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Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022; 2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.
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Affiliation(s)
- Phuong Hoang Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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Prediction of suitable T and B cell epitopes for eliciting immunogenic response against SARS-CoV-2 and its mutant. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS 2021; 11:1. [PMID: 34849327 PMCID: PMC8619655 DOI: 10.1007/s13721-021-00348-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/21/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Spike glycoprotein of SARS-CoV-2 is mainly responsible for the recognition and membrane fusion within the host and this protein has an ability to mutate. Hence, T cell and B cell epitopes were derived from the spike glycoprotein sequence of wild SARS-CoV-2. The proposed T cell and B cell epitopes were found to be antigenic and conserved in the sequence of SARS-CoV-2 mutant (B.1.1.7). Thus, the proposed epitopes are effective against SARS-CoV-2 and its B.1.1.7 mutant. MHC-I that best interacts with the proposed T cell epitopes were found, using immune epitope database. Molecular docking and molecular dynamic simulations were done for ensuring a good binding between the proposed MHC-I and T cell epitopes. The finally proposed T cell epitope was found to be antigenic, non-allergenic, non-toxic and stable. Further, the finally proposed B cell epitopes were also found to be antigenic. The population conservation analysis has ensured the presence of MHC-I molecule (respective to the finally proposed T cell) in human population of most affected countries with SARS-CoV-2. Thus the proposed T and B cell epitope could be effective in designing an epitope-based vaccine, which is effective on SARS-CoV-2 and its B.1.1.7mutant. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13721-021-00348-w.
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Timmons PB, Hewage CM. APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures. Brief Bioinform 2021; 22:bbab308. [PMID: 34396417 PMCID: PMC8575040 DOI: 10.1093/bib/bbab308] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 01/29/2023] Open
Abstract
Good knowledge of a peptide's tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5-40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and PepLook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.
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Affiliation(s)
- Patrick Brendan Timmons
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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Teixeira SPB, Reis RL, Peppas NA, Gomes ME, Domingues RMA. Epitope-imprinted polymers: Design principles of synthetic binding partners for natural biomacromolecules. SCIENCE ADVANCES 2021; 7:eabi9884. [PMID: 34714673 PMCID: PMC8555893 DOI: 10.1126/sciadv.abi9884] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/07/2021] [Indexed: 05/27/2023]
Abstract
Molecular imprinting (MI) has been explored as an increasingly viable tool for molecular recognition in various fields. However, imprinting of biologically relevant molecules like proteins is severely hampered by several problems. Inspired by natural antibodies, the use of epitopes as imprinting templates has been explored to circumvent those limitations, offering lower costs and greater versatility. Here, we review the latest innovations in this technology, as well as different applications where MI polymers (MIPs) have been used to target biomolecules of interest. We discuss the several steps in MI, from the choice of epitope and functional monomers to the different production methods and possible applications. We also critically explore how MIP performance can be assessed by various parameters. Last, we present perspectives on future breakthroughs and advances, offering insights into how MI techniques can be expanded to new fields such as tissue engineering.
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Affiliation(s)
- Simão P. B. Teixeira
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L. Reis
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nicholas A. Peppas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1801, USA
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Pediatrics, Dell Medical School, University of Texas at Austin, Austin, TX 78712-1801, USA
- Department of Surgery and Perioperative Care, Dell Medical School, University of Texas at Austin, Austin, TX 78712-1801, USA
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, University of Texas at Austin, Austin, TX 78712-1801, USA
| | - Manuela E. Gomes
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui M. A. Domingues
- 3B’s Research Group, I3Bs—Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark—Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga, Guimarães, Portugal
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Making ERRFI1-Derived Peptides ‘Bindable’ to the Allosteric Dimerization Interface of Breast Cancer ERBB3 Kinase by Adding a Nonbonded Interaction System. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10298-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gascoigne L, Magana JR, Atkins DL, Sproncken CCM, Gumi-Audenis B, Schoenmakers SMC, Wakeham D, Wanless EJ, Voets IK. Fractal-like R5 assembly promote the condensation of silicic acid into silica particles. J Colloid Interface Sci 2021; 598:206-212. [PMID: 33905996 DOI: 10.1016/j.jcis.2021.04.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/29/2022]
Abstract
HYPOTHESIS Despite advances in understanding the R5 (SSKKSGSYSGKSGSKRRIL) peptide-driven bio-silica process, there remains significant discrepancies regarding the physicochemical characterization and the self-assembling mechanistic driving forces of the supramolecular R5 template. This paper investigates the self-assembly of R5 as a function of monovalent (sodium chloride) and multivalent salt (phosphate) to determine if assembly is phosphate ion concentration dependent. Additionally, we hypothesize that the assembled R5 aggregates do not resemble a micelle or unimer structure as proposed in current literature. EXPERIMENTS R5 peptides were synthesized, and aggregates evaluated for their size, morphology, and association state as a function of salt and ionic strength concentration via dynamic and static light scattering, small angle X-ray and neutron scattering and cryogenic transmission electron microscopy. Furthermore, we compare the proposed R5 template to precipitated silica by scanning electron microscopy. FINDINGS R5 peptides assemble into large aggregates due to multivalence bridging and the decrease in electrostatic repulsion due to ionic strength. We elucidate the structure of R5 aggregates as mass-fractals composed of small spherical aggregates. Moreover, we discover that phosphate ions not only have a significant role in driving the growth of the R5 scaffold, but additionally in driving the polycondensation of silicic acid during the bio-silification process via electrostatic interactions.
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Affiliation(s)
- Levena Gascoigne
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands; School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
| | - Jose Rodrigo Magana
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Dylan Luke Atkins
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Christian C M Sproncken
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Berta Gumi-Audenis
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Sandra M C Schoenmakers
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands
| | - Deborah Wakeham
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW 2234, Australia
| | - Erica J Wanless
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Ilja Karina Voets
- Laboratory of Self-Organizing Soft Matter & Institute for Complex Molecular Systems, Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, De Zaale, 5612 AZ Eindhoven the Netherlands.
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Immunoinformatics aided design of peptide-based vaccines against ebolaviruses. VITAMINS AND HORMONES 2021; 117:157-187. [PMID: 34420579 DOI: 10.1016/bs.vh.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ebolaviruses are at the forefront of emerging viruses and present a very perceptible threat to global peace and harmony. In the last decade, Ebola virus disease has claimed more than 90% of total lives since its inception in 1976. Owing to multiple host immune evasion methods employed by the virus and the limitations of traditional vaccine development approaches, finding a globally effective and reliable counter measure against Ebola virus remains a challenge. Highly conserved peptide fragments belonging to critical viral proteins and containing multiple epitopes which have the capacity to interact with a wide array of HLA molecules present a viable solution. Immunoinformatics or computational immunology enables rapid screening and shortlisting of plausible epitopes with a high immunogenic potential, thus, supporting expeditious elucidation of efficacious vaccine candidates. In light of above facts, we describe a computational methodology in this chapter for identification of potent peptide vaccine candidates against human infecting viruses. By applying this stringent methodology, we were able to identify multiple, immunogenic ebolavirus peptide fragments which, after verification in animal models, might be considered as part of future synthetic Ebola vaccine.
