors. Our results identified important TMPRSS2 variations that could be useful to develop high affinity and personalized drugs for treating COVID-19 patients.
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187
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Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds. Int J Mol Sci 2022; 23:ijms23031514. [PMID: 35163439 PMCID: PMC8835989 DOI: 10.3390/ijms23031514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 01/12/2023] Open
Abstract
The presence of protein structures with atypical folds in the Protein Data Bank (PDB) is rare and may result from naturally occurring knots or crystallographic errors. Proper characterisation of such folds is imperative to understanding the basis of naturally existing knots and correcting crystallographic errors. If left uncorrected, such errors can frustrate downstream experiments that depend on the structures containing them. An atypical fold has been identified in P. falciparum dihydrofolate reductase (PfDHFR) between residues 20–51 (loop 1) and residues 191–205 (loop 2). This enzyme is key to drug discovery efforts in the parasite, necessitating a thorough characterisation of these folds. Using multiple sequence alignments (MSA), a unique insert was identified in loop 1 that exacerbates the appearance of the atypical fold-giving it a slipknot-like topology. However, PfDHFR has not been deposited in the knotted proteins database, and processing its structure failed to identify any knots within its folds. The application of protein homology modelling and molecular dynamics simulations on the DHFR domain of P. falciparum and those of two other organisms (E. coli and M. tuberculosis) that were used as molecular replacement templates in solving the PfDHFR structure revealed plausible unentangled or open conformations of these loops. These results will serve as guides for crystallographic experiments to provide further insights into the atypical folds identified.
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188
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Fakhouri LI, Al-Shar'i NA. The design of TOPK inhibitors using structure-based pharmacophore modeling and molecular docking based on an MD-refined homology model. Mol Divers 2022; 26:2679-2702. [PMID: 35031933 DOI: 10.1007/s11030-021-10361-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022]
Abstract
The TOPK enzyme (also known as PBK) is a serine-threonine protein kinase that is rarely detected in normal tissues yet is found to be overexpressed and activated in a variety of cancers such as lung, colorectal, breast, and esophageal cancer. Its prevalence in cancerous cells is associated with their poor prognosis and responsiveness to treatment. This enzyme plays a vital role in cell division, specifically in regulating cytokinesis. Unlike drugs targeting early phases in mitosis, inhibition of cytokinesis by targeting biomolecules that are unique to multiplying cells poses no threat to the normal function of non-multiplying cells. Studies have shown that inhibition of cytokinesis is promising in suppressing the growth of proliferating cancerous cells as exemplified by the complete tumor regression seen with the suppression of TOPK. Herein, we report the identification of potent TOPK inhibitors with anticancer potential using a structure-based drug design approach. The only available crystal structure of TOPK corresponds to a double mutant (T9E and T198E) dimer with a distorted N-lobe conformation, thus 3D homology modeling was implemented to rebuild the enzyme's native conformation. The resulting refined model was used to generate 3D pharmacophore models for the virtual screening of small molecules databases. Retrieved hits were filtered, docked into the ATP binding site of the enzyme, rescored, and the binding free energies for the top consensually scoring hits were calculated. Consequently, 45 compounds were selected and their in vitro inhibitory activity against TOPK was tested revealing four potential hits with the most active compound having an IC50 of 3.85 µM. This compound will be chosen as a lead compound to synthesize analogs aiming to enhance potency and drug-like properties and to enrich the SAR data.
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Affiliation(s)
- Lara I Fakhouri
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan.
| | - Nizar A Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan.