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Sakib MMH, Nishat AA, Islam MT, Raihan Uddin MA, Iqbal MS, Bin Hossen FF, Ahmed MI, Bashir MS, Hossain T, Tohura US, Saif SI, Jui NR, Alam M, Islam MA, Hasan MM, Sufian MA, Ali MA, Islam R, Hossain MA, Halim MA. Computational screening of 645 antiviral peptides against the receptor-binding domain of the spike protein in SARS-CoV-2. Comput Biol Med 2021; 136:104759. [PMID: 34403938 PMCID: PMC8352665 DOI: 10.1016/j.compbiomed.2021.104759] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/03/2021] [Accepted: 08/07/2021] [Indexed: 11/29/2022]
Abstract
The receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein plays a vital role in binding and internalization through the alpha-helix (AH) of human angiotensin-converting enzyme 2 (hACE2). Thus, it is a potential target for designing and developing antiviral agents. Inhibition of RBD activity of the S protein may be achieved by blocking RBD interaction with hACE2. In this context, inhibitors with large contact surface area are preferable as they can form a potentially stable complex with RBD of S protein and would not allow RBD to come in contact with hACE2. Peptides represent excellent features as potential anti-RBD agents due to better efficacy, safety, and tolerability in humans compared to that of small molecules. The present study has selected 645 antiviral peptides known to inhibit various viruses and computationally screened them against the RBD of SARS-CoV-2 S protein. In primary screening, 27 out of 645 peptides exhibited higher affinity for the RBD of S protein compared to that of AH of the hACE2 receptor. Subsequently, AVP1795 appeared as the most promising candidate that could inhibit hACE2 recognition by SARS-CoV 2 as was predicted by the molecular dynamics simulation. The critical residues in RBD found for protein-peptide interactions are TYR 489, GLY 485, TYR 505, and GLU 484. Peptide-protein interactions were substantially influenced by hydrogen bonding and hydrophobic interactions. This comprehensive computational screening may provide a guideline to design the most effective peptides targeting the spike protein, which could be studied further in vitro and in vivo for assessing their anti-SARS CoV-2 activity.
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Affiliation(s)
- Md Minhas Hossain Sakib
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Aktiya Anjum Nishat
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mohammad Tarequl Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mohammad Abu Raihan Uddin
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Shahriar Iqbal
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Farhan Fuad Bin Hossen
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mohammad Imran Ahmed
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Samiul Bashir
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Takbir Hossain
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Umma Sumia Tohura
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Saiful Islam Saif
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Nabilah Rahman Jui
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mosharaf Alam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Aminul Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Mehadi Hasan
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Md Abu Sufian
- School of Pharmacy, Temple University, Philadelphia, PA, 19140, USA
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka, 1215, Bangladesh
| | - Mohammed Akhter Hossain
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Mohammad A Halim
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, Arkansas 72913, USA.
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Rossi E, Kauskot A, Saller F, Frezza E, Poirault-Chassac S, Lokajczyk A, Bourdoncle P, Saubaméa B, Gaussem P, Pericacho M, Bobe R, Bachelot-Loza C, Pasquali S, Bernabeu C, Smadja DM. Endoglin Is an Endothelial Housekeeper against Inflammation: Insight in ECFC-Related Permeability through LIMK/Cofilin Pathway. Int J Mol Sci 2021; 22:ijms22168837. [PMID: 34445542 PMCID: PMC8396367 DOI: 10.3390/ijms22168837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Endoglin (Eng) is an endothelial cell (EC) transmembrane glycoprotein involved in adhesion and angiogenesis. Eng mutations result in vessel abnormalities as observed in hereditary hemorrhagic telangiectasia of type 1. The role of Eng was investigated in endothelial functions and permeability under inflammatory conditions, focusing on the actin dynamic signaling pathway. Endothelial Colony-Forming Cells (ECFC) from human cord blood and mouse lung/aortic EC (MLEC, MAEC) from Eng+/+ and Eng+/- mice were used. ECFC silenced for Eng with Eng-siRNA and ctr-siRNA were used to test tubulogenesis and permeability +/- TNFα and +/- LIM kinase inhibitors (LIMKi). In silico modeling of TNFα-Eng interactions was carried out from PDB IDs 5HZW and 5HZV. Calcium ions (Ca2+) flux was studied by Oregon Green 488 in epifluorescence microscopy. Levels of cofilin phosphorylation and tubulin post-translational modifications were evaluated by Western blot. F-actin and actin-tubulin distribution/co-localization were evaluated in cells by confocal microscopy. Eng silencing in ECFCs resulted in a decrease of cell sprouting by 50 ± 15% (p < 0.05) and an increase in pseudo-tube width (41 ± 4.5%; p < 0.001) compared to control. Upon TNFα stimulation, ECFC Eng-siRNA displayed a significant higher permeability compared to ctr-siRNA (p < 0.01), which is associated to a higher Ca2+ mobilization (p < 0.01). Computational analysis suggested that Eng mitigated TNFα activity. F-actin polymerization was significantly increased in ECFC Eng-siRNA, MAEC+/-, and MLEC+/- compared to controls (p < 0.001, p < 0.01, and p < 0.01, respectively) as well as actin/tubulin distribution (p < 0.01). Furthermore, the inactive form of cofilin (P-cofilin at Ser3) was significantly decreased by 36.7 ± 4.8% in ECFC Eng-siRNA compared to ctr-siRNA (p < 0.001). Interestingly, LIMKi reproduced the absence of Eng on TNFα-induced ECFC-increased permeability. Our data suggest that Eng plays a critical role in the homeostasis regulation of endothelial cells under inflammatory conditions (TNFα), and loss of Eng influences ECFC-related permeability through the LIMK/cofilin/actin rearrangement-signaling pathway.
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Affiliation(s)
- Elisa Rossi
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- IThEM, Inserm UMR-S 1140, F-75006 Paris, France
- Correspondence:
| | - Alexandre Kauskot
- HITh, UMR-S 1176, INSERM—Faculty of Medicine, University Paris-Saclay, F-94270 Le Kremlin-Bicêtre, France; (A.K.); (F.S.); (R.B.)
| | - François Saller
- HITh, UMR-S 1176, INSERM—Faculty of Medicine, University Paris-Saclay, F-94270 Le Kremlin-Bicêtre, France; (A.K.); (F.S.); (R.B.)
| | - Elisa Frezza
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- CiTCoM, CNRS, Université de Paris, F-75006 Paris, France
| | - Sonia Poirault-Chassac
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- IThEM, Inserm UMR-S 1140, F-75006 Paris, France
| | - Anna Lokajczyk
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- IThEM, Inserm UMR-S 1140, F-75006 Paris, France
| | - Pierre Bourdoncle
- Plate-Forme IMAG’IC Institut Cochin Inserm U1016-CNRS UMR8104, Université Paris Descartes, F-75006 Paris, France;
| | - Bruno Saubaméa
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- UMR-S 1144, F-75006 Paris, France
| | - Pascale Gaussem
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- IThEM, Inserm UMR-S 1140, F-75006 Paris, France
- AP-HP, Hematology Department, Hôpital Européen Georges Pompidou, F-75015 Paris, France
| | - Miguel Pericacho
- Department of Physiology and Pharmacology, Universidad de Salamanca, 37008 Salamanca, Spain;
| | - Regis Bobe
- HITh, UMR-S 1176, INSERM—Faculty of Medicine, University Paris-Saclay, F-94270 Le Kremlin-Bicêtre, France; (A.K.); (F.S.); (R.B.)
| | - Christilla Bachelot-Loza
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- IThEM, Inserm UMR-S 1140, F-75006 Paris, France
| | - Samuela Pasquali
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- CiTCoM, CNRS, Université de Paris, F-75006 Paris, France
| | - Carmelo Bernabeu
- Centro de Investigaciones Biológicas Margarita Salas, 28040 Madrid, Spain;
- Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28040 Madrid, Spain
| | - David M. Smadja
- Faculty of Pharmacy, University of Paris, F-75006 Paris, France; (E.F.); (S.P.-C.); (A.L.); (B.S.); (P.G.); (C.B.-L.); (S.P.); (D.M.S.)
- IThEM, Inserm UMR-S 1140, F-75006 Paris, France
- AP-HP, Hematology Department, Hôpital Européen Georges Pompidou, F-75015 Paris, France
- Biosurgical Research Lab (Carpentier Foundation), F-75000 Paris, France
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Effect of L- to D-Amino Acid Substitution on Stability and Activity of Antitumor Peptide RDP215 against Human Melanoma and Glioblastoma. Int J Mol Sci 2021; 22:ijms22168469. [PMID: 34445175 PMCID: PMC8395111 DOI: 10.3390/ijms22168469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022] Open
Abstract
The study investigates the antitumor effect of two cationic peptides, R-DIM-P-LF11-215 (RDP215) and the D-amino acid variant 9D-R-DIM-P-LF11-215 (9D-RDP215), targeting the negatively charged lipid phosphatidylserine (PS) exposed by cancer cells, such as of melanoma and glioblastoma. Model studies mimicking cancer and non-cancer membranes revealed the specificity for the cancer-mimic PS by both peptides with a slightly stronger impact by the D-peptide. Accordingly, membrane effects studied by DSC, leakage and quenching experiments were solely induced by the peptides when the cancer mimic PS was present. Circular dichroism revealed a sole increase in β-sheet conformation in the presence of the cancer mimic for both peptides; only 9D-RDP215 showed increased structure already in the buffer. Ex vitro stability studies by SDS-PAGE as well as in vitro with melanoma A375 revealed a stabilizing effect of D-amino acids in the presence of serum, which was also confirmed in 2D and 3D in vitro experiments on glioblastoma LN-229. 9D-RDP215 was additionally able to pass a BBB model, whereupon it induced significant levels of cell death in LN-229 spheroids. Summarized, the study encourages the introduction of D-amino acids in the design of antitumor peptides for the improvement of their stable antitumor activity.
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Tooyserkani R, Rasaee MJ, Bandehpour M, W P M Löwik D. Novel anti-PD-L1 peptide selected from combinatorial phage library inhibits tumor cell growth and restores T-cell activity. J Drug Target 2021; 29:771-782. [PMID: 33478285 DOI: 10.1080/1061186x.2021.1879087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PD-L1 overexpression on tumour cells forms a protective shield against cytotoxic T-cell killing, which consequently leads to immune evasion. Engagement of PD-1 in tumour infiltrating T cells with PD-L1 results in an exhausted T-cell phenotype, thus preventing an effective immune response against tumour cells. In the present study, we employed phage display combinatorial peptide library to discover anti-PD-L1 peptides. The peptides discovered here, could computationally exhibit specific interactions with PD-L1 at residues with which PD-1 also interacts. Binding affinity and specificity of the peptides were examined by flow cytometry. Anti- tumour activity of peptides was also investigated using several cell-based assays. Surprisingly, we demonstrated that Pep-39 can inhibit PDL-1, and reduce MDA-MB-231, CT-26, and DU-145 cells survival. In co-culture experiments, Pep-39 restored proliferation of Jurkat cells cultured in the presence of MDA-MB-231 cells. In addition, Jurkat cells apoptosis was impeded, indicating blocking potential of Pep-39 against PD-1/PD-L1 interaction.
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Affiliation(s)
- Raheleh Tooyserkani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mojgan Bandehpour
- Cellular & Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Dennis W P M Löwik
- Institute for Molecules and Materials, Radboud University Nijmegen, AJ Nijmegen, The Netherlands
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Dasmeh P, Wagner A. Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution. Mol Biol Evol 2021; 38:940-951. [PMID: 33022038 PMCID: PMC7947763 DOI: 10.1093/molbev/msaa258] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein phase separation can help explain the formation of many nonmembranous organelles. However, we know little about its ability to change in evolution. Here we studied the evolution of the mammalian RNA-binding protein Fused in Sarcoma (FUS), a protein whose prion-like domain (PLD) contributes to the formation of stress granules through liquid–liquid phase separation. Although the PLD evolves three times as rapidly as the remainder of FUS, it harbors absolutely conserved tyrosine residues that are crucial for phase separation. Ancestral reconstruction shows that the phosphorylation sites within the PLD are subject to stabilizing selection. They toggle among a small number of amino acid states. One exception to this pattern is primates, where the number of such phosphosites has increased through positive selection. In addition, we find frequent glutamine to proline changes that help maintain the unstructured state of FUS that is necessary for phase separation. Our work provides evidence that natural selection has stabilized the liquid forming potential of FUS and minimized the propensity of cytotoxic liquid-to-solid phase transitions during 160 My of mammalian evolution.
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Affiliation(s)
- Pouria Dasmeh
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andreas Wagner
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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BING, a novel antimicrobial peptide isolated from Japanese medaka plasma, targets bacterial envelope stress response by suppressing cpxR expression. Sci Rep 2021; 11:12219. [PMID: 34108601 PMCID: PMC8190156 DOI: 10.1038/s41598-021-91765-4] [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] [Received: 02/26/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) have emerged as a promising alternative to small molecule antibiotics. Although AMPs have previously been isolated in many organisms, efforts on the systematic identification of AMPs in fish have been lagging. Here, we collected peptides from the plasma of medaka (Oryzias latipes) fish. By using mass spectrometry, 6399 unique sequences were identified from the isolated peptides, among which 430 peptides were bioinformatically predicted to be potential AMPs. One of them, a thermostable 13-residue peptide named BING, shows a broad-spectrum toxicity against pathogenic bacteria including drug-resistant strains, at concentrations that presented relatively low toxicity to mammalian cell lines and medaka. Proteomic analysis indicated that BING treatment induced a deregulation of periplasmic peptidyl-prolyl isomerases in gram-negative bacteria. We observed that BING reduced the RNA level of cpxR, an upstream regulator of envelope stress responses. cpxR is known to play a crucial role in the development of antimicrobial resistance, including the regulation of genes involved in drug efflux. BING downregulated the expression of efflux pump components mexB, mexY and oprM in P. aeruginosa and significantly synergised the toxicity of antibiotics towards these bacteria. In addition, exposure to sublethal doses of BING delayed the development of antibiotic resistance. To our knowledge, BING is the first AMP shown to suppress cpxR expression in Gram-negative bacteria. This discovery highlights the cpxR pathway as a potential antimicrobial target.
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Obaidullah AJ, Alanazi MM, Alsaif NA, Albassam H, Almehizia AA, Alqahtani AM, Mahmud S, Sami SA, Emran TB. Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2. RSC Adv 2021; 11:18103-18121. [PMID: 35480208 PMCID: PMC9033181 DOI: 10.1039/d1ra02885e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a contagious respiratory tract infection that has become a global burden since the end of 2019. Notably, fewer patients infected with SARS-CoV-2 progress from acute disease onset to death compared with the progression rate associated with two other coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Several research organizations and pharmaceutical industries have attempted to develop successful vaccine candidates for the prevention of COVID-19. However, increasing evidence indicates that the SARS-CoV-2 genome undergoes frequent mutation; thus, an adequate analysis of the viral strain remains necessary to construct effective vaccines. The current study attempted to design a multi-epitope vaccine by utilizing an approach based on the SARS-CoV-2 structural proteins. We predicted the antigenic T- and B-lymphocyte responses to four structural proteins after screening all structural proteins according to specific characteristics. The predicted epitopes were combined using suitable adjuvants and linkers, and a secondary structure profile indicated that the vaccine shared similar properties with the native protein. Importantly, the molecular docking analysis and molecular dynamics simulations revealed that the constructed vaccine possessed a high affinity for toll-like receptor 4 (TLR4). In addition, multiple descriptors were obtained from the simulation trajectories, including the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (R g), demonstrating the rigid nature and inflexibility of the vaccine and receptor molecules. In addition, codon optimization, based on Escherichia coli K12, was used to determine the GC content and the codon adaptation index (CAI) value, which further followed for the incorporation into the cloning vector pET28+(a). Collectively, these findings suggested that the constructed vaccine could be used to modulate the immune reaction against SARS-CoV-2.