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189
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Kimura I, Kosugi Y, Wu J, Zahradnik J, Yamasoba D, Butlertanaka EP, Tanaka YL, Uriu K, Liu Y, Morizako N, Shirakawa K, Kazuma Y, Nomura R, Horisawa Y, Tokunaga K, Ueno T, Takaori-Kondo A, Schreiber G, Arase H, Motozono C, Saito A, Nakagawa S, Sato K. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep 2022; 38:110218. [PMID: 34968415 DOI: 10.1101/2021.07.28.454085] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 05/22/2023] Open
Abstract
SARS-CoV-2 Lambda, a variant of interest, has spread in some South American countries; however, its virological features and evolutionary traits remain unclear. In this study, we use pseudoviruses and reveal that the spike protein of the Lambda variant is more infectious than that of other variants due to the T76I and L452Q mutations. The RSYLTPGD246-253N mutation, a unique 7-amino acid deletion in the N-terminal domain of the Lambda spike protein, is responsible for evasion from neutralizing antibodies and further augments antibody-mediated enhancement of infection. Although this mutation generates a nascent N-linked glycosylation site, the additional N-linked glycan is dispensable for the virological property conferred by this mutation. Since the Lambda variant has dominantly spread according to the increasing frequency of the isolates harboring the RSYLTPGD246-253N mutation, our data suggest that the RSYLTPGD246-253N mutation is closely associated with the substantial spread of the Lambda variant in South America.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Faculty of Medicine, Kobe University, Hyogo 6500017, Japan
| | - Erika P Butlertanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
| | - Yuri L Tanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, The University of Tokyo, 1130033 Tokyo, Japan
| | - Yafei Liu
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 5650871, Japan
| | - Nanami Morizako
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Ryosuke Nomura
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 1628640, Japan
| | - Takamasa Ueno
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hisashi Arase
- Graduate School of Medicine, The University of Tokyo, 1130033 Tokyo, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 5650871, Japan
| | - Chihiro Motozono
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki 8892192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 8892192, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan; Graduate School of Medicine, The University of Tokyo, 1130033 Tokyo, Japan.
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190
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Ikedife J, He J, Wei Y. PEA-15 engages in allosteric interactions using a common scaffold in a phosphorylation-dependent manner. Sci Rep 2022; 12:116. [PMID: 34997083 PMCID: PMC8742051 DOI: 10.1038/s41598-021-04099-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
Phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) is a death-effector domain (DED) containing protein involved in regulating mitogen-activated protein kinase and apoptosis pathways. In this molecular dynamics study, we examined how phosphorylation of the PEA-15 C-terminal tail residues, Ser-104 and Ser-116, allosterically mediates conformational changes of the DED and alters the binding specificity from extracellular-regulated kinase (ERK) to Fas-associated death domain (FADD) protein. We delineated that the binding interfaces between the unphosphorylated PEA-15 and ERK2 and between the doubly phosphorylated PEA-15 and FADD are similarly composed of a scaffold that includes both the DED and the C-terminal tail residues of PEA-15. While the unphosphorylated serine residues do not directly interact with ERK2, the phosphorylated Ser-116 engages in strong electrostatic interactions with arginine residues on FADD DED. Upon PEA-15 binding, FADD repositions its death domain (DD) relative to the DED, an essential conformational change to allow the death-inducing signaling complex (DISC) assembly.
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Affiliation(s)
- Joyce Ikedife
- Department of Chemistry, New Jersey City University, Jersey City, NJ, 07305, USA
| | - Jianlin He
- Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, Fujian, China
| | - Yufeng Wei
- Department of Chemistry, New Jersey City University, Jersey City, NJ, 07305, USA.
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191
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Ahmed T, Nisler CR, Fluck EC, Walujkar S, Sotomayor M, Moiseenkova-Bell VY. Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium. Structure 2022; 30:139-155.e5. [PMID: 34453887 PMCID: PMC8741645 DOI: 10.1016/j.str.2021.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 01/14/2023]
Abstract
Transient receptor potential (TRP) channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the structure and details of channel modulation remain elusive. Here, we describe the full-length cryoelectron microscopy structure of TRPY1 at 3.1 Å resolution in a closed state. The structure, despite containing an evolutionarily conserved and archetypical transmembrane domain, reveals distinctive structural folds for the cytosolic N and C termini, compared with other eukaryotic TRP channels. We identify an inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid-binding site, along with two Ca2+-binding sites: a cytosolic site, implicated in channel activation and a vacuolar lumen site, implicated in inhibition. These findings, together with data from microsecond-long molecular dynamics simulations and a model of a TRPY1 open state, provide insights into the basis of TRPY1 channel modulation by lipids and Ca2+, and the molecular evolution of TRP channels.
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Affiliation(s)
- Tofayel Ahmed
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Collin R Nisler
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sanket Walujkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Chemical Physics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Chemical Physics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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192
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Mikhailovskii O, Xue Y, Skrynnikov NR. Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber. IUCRJ 2022; 9:114-133. [PMID: 35059216 PMCID: PMC8733891 DOI: 10.1107/s2052252521011891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program Amber. The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new Amber-based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower R free values compared with those reported in the original PDB depositions or obtained by means of the industry-standard phenix.refine program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, Amber-refined structures consistently show superior MolProbity scores. The new approach offers a highly realistic representation of protein-protein interactions in the crystal, as well as of protein-water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.