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Affiliation(s)
- Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Nawaf A Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Hussam Albassam
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Abdulrahman A Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University Abha 62529 Saudi Arabia
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi Rajshahi 6205 Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong Chittagong 4331 Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh Chittagong 4381 Bangladesh
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65
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Mahmud S, Paul GK, Biswas S, Afrose S, Mita MA, Hasan MR, Shimu MSS, Hossain A, Promi MM, Ema FK, Chidambaram K, Chandrasekaran B, Alqahtani AM, Emran TB, Saleh MA. Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2. Front Mol Biosci 2021; 8:628585. [PMID: 34041263 PMCID: PMC8142691 DOI: 10.3389/fmolb.2021.628585] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/22/2021] [Indexed: 12/12/2022] Open
Abstract
The recently emerged coronavirus (SARS-CoV-2) has created a crisis in world health, and economic sectors as an effective treatment or vaccine candidates are still developing. Besides, negative results in clinical trials and effective cheap solution against this deadly virus have brought new challenges. The viral protein, the main protease from SARS-CoV-2, can be effectively targeted due to its viral replication and pathogenesis role. In this study, we have enlisted 88 peptides from the AVPdb database. The peptide molecules were modeled to carry out the docking interactions. The four peptides molecules, P14, P39, P41, and P74, had more binding energy than the rest of the peptides in multiple docking programs. Interestingly, the active points of the main protease from SARS-CoV-2, Cys145, Leu141, Ser139, Phe140, Leu167, and Gln189, showed nonbonded interaction with the peptide molecules. The molecular dynamics simulation study was carried out for 200 ns to find out the docked complex’s stability where their stability index was proved to be positive compared to the apo and control complex. Our computational works based on peptide molecules may aid the future development of therapeutic options against SARS-CoV-2.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Fahmida Khan Ema
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Balakumar Chandrasekaran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Philadelphia University-Jordan, Amman, Jordan
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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66
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A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing. MATHEMATICAL AND COMPUTATIONAL APPLICATIONS 2021. [DOI: 10.3390/mca26020039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.
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67
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Ropero-Vega JL, Redondo-Ortega JF, Galvis-Curubo YJ, Rondón-Villarreal P, Flórez-Castillo JM. A Bioinspired Peptide in TIR Protein as Recognition Molecule on Electrochemical Biosensors for the Detection of E. coli O157:H7 in an Aqueous Matrix. Molecules 2021; 26:molecules26092559. [PMID: 33924762 PMCID: PMC8124904 DOI: 10.3390/molecules26092559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/06/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Currently, the detection of pathogens such as Escherichia coli through instrumental alternatives with fast response and excellent sensitivity and selectivity are being studied. Biosensors are systems consisting of nanomaterials and biomolecules that exhibit remarkable properties such as simplicity, portable, affordable, user‑friendly, and deliverable to end‑users. For this, in this work we report for the first time, to our knowledge, the bioinformatic design of a new peptide based on TIR protein, a receptor of Intimin membrane protein which is characteristic of E. coli. This peptide (named PEPTIR‑1.0) was used as recognition element in a biosensor based on AuNPs‑modified screen‑printed electrodes for the detection of E. coli. The morphological and electrochemical characteristics of the biosensor obtained were studied. Results show that the biosensor can detect the bacteria with limits of detection and quantification of 2 and 6 CFU/mL, respectively. Moreover, the selectivity of the system is statistically significant towards the detection of the pathogen in the presence of other microorganisms such as P. aeruginosa and S. aureus. This makes this new PEPTIR‑1.0 based biosensor can be used in the rapid, sensitive, and selective detection of E. coli in aqueous matrices.
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Affiliation(s)
- Jose Luis Ropero-Vega
- Facultad de Ciencias Exactas, Naturales y Agropecuarias, Ciencias Básicas y Aplicadas Para la Sostenibilidad—CIBAS, Universidad de Santander, Calle 70 No. 55-210, Bucaramanga C.P. 680003, Santander, Colombia; (Y.J.G.-C.); (J.M.F.-C.)
- Correspondence: (J.L.R.-V.); (J.F.R.-O.); Tel.: +57-7-6516500 (ext. 1665) (J.L.R.-V.)
| | - Joshua Felipe Redondo-Ortega
- Facultad de Ciencias Exactas, Naturales y Agropecuarias, Ciencias Básicas y Aplicadas Para la Sostenibilidad—CIBAS, Universidad de Santander, Calle 70 No. 55-210, Bucaramanga C.P. 680003, Santander, Colombia; (Y.J.G.-C.); (J.M.F.-C.)
- Correspondence: (J.L.R.-V.); (J.F.R.-O.); Tel.: +57-7-6516500 (ext. 1665) (J.L.R.-V.)
| | - Yuli Juliana Galvis-Curubo
- Facultad de Ciencias Exactas, Naturales y Agropecuarias, Ciencias Básicas y Aplicadas Para la Sostenibilidad—CIBAS, Universidad de Santander, Calle 70 No. 55-210, Bucaramanga C.P. 680003, Santander, Colombia; (Y.J.G.-C.); (J.M.F.-C.)
| | - Paola Rondón-Villarreal
- Facultad de Ciencias de la Salud, Grupo de Investigación en Biología Molecular y Biotecnología, Universidad de Santander, Calle 70 No. 55-210, Bucaramanga C.P. 680003, Santander, Colombia;
| | - Johanna Marcela Flórez-Castillo
- Facultad de Ciencias Exactas, Naturales y Agropecuarias, Ciencias Básicas y Aplicadas Para la Sostenibilidad—CIBAS, Universidad de Santander, Calle 70 No. 55-210, Bucaramanga C.P. 680003, Santander, Colombia; (Y.J.G.-C.); (J.M.F.-C.)
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Hashemi ZS, Zarei M, Fath MK, Ganji M, Farahani MS, Afsharnouri F, Pourzardosht N, Khalesi B, Jahangiri A, Rahbar MR, Khalili S. In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions. Front Mol Biosci 2021; 8:669431. [PMID: 33996914 PMCID: PMC8113820 DOI: 10.3389/fmolb.2021.669431] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Large contact surfaces of protein-protein interactions (PPIs) remain to be an ongoing issue in the discovery and design of small molecule modulators. Peptides are intrinsically capable of exploring larger surfaces, stable, and bioavailable, and therefore bear a high therapeutic value in the treatment of various diseases, including cancer, infectious diseases, and neurodegenerative diseases. Given these promising properties, a long way has been covered in the field of targeting PPIs via peptide design strategies. In silico tools have recently become an inevitable approach for the design and optimization of these interfering peptides. Various algorithms have been developed to scrutinize the PPI interfaces. Moreover, different databases and software tools have been created to predict the peptide structures and their interactions with target protein complexes. High-throughput screening of large peptide libraries against PPIs; "hotspot" identification; structure-based and off-structure approaches of peptide design; 3D peptide modeling; peptide optimization strategies like cyclization; and peptide binding energy evaluation are among the capabilities of in silico tools. In the present study, the most recent advances in the field of in silico approaches for the design of interfering peptides against PPIs will be reviewed. The future perspective of the field and its advantages and limitations will also be pinpointed.
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Affiliation(s)
- Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, Academic Center for Education, Culture and Research, Tehran, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahboube Shahrabi Farahani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Afsharnouri
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Department of Biochemistry, Guilan University of Medical Sciences, Rasht, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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69
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Onime LA, Oyama LB, Thomas BJ, Gani J, Alexander P, Waddams KE, Cookson A, Fernandez-Fuentes N, Creevey CJ, Huws SA. The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential. BMC Microbiol 2021; 21:105. [PMID: 33832427 PMCID: PMC8034185 DOI: 10.1186/s12866-021-02172-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The rise of microbial antibiotic resistance is a leading threat to the health of the human population. As such, finding new approaches to tackle these microbes, including development of novel antibiotics is vital. RESULTS In this study, we mined a rumen eukaryotic metatranscriptomic library for novel Antimicrobial peptides (AMPs) using computational approaches and thereafter characterised the therapeutic potential of the AMPs. We identified a total of 208 potentially novel AMPs from the ruminal eukaryotome, and characterised one of those, namely Lubelisin. Lubelisin (GIVAWFWRLAR) is an α-helical peptide, 11 amino acid long with theoretical molecular weight of 1373.76 D. In the presence of Lubelisin, strains of methicillin-resistant Staphylococcus aureus (MRSA) USA300 and EMRSA-15 were killed within 30 min of exposure with ≥103 and 104 CFU/mL reduction in viable cells respectively. Cytotoxicity of Lubelisin against both human and sheep erythrocytes was low resulting in a therapeutic index of 0.43. Membrane permeabilisation assays using propidium iodide alongside transmission electron microscopy revealed that cytoplasmic membrane damage may contribute to the antimicrobial activities of Lubelisin. CONCLUSIONS We demonstrate that the rumen eukaryotome is a viable source for the discovery of antimicrobial molecules for the treatment of bacterial infections and further development of these may provide part of the potential solution to the ongoing problem of antimicrobial resistance. The role of these AMPs in the ecological warfare within the rumen is also currently unknown.
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Affiliation(s)
- Lucy A Onime
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Linda B Oyama
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Benjamin J Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Jurnorain Gani
- Institute of Infection and Immunity, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Peter Alexander
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Kate E Waddams
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Alan Cookson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK
| | - Sharon A Huws
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, Northern Ireland, BT9 5DL, UK.
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70
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Raza MT, Mizan S, Yasmin F, Akash AS, Shahik SM. Epitope-based universal vaccine for Human T-lymphotropic virus-1 (HTLV-1). PLoS One 2021; 16:e0248001. [PMID: 33798232 PMCID: PMC8018625 DOI: 10.1371/journal.pone.0248001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/17/2021] [Indexed: 12/26/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) was the first oncogenic human retrovirus identified in humans which infects at least 10-15 million people worldwide. Large HTLV-1 endemic areas exist in Southern Japan, the Caribbean, Central and South America, the Middle East, Melanesia, and equatorial regions of Africa. HTLV-1 TAX viral protein is thought to play a critical role in HTLV-1 associated diseases. We have used numerous bio-informatics and immuno-informatics implements comprising sequence and construction tools for the construction of a 3D model and epitope prediction for HTLV-1 Tax viral protein. The conformational linear B-cell and T-cell epitopes for HTLV-1 TAX viral protein have been predicted for their possible collective use as vaccine candidates. Based on in silico investigation two B cell epitopes, KEADDNDHEPQISPGGLEPPSEKHFR and DGTPMISGPCPKDGQPS spanning from 324-349 and 252-268 respectively; and T cell epitopes, LLFGYPVYV, ITWPLLPHV and GLLPFHSTL ranging from 11-19, 163-171 and 233-241 were found most antigenic and immunogenic epitopes. Among different vaccine constructs generated by different combinations of these epitopes our predicted vaccine construct was found to be most antigenic with a score of 0.57. T cell epitopes interacted strongly with HLA-A*0201 suggesting a significant immune response evoked by these epitopes. Molecular docking study also showed a high binding affinity of the vaccine construct for TLR4. The study was carried out to predict antigenic determinants of the Tax protein along with the 3D protein modeling. The study revealed a potential multi epitope vaccine that can raise the desired immune response against HTLV-1 and be useful in developing effective vaccines against Human T-lymphotropic virus.
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Affiliation(s)
- Md. Thosif Raza
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Shagufta Mizan
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Farhana Yasmin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Al-Shahriar Akash
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Shah Md. Shahik
- Bioinformatics Division, Disease Biology and Molecular Epidemiology Research Group, Chattogram, Bangladesh
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Chukwudozie OS, Gray CM, Fagbayi TA, Chukwuanukwu RC, Oyebanji VO, Bankole TT, Adewole RA, Daniel EM. Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein. PLoS One 2021; 16:e0248061. [PMID: 33730022 PMCID: PMC7968690 DOI: 10.1371/journal.pone.0248061] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
Developing an efficacious vaccine for SARS-CoV-2 infection is critical to stemming COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in designing an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers and 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC I and II alleles, respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. With our In silico test, the vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was also characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We, therefore, propose that potential vaccine designs consider this approach.
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Affiliation(s)
| | - Clive M. Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tawakalt A. Fagbayi
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Rebecca C. Chukwuanukwu
- Immunology Unit, Medical Laboratory Science Department, Nnamdi Azikiwe University, Nnewi, Nigeria
| | - Victor O. Oyebanji
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
| | - Taiwo T. Bankole
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Richard A. Adewole
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | - Eze M. Daniel
- Public Health Biotechnology Unit, Institute of Child Health, University College Hospital, University of Ibadan, Ibadan, Nigeria
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72
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Gaurav N, Tripathi PK, Kumar V, Chugh A, Sundd M, Patel AK. Role of nuclear localization signals in the DNA delivery function of Chikungunya virus capsid protein. Arch Biochem Biophys 2021; 702:108822. [PMID: 33722536 DOI: 10.1016/j.abb.2021.108822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Capsids of several RNA viruses are reported to have unconventional roles attributed to their subcellular trafficking property. The capsid of CHIKV is also found to localize in the nucleus, but the rationale is not yet clear. To understand the role of the nuclear-localized capsid, we examined the nucleic acid binding and cargo delivery activity of the CHIKV capsid. We used bacterially purified capsid protein to probe the binding affinity with CHIKV genome-specific and non-specific nucleic acids. We found that the capsid was able to bind non-specifically to different forms of nucleic acids. The successful transfection of GFP-tagged plasmid DNA by CHIKV capsid protein shows the DNA delivery ability of the protein. Further, we selected and investigated the DNA binding and cargo delivery activity of commercially synthesized Nuclear Localization Signal sequences (NLS 1 and NLS2) of capsid protein. Both peptides showed comparable DNA binding affinity, however, only the NLS1 peptide was capable of delivering plasmid DNA inside the cell. Furthermore, the cellular uptake study using the FITC-labelled NLS1 peptide was performed to highlight the membrane penetrating ability. Structural analysis was performed using circular dichroism and NMR spectroscopy to elucidate the transfection ability of the NLS1 peptides. Our findings suggest that the capsid of CHIKV might influence cellular trafficking in the infected cell via non-specific interactions. Our study also indicates the significance of NLS sequences in the multifunctionality of CHIKV capsid protein.
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Affiliation(s)
- Nitika Gaurav
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Praveen Kumar Tripathi
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Vivek Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110067, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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73
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Pandey RK, Dikhit MR, Lokhande KB, Pandey K, Das P, Bimal S. An immunoprophylactic evaluation of Ld-ODC derived HLA-A0201 restricted peptides against visceral leishmaniasis. J Biomol Struct Dyn 2021; 40:6086-6096. [PMID: 33602055 DOI: 10.1080/07391102.2021.1876773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Five (5) HLA-A 0201 restricted epitopes of ornithine decarboxylase derived from Leishmania donovani (Ld-ODC) were examined by reverse vaccinology to develop prophylactics against visceral leishmaniasis (VL). These consensus epitopes comprising (P1: RLMPSAHAI, P2: LLDQYQIHL, P3: GLYHSFNCI, P4: AVLEVLSAL and P5: RLPASPAAL) were observed and presented by diverse HLA alleles screened by immune-informatics tools. These epitopes were also observed for strong stability for appropriate immune response in in silico screening and molecular dynamics. Top five selected epitopes filtered from population coverage analysis and TAP binding affinity were identified and evaluated against treated cases of VL subjects. Experiments were run individually with synthetic peptides or as the cocktail of peptides. A major population of CD8+ T cells were predominantly IFN-γ producers but not the IL-10 cytokines and shown with granzyme-B activity. Therefore, it can be concluded that the screened HLA-A0201 restricted epitope hotspots derived from Leishmania ODC can trigger CD8+ T cells, which can skew other immune cells functions toward protection. However, a detailed analysis can explore its potentiality as a vaccine candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Raj Kishor Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research, Hajipur, India.,Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Kiran Bharat Lokhande
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Sanjiva Bimal
- Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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74
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Rehman Z, Fahim A, Bhatti MF. Scouting the receptor-binding domain of SARS coronavirus 2: a comprehensive immunoinformatics inquisition. Future Virol 2021. [PMCID: PMC7899787 DOI: 10.2217/fvl-2020-0269] [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: 12/24/2022]
Abstract
Aim: December 2019 witnessed the emergence of a worldwide outbreak of a novel strain of coronavirus (CoV) termed SARS-CoV-2. Several preventive strategies are being developed, such as vaccines, to stop the spread of infection. Materials & methods: A comprehensive immunoinformatics approach was used to map conserved peptide sequences on the receptor binding domain of SARS-CoV-2 for their B-cell, T-helper & T-cytotoxic cell epitope profiles. Results & conclusion: The antigenic B-cell epitopes were LFRKSN and SYGFQPT. Among T-cell epitopes, CVADYSVLY and FTNVYADSF exhibited affinity for MHC class I, while YRLFRKSNL and VYAWNRKRI exhibited affinity for of MHC class II alleles. The overlapping epitope between B- and T-cells was YRLFRKSNL. The deployment of these epitopes in potential vaccine development against COVID-19 may help in slowing down the SARS-CoV-2 spread.