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Affiliation(s)
- Oleg Mikhailovskii
- Laboratory of Biomolecular NMR, St Petersburg State University, St Petersburg 199034, Russian Federation
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yi Xue
- School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, People’s Republic of China
- Tsinghua University–Peking University Joint Center for Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR, St Petersburg State University, St Petersburg 199034, Russian Federation
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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193
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Molecular dynamics simulations and Gaussian network model for designing antibody mimicking protein towards dengue envelope protein. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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194
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195
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Cheng Y, Peng X. In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2. Phys Chem Chem Phys 2022; 24:16876-16883. [DOI: 10.1039/d2cp01724e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The COVID-19 epidemic, caused by virus SARS-CoV-2, has been a pandemic and threatening everyone's health in the past two years. In SARS-CoV-2, ORF8 is one of the most important accessory...
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196
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Raybould MIJ, Deane CM. The Therapeutic Antibody Profiler for Computational Developability Assessment. Methods Mol Biol 2022; 2313:115-125. [PMID: 34478133 DOI: 10.1007/978-1-0716-1450-1_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The need to consider an antibody's "developability" (immunogenicity, solubility, specificity, stability, manufacturability, and storability) is now well understood in therapeutic antibody design. Predicting these properties rapidly and inexpensively is critical to industrial workflows, to avoid devoting resources to non-productive candidates. Here, we describe a high-throughput computational developability assessment tool, the Therapeutic Antibody Profiler (TAP), which assesses the physicochemical "druglikeness" of an antibody candidate. Input variable domain sequences are converted to three-dimensional structural models, and then five developability-linked molecular surface descriptors are calculated and compared to advanced-stage clinical therapeutics. Values at the extremes of/outside of the distributions seen in therapeutics imply an increased risk of developability issues. Therefore, TAP, starting only from sequence information, provides a route to rapidly identifying drug candidate antibodies that are likely to have poor developability. Our web application ( opig.stats.ox.ac.uk/webapps/tap ) profiles input antibody sequences against a continually updated reference set of clinical therapeutics.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK.
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197
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Structural basis of sphingosine-1-phosphate receptor 1 activation and biased agonism. Nat Chem Biol 2021; 18:281-288. [PMID: 34937912 DOI: 10.1038/s41589-021-00930-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/21/2021] [Indexed: 12/20/2022]
Abstract
Sphingosine-1-phosphate receptor 1 (S1PR1) is a master regulator of lymphocyte egress from the lymph node and an established drug target for multiple sclerosis (MS). Mechanistically, therapeutic S1PR1 modulators activate the receptor yet induce sustained internalization through a potent association with β-arrestin. However, a structural basis of biased agonism remains elusive. Here, we report the cryo-electron microscopy (cryo-EM) structures of Gi-bound S1PR1 in complex with S1P, fingolimod-phosphate (FTY720-P) and siponimod (BAF312). In combination with functional assays and molecular dynamics (MD) studies, we reveal that the β-arrestin-biased ligands direct a distinct activation path in S1PR1 through the extensive interplay between the PIF and the NPxxY motifs. Specifically, the intermediate flipping of W2696.48 and the retained interaction between F2656.44 and N3077.49 are the key features of the β-arrestin bias. We further identify ligand-receptor interactions accounting for the S1PR subtype specificity of BAF312. These structural insights provide a rational basis for designing novel signaling-biased S1PR modulators.
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198
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Elisi GM, Scalvini L, Lodola A, Mor M, Rivara S. Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. J Chem Inf Model 2021; 62:210-222. [PMID: 34932329 PMCID: PMC8757440 DOI: 10.1021/acs.jcim.1c01183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
The effects of the
neurohormone melatonin are mediated by the activation
of the GPCRs MT1 and MT2 in a variety of tissues.
Crystal structures suggest ligand access to the orthosteric binding
site of MT1 and MT2 receptors through a lateral
channel between transmembrane (TM) helices IV and V. We investigated
the feasibility of this lipophilic entry route for 2-iodomelatonin,
a nonselective agonist with a slower dissociation rate from the MT2 receptor, applying enhanced sampling simulations and free-energy
calculations. 2-Iodomelatonin unbinding was investigated with steered
molecular dynamics simulations which revealed different trajectories
passing through the gap between TM helices IV and V for both receptors.