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Affiliation(s)
- Zaira Rehman
- Department of Virology, National Institute of Health (NIH), Islamabad, Pakistan
| | - Ammad Fahim
- Department of Multidisciplinary Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB),National University of Sciences & Technology (NUST), Sector H-12, Islamabad, Pakistan
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75
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Immuno-informatics approach for B-cell and T-cell epitope based peptide vaccine design against novel COVID-19 virus. Vaccine 2021; 39:1087-1095. [PMID: 33478787 PMCID: PMC7796797 DOI: 10.1016/j.vaccine.2021.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/08/2020] [Accepted: 01/04/2021] [Indexed: 02/02/2023]
Abstract
COVID-19 has brought the world to a standstill with a wave of destruction in country after country with tremendous loss of lives and livelihood in advanced to developing nations. Whole world is staring at the prospect of repeated lockdowns with another wave of COVID-19 predicted to hit the world in September of 2020. The second wave is assumed to be even more destructive with severe impact across much of the world. The only way to defeat this pandemic is to quickly develop a safe and effective vaccine against this raging menace and initiate a global vaccination drive. Our study is an attempt to deploy various computational methods to identify B-cell and T-cell epitopes from the spike surface glycoprotein of SARS-COV-2 which have the novel potential for vaccine development against COVID-19. For this we have taken 8 unique strains with one each from India, China, France, USA, Italy, Australia, Iran and Pakistan. The strain data was extracted from NCBI Database. By analyzing the immune parameters like surface accessibility, antigenicity, variability, conservancy, flexibility, hydrophilicity, allergenicity and toxicity of the conserved sequences of spike glycoprotein using various databases and bioinformatics tools, we identified two potential novel linear (SGTNGTKRFDN and ASVYAWNRK) and one structural B-cell epitope as well as two T-cell epitopes (RLFRKSNLK and IPTNFTISV) which can be used as epitope-based peptide vaccines. Docking simulation assay revealed that above T-cell epitopes have minimum free binding energy and showed strong hydrogen bond interaction which strengthened its potential as being a T-cell epitope for the epitope-based novel vaccine against SARS-CoV-2. This study allows us to claim that B-cell and T-cell epitopes mentioned above provide potential pathways for developing an exploratory vaccine against spike surface glycoprotein of SARS-CoV-2 with high confidence for the identified strains. We will need to confirm our findings with biological assays.
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76
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Chen Z, Ruan P, Wang L, Nie X, Ma X, Tan Y. T and B cell Epitope analysis of SARS-CoV-2 S protein based on immunoinformatics and experimental research. J Cell Mol Med 2021; 25:1274-1289. [PMID: 33325143 PMCID: PMC7812294 DOI: 10.1111/jcmm.16200] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/22/2020] [Accepted: 11/28/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 is pandemic with a severe morbidity and mortality rate across the world. Despite the race for effective vaccine and drug against further expansion and fatality rate of this novel coronavirus, there is still lack of effective antiviral therapy. To this effect, we deemed it necessary to identify potential B and T cell epitopes from the envelope S protein. This can be used as potential targets to develop anti-SARS-CoV-2 vaccine preparations. In this study, we used immunoinformatics to identify conservative B and T cell epitopes for S proteins of SARS-CoV-2, which might play roles in the initiation of SARS-CoV-2 infection. We identified the B cell and T cell peptide epitopes of S protein and their antigenicity, as well as the interaction between the peptide epitopes and human leucocyte antigen (HLA). Among the B cell epitopes, 'EILDITPCSFGGVS' has the highest score of antigenicity and great immunogenicity. In T cell epitopes, MHC-I peptide 'KIADYNYKL' and MHC-II peptide 'LEILDITPC' were identified as high antigens. Besides, docking analysis showed that the predicted peptide 'KIADYNYKL' was closely bound to the HLA-A*0201. The results of molecular dynamics simulation through GROMACS software showed that 'HLA-A*0201~peptide' complex was very stable. And the peptide we selected could induce the T cell response similar to that of SARS-CoV-2 infection. Moreover, the predicted peptides were highly conserved in different isolates from different countries. The antigenic epitopes presumed in this study were effective new vaccine targets to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Ziwei Chen
- Department of Medical MicrobiologyXiangya School of MedicineCentral South UniversityChangshaChina
- Department of Clinical LaboratoryThird Xiangya HospitalCentral South UniversityChangshaChina
- Department of NHC Key Laboratory of Medical Virology and Viral DiseasesNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Pinglang Ruan
- Department of Medical MicrobiologyXiangya School of MedicineCentral South UniversityChangshaChina
| | - Lili Wang
- Department of Medical MicrobiologyXiangya School of MedicineCentral South UniversityChangshaChina
| | - Xinmin Nie
- Department of Clinical LaboratoryThird Xiangya HospitalCentral South UniversityChangshaChina
| | - Xuejun Ma
- Department of NHC Key Laboratory of Medical Virology and Viral DiseasesNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Yurong Tan
- Department of Medical MicrobiologyXiangya School of MedicineCentral South UniversityChangshaChina
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77
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Kurabi A, Cooper M, Spriggs M, Xu Y, Schaerer D, Ryan AF. Molecular Screening Strategy to Identify a Non-invasive Delivery Mechanism for the Treatment of Middle Ear Disorders. Front Med (Lausanne) 2020; 7:503819. [PMID: 33392211 PMCID: PMC7775502 DOI: 10.3389/fmed.2020.503819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Middle ear ailments include a broad range of pathological conditions. Otitis media is the leading middle ear disease of childhood, which incurs significant health care resources in developed countries and, in developing countries, causes significant mortality and morbidity. Recurrent and chronic infections of the middle ear lead to the prolonged presence of inflammatory factors and cellular infiltrates resulting in temporary hearing loss. However, long-term alteration of the middle ear space can pose the risk of permanent damage to the delicate ear structures and cause tissue remodeling. While the etiopathogenesis of middle ear diseases is multifactorial, targeting the biological mechanisms and molecular networks that drive disease development is critical. Yet, a pivotal step in realizing the potential of molecular therapies is the development of methods for local drug delivery, since systemic application risks side effects. Utilizing bacteriophage display in the rat, we discovered rare peptides that are able to transit the intact tympanic membrane from the external canal to the middle ear cavity by an active process. An in vitro assay demonstrated that transport occurs across the tympanic membranes of humans and that the peptides cross the membrane independent of phage. Transport of phage, which is ~900 nm in length, suggests that these peptides could non-invasively deliver drug packages or gene therapy vectors into the middle ear.
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Affiliation(s)
- Arwa Kurabi
- Department of Surgery/Otolaryngology, UCSD School of Medicine, San Diego, CA, United States
| | - Molly Cooper
- Department of Surgery/Otolaryngology, UCSD School of Medicine, San Diego, CA, United States
| | - Meghan Spriggs
- Department of Surgery/Otolaryngology, UCSD School of Medicine, San Diego, CA, United States
| | - Yuge Xu
- Department of Surgery/Otolaryngology, UCSD School of Medicine, San Diego, CA, United States
| | - Daniel Schaerer
- Department of Surgery/Otolaryngology, UCSD School of Medicine, San Diego, CA, United States
| | - Allen F Ryan
- Department of Surgery/Otolaryngology, UCSD School of Medicine, San Diego, CA, United States.,Department of Neurosciences, UCSD School of Medicine, San Diego, CA, United States.,San Diego VA Healthcare System, San Diego, CA, United States
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78
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Pirkhezranian Z, Tahmoorespur M, Monhemi H, Sekhavati MH. Computational Peptide Engineering Approach for Selection the Best Engendered Camel Lactoferrin-Derive Peptide with Potency to Interact with DNA. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-10012-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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79
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Ross JN, Fields FR, Kalwajtys VR, Gonzalez AJ, O’Connor S, Zhang A, Moran TE, Hammers DE, Carothers KE, Lee SW. Synthetic Peptide Libraries Designed From a Minimal Alpha-Helical Domain of AS-48-Bacteriocin Homologs Exhibit Potent Antibacterial Activity. Front Microbiol 2020; 11:589666. [PMID: 33281785 PMCID: PMC7689250 DOI: 10.3389/fmicb.2020.589666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022] Open
Abstract
The circularized bacteriocin enterocin AS-48 produced by Enterococcus sp. exhibits antibacterial activity through membrane disruption. The membrane-penetrating activity of enterocin AS-48 has been attributed to a specific alpha-helical region on the circular peptide. Truncated, linearized forms containing these domains have been shown to preserve limited bactericidal activity. We utilized the amino acid sequence of the active helical domain of enterocin AS-48 to perform a homology-based search of similar sequences in other bacterial genomes. We identified similar domains in three previously uncharacterized AS-48-like bacteriocin genes in Clostridium sordellii, Paenibacillus larvae, and Bacillus xiamenensis. Enterocin AS-48 and homologs from these bacterial species were used as scaffolds for the design of a minimal peptide library based on the active helical domain of each bacteriocin sequence. 95 synthetic peptide variants of each scaffold peptide, designated Syn-enterocin, Syn-sordellicin, Syn-larvacin, and Syn-xiamensin, were designed and synthesized from each scaffold sequence based on defined biophysical parameters. A total of 384 total peptides were assessed for antibacterial activity against Gram-negative and Gram-positive bacteria. Minimal Inhibitory Concentrations (MICs) as low as 15.6 nM could be observed for the most potent peptide candidate tested, with no significant cytotoxicity to eukaryotic cells. Our work demonstrates for the first time a general workflow of using minimal domains of natural bacteriocin sequences as scaffolds to design and rapidly synthesize a library of bacteriocin-based antimicrobial peptide variants for evaluation.
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Affiliation(s)
- Jessica N. Ross
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Francisco R. Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Veronica R. Kalwajtys
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Alejandro J. Gonzalez
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Samantha O’Connor
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Angela Zhang
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Thomas E. Moran
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Daniel E. Hammers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Katelyn E. Carothers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Shaun W. Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
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80
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Zheng W, Lan J, Feng L, Chen Z, Feng S, Gao Y, Ren F, Chen Y. Structure-Based Optimization of Conformationally Constrained Peptides to Target Esophageal Cancer TEAD Transcription Factor. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10138-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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81
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Rakib A, Sami SA, Islam MA, Ahmed S, Faiz FB, Khanam BH, Marma KKS, Rahman M, Uddin MMN, Nainu F, Emran TB, Simal-Gandara J. Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2. Molecules 2020; 25:E5088. [PMID: 33147821 PMCID: PMC7663370 DOI: 10.3390/molecules25215088] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Md. Ashiqul Islam
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
- Department of Pharmacy, Mawlana Bhashani Science & Technology University, Santosh, Tangail 1902, Bangladesh
| | - Shahriar Ahmed
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Farhana Binta Faiz
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Bibi Humayra Khanam
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Kay Kay Shain Marma
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Maksuda Rahman
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan 90245, Indonesia;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain
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82
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Hu K, Xie L, Hanyu M, Zhang Y, Li L, Ma X, Nagatsu K, Suzuki H, Wang W, Zhang MR. Harnessing the PD-L1 interface peptide for positron emission tomography imaging of the PD-1 immune checkpoint. RSC Chem Biol 2020; 1:214-224. [PMID: 34458761 PMCID: PMC8341843 DOI: 10.1039/d0cb00070a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/04/2020] [Indexed: 12/18/2022] Open
Abstract
Interface peptides that mediate protein–protein interactions (PPI) are a class of important lead compounds for designing PPI inhibitors. However, their potential as precursors for radiotracers has never been exploited. Here we report that the interface peptides from programmed death-ligand 1 (PD-L1) can be used in positron emission tomography (PET) imaging of programmed cell death 1 (PD-1) with high accuracy and sensitivity. Moreover, the performance differentiation between murine PD-L1 derived interface peptide (mPep-1) and human PD-L1 derived interface peptide (hPep-1) as PET tracers for PD-1 unveiled an unprecedented role of a non-critical residue in target binding, highlighting the significance of PET imaging as a companion diagnostic in drug development. Collectively, this study not only provided a first-of-its-kind peptide-based PET tracer for PD-1 but also conveyed a unique paradigm for developing imaging agents for highly challenging protein targets, which could be used to identify other protein biomarkers involved in the PPI networks. Leveraging interface peptides in PD-L1 for PET imaging of PD-1, providing a new paradigm for radiotracer development.![]()
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Affiliation(s)
- Kuan Hu
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
| | - Lin Xie
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
| | - Masayuki Hanyu
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
| | - Yiding Zhang
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
| | - Lingyun Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 P. R. China
| | - Xiaohui Ma
- Department of Vascular Surgery, General Hospital of People's Liberation Army Beijing 100853 P. R. China
| | - Kotaro Nagatsu
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
| | - Hisashi Suzuki
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
| | - Weizhi Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 P. R. China
| | - Ming-Rong Zhang
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology Chiba, 263-8555 Japan
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Sunita, Singhvi N, Singh Y, Shukla P. Computational approaches in epitope design using DNA binding proteins as vaccine candidate in Mycobacterium tuberculosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 83:104357. [PMID: 32438080 DOI: 10.1016/j.meegid.2020.104357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a successful pathogen in the history of mankind. A high rate of mortality and morbidity raises the need for vaccine development. Mechanism of pathogenesis, survival strategy and virulence determinant are needed to be explored well for this pathogen. The involvement of DNA binding proteins in the regulation of virulence genes, transcription, DNA replication, repair make them more significant. In present work, we have identified 1453 DNA binding proteins (DBPs) in the 4173 genes of Mtb through the DNABIND tool and they were subjected for further screening by incorporating different bioinformatics tools. The eighteen DBPs were selected for the B-cell epitope prediction by using ABCpred server. Moreover, the B-cell epitope bearing the antigenic and non- allergenic property were selected for T-cell epitope prediction using ProPredI, and ProPred server. Finally, DGIGSAVSV (Rv1088), IRALPSSRH (Rv3923c), LTISPIANS (Rv3235), VQPSGKGGL (Rv2871) VPRPGPRPG (Rv2731) and VGQKINPHG (Rv0707) were identified as T-cell epitopes. The structural modelling of these epitopes and DBPs was performed to ensure the localization of these epitopes on the respective proteins. The interaction studies of these epitopes with human HLA confirmed their validation to be used as potential vaccine candidates. Collectively, these results revealed that the DBPs- Rv2731, Rv3235, Rv1088, Rv0707, Rv3923c and Rv2871 are the most appropriate vaccine candidates. In our knowledge, it is the first report of using the DBPs of Mtb for epitope prediction. Significantly, this study also provides evidence to be useful for designing a peptide-based vaccine against tuberculosis.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India; Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Nirjara Singhvi
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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84
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Rakib A, Sami SA, Mimi NJ, Chowdhury MM, Eva TA, Nainu F, Paul A, Shahriar A, Tareq AM, Emon NU, Chakraborty S, Shil S, Mily SJ, Ben Hadda T, Almalki FA, Emran TB. Immunoinformatics-guided design of an epitope-based vaccine against severe acute respiratory syndrome coronavirus 2 spike glycoprotein. Comput Biol Med 2020; 124:103967. [PMID: 32828069 PMCID: PMC7423576 DOI: 10.1016/j.compbiomed.2020.103967] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/08/2020] [Accepted: 08/08/2020] [Indexed: 02/07/2023]
Abstract
AIMS With a large number of fatalities, coronavirus disease-2019 (COVID-19) has greatly affected human health worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19. The World Health Organization has declared a global pandemic of this contagious disease. Researchers across the world are collaborating in a quest for remedies to combat this deadly virus. It has recently been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator by which the virus enters host cells. MAIN METHODS Our group comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis and a phylogenetic analysis. We predicted the strongest immunogenic epitopes of the SGP for both B cells and T cells. KEY FINDINGS We focused on predicting peptides that would bind major histocompatibility complex class I. Two optimal epitopes were identified, WTAGAAAYY and GAAAYYVGY. They interact with the HLA-B*15:01 allele, which was further validated by molecular docking simulation. This study also found that the selected epitopes are able to be recognized in a large percentage of the world's population. Furthermore, we predicted CD4+ T-cell epitopes and B-cell epitopes. SIGNIFICANCE Our study provides a strong basis for designing vaccine candidates against SARS-CoV-2. However, laboratory work is required to validate our theoretical results, which would lay the foundation for the appropriate vaccine manufacturing and testing processes.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Vaccines
- Computational Biology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Drug Design
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- HLA-B15 Antigen/chemistry
- HLA-B15 Antigen/metabolism
- HLA-DRB1 Chains/chemistry
- HLA-DRB1 Chains/metabolism
- Humans
- Molecular Docking Simulation
- Pandemics/prevention & control
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/immunology
- Viral Vaccines/chemistry
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nusrat Jahan Mimi
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Md Mustafiz Chowdhury
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Taslima Akter Eva
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan, 90245, Indonesia
| | - Arkajyoti Paul
- Drug Discovery, GUSTO A Research Group, Chittagong, 4203, Bangladesh; Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Asif Shahriar
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217, Bangladesh
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Nazim Uddin Emon
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Sajal Chakraborty
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Sagar Shil
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh
| | - Sabrina Jahan Mily
- Department of Gynaecology and Obstetrics, Banshkhali Upazila Health Complex, Jaldi Union, Chittagong, 4390, Bangladesh
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, University Mohammed the First, BP 524, 60000, Oujda, Morocco; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, 21955, Saudi Arabia.