For one of these unbinding trajectories from the MT1 receptor,
an umbrella-sampling protocol with path-collective variables provided
a calculated energy barrier consistent with the experimental dissociation
rate. The side-chain flexibility of Tyr5.38 was significantly different
in the two receptor subtypes, as assessed by metadynamics simulations,
and during ligand unbinding it frequently assumes an open conformation
in the MT1 but not in the MT2 receptor, favoring
2-iodomelatonin egress. Taken together, our simulations are consistent
with the possibility that the gap between TM IV and V is a way of
connecting the orthosteric binding site and the membrane core for
lipophilic melatonin receptor ligands. Our simulations also suggest
that the open state of Tyr5.38 generates a small pocket on the surface
of MT1 receptor, which could participate in the recognition
of MT1-selective ligands and may be exploited in the design
of new selective compounds.
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Affiliation(s)
- Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy.,Microbiome Research Hub, University of Parma, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
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199
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Kihn KC, Wilson T, Smith AK, Bradshaw RT, Wintrode PL, Forrest LR, Wilks A, Deredge DJ. Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting. Biophys J 2021; 120:5141-5157. [PMID: 34767787 PMCID: PMC8715216 DOI: 10.1016/j.bpj.2021.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/13/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
The cytoplasmic heme binding protein from Pseudomonas aeruginosa, PhuS, plays two essential roles in regulating heme uptake and iron homeostasis. First, PhuS shuttles exogenous heme to heme oxygenase (HemO) for degradation and iron release. Second, PhuS binds DNA and modulates the transcription of the prrF/H small RNAs (sRNAs) involved in the iron-sparing response. Heme binding to PhuS regulates this dual function, as the unliganded form binds DNA, whereas the heme-bound form binds HemO. Crystallographic studies revealed nearly identical structures for apo- and holo-PhuS, and yet numerous solution-based measurements indicate that heme binding is accompanied by large conformational rearrangements. In particular, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of apo- versus holo-PhuS revealed large differences in deuterium uptake, notably in α-helices 6, 7, and 8 (α6,7,8), which contribute to the heme binding pocket. These helices were mostly labile in apo-PhuS but largely protected in holo-PhuS. In contrast, in silico-predicted deuterium uptake levels of α6,7,8 from molecular dynamics (MD) simulations of the apo- and holo-PhuS structures are highly similar, consistent only with the holo-PhuS HDX-MS data. To rationalize this discrepancy between crystal structures, simulations, and observed HDX-MS, we exploit a recently developed computational approach (HDXer) that fits the relative weights of conformational populations within an ensemble of structures to conform to a target set of HDX-MS data. Here, a combination of enhanced sampling MD, HDXer, and dimensionality reduction analysis reveals an apo-PhuS conformational landscape in which α6, 7, and 8 are significantly rearranged compared to the crystal structure, including a loss of secondary structure in α6 and the displacement of α7 toward the HemO binding interface. Circular dichroism analysis confirms the loss of secondary structure, and the extracted ensembles of apo-PhuS and of heme-transfer-impaired H212R mutant, are consistent with known heme binding and transfer properties. The proposed conformational landscape provides structural insights into the modulation by heme of the dual function of PhuS.
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Affiliation(s)
- Kyle C Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Tyree Wilson
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Ally K Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | | | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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200
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. eLife 2021; 10:e73027. [PMID: 34874007 PMCID: PMC8651292 DOI: 10.7554/elife.73027] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/07/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that indeed these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind to distinct sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
- Department of Chemistry, St. John’s UniversityQueensUnited States
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller UniversityNew YorkUnited States
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller UniversityNew YorkUnited States
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller UniversityNew YorkUnited States
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research InstituteSeattleUnited States
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children’s Research InstituteSeattleUnited States
| | - Nicholas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of MedicineNew YorkUnited States
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | | | | | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
- Division of Pulmonary and Sleep Medicine, Seattle Children’s HospitalSeattleUnited States
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of MedicineNew YorkUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San FranciscoSan FranciscoUnited States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research InstituteSeattleUnited States
- Department of Pediatrics, University of WashingtonSeattleUnited States
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller UniversityNew YorkUnited States
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller UniversityNew YorkUnited States
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