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, 21955, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh.
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85
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Kennedy K, Cal R, Casey R, Lopez C, Adelfio A, Molloy B, Wall AM, Holton TA, Khaldi N. The anti-ageing effects of a natural peptide discovered by artificial intelligence. Int J Cosmet Sci 2020; 42:388-398. [PMID: 32453870 DOI: 10.1111/ics.12635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/08/2020] [Accepted: 05/20/2020] [Indexed: 01/03/2023]
Abstract
OBJECTIVE As skin ages, impaired extracellular matrix (ECM) protein synthesis and increased action of degradative enzymes manifest as atrophy, wrinkling and laxity. There is mounting evidence for the functional role of exogenous peptides across many areas, including in offsetting the effects of cutaneous ageing. Here, using an artificial intelligence (AI) approach, we identified peptide RTE62G (pep_RTE62G), a naturally occurring, unmodified peptide with ECM stimulatory properties. The AI-predicted anti-ageing properties of pep_RTE62G were then validated through in vitro, ex vivo and proof of concept clinical testing. METHODS A deep learning approach was applied to unlock pep_RTE62G from a plant source, Pisum sativum (pea). Cell culture assays of human dermal fibroblasts (HDFs) and keratinocytes (HaCaTs) were subsequently used to evaluate the in vitro effect of pep_RTE62G. Distinct activities such as cell proliferation and ECM protein production properties were determined by ELISA assays. Cell migration was assessed using a wound healing assay, while ECM protein synthesis and gene expression were analysed, respectively, by immunofluorescence microscopy and PCR. Immunohistochemistry of human skin explants was employed to further investigate the induction of ECM proteins by pep_RTE62G ex vivo. Finally, the clinical effect of pep_RTE626 was evaluated in a proof of concept 28-day pilot study. RESULTS In vitro testing confirmed that pep_RTE62G is an effective multi-functional anti-ageing ingredient. In HaCaTs, pep_RTE62G treatment significantly increases both cellular proliferation and migration. Similarly, in HDFs, pep_RTE62G consistently induced the neosynthesis of ECM protein elastin and collagen, effects that are upheld in human skin explants. Lastly, in our proof of concept clinical study, application of pep_RTE626 over 28 days demonstrated anti-wrinkle and collagen stimulatory potential. CONCLUSION pep_RTE62G represents a natural, unmodified peptide with AI-predicted and experimentally validated anti-ageing properties. Our results affirm the utility of AI in the discovery of novel, functional topical ingredients.
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Affiliation(s)
- K Kennedy
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - R Cal
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - R Casey
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - C Lopez
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - A Adelfio
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - B Molloy
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - A M Wall
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - T A Holton
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
| | - N Khaldi
- Nuritas Ltd, Joshua Dawson House, Dawson St, Dublin 2, D02 RY95, Ireland
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86
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Haddad Y, Charousova M, Zivotska H, Splichal Z, Merlos Rodrigo MA, Michalkova H, Krizkova S, Tesarova B, Richtera L, Vitek P, Stokowa-Soltys K, Hynek D, Milosavljevic V, Rex S, Heger Z. Norepinephrine transporter-derived homing peptides enable rapid endocytosis of drug delivery nanovehicles into neuroblastoma cells. J Nanobiotechnology 2020; 18:95. [PMID: 32660596 PMCID: PMC7359476 DOI: 10.1186/s12951-020-00654-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Currently, the diagnosis and treatment of neuroblastomas-the most frequent solid tumors in children-exploit the norepinephrine transporter (hNET) via radiolabeled norepinephrine analogs. We aim to develop a nanomedicine-based strategy towards precision therapy by targeting hNET cell-surface protein with hNET-derived homing peptides. RESULTS The peptides (seq. GASNGINAYL and SLWERLAYGI) were shown to bind high-resolution homology models of hNET in silico. In particular, one unique binding site has marked the sequence and structural similarities of both peptides, while most of the contribution to the interaction was attributed to the electrostatic energy of Asn and Arg (< - 228 kJ/mol). The peptides were comprehensively characterized by computational and spectroscopic methods showing ~ 21% β-sheets/aggregation for GASNGINAYL and ~ 27% α-helix for SLWERLAYGI. After decorating 12-nm ferritin-based nanovehicles with cysteinated peptides, both peptides exhibited high potential for use in actively targeted neuroblastoma nanotherapy with exceptional in vitro biocompatibility and stability, showing minor yet distinct influences of the peptides on the global expression profiles. Upon binding to hNET with fast binding kinetics, GASNGINAYLC peptides enabled rapid endocytosis of ferritins into neuroblastoma cells, leading to apoptosis due to increased selective cytotoxicity of transported payload ellipticine. Peptide-coated nanovehicles significantly showed higher levels of early apoptosis after 6 h than non-coated nanovehicles (11% and 7.3%, respectively). Furthermore, targeting with the GASNGINAYLC peptide led to significantly higher degree of late apoptosis compared to the SLWERLAYGIC peptide (9.3% and 4.4%, respectively). These findings were supported by increased formation of reactive oxygen species, down-regulation of survivin and Bcl-2 and up-regulated p53. CONCLUSION This novel homing nanovehicle employing GASNGINAYLC peptide was shown to induce rapid endocytosis of ellipticine-loaded ferritins into neuroblastoma cells in selective fashion and with successful payload. Future homing peptide development via lead optimization and functional analysis can pave the way towards efficient peptide-based active delivery of nanomedicines to neuroblastoma cells.
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Affiliation(s)
- Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Marketa Charousova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Hana Zivotska
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Zbynek Splichal
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Miguel Angel Merlos Rodrigo
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Hana Michalkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Barbora Tesarova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Petr Vitek
- Global Change Research Institute of the Czech Academy of Sciences, Belidla 986/4a, 603 00, Brno, Czechia
| | - Kamila Stokowa-Soltys
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - David Hynek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia
| | - Simona Rex
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia.
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia.
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia.
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00, Brno, Czechia.
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87
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Panda PK, Arul MN, Patel P, Verma SK, Luo W, Rubahn HG, Mishra YK, Suar M, Ahuja R. Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. SCIENCE ADVANCES 2020; 6:eabb8097. [PMID: 32691011 PMCID: PMC7319274 DOI: 10.1126/sciadv.abb8097] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/27/2020] [Indexed: 05/19/2023]
Abstract
The prevalence of respiratory illness caused by the novel SARS-CoV-2 virus associated with multiple organ failures is spreading rapidly because of its contagious human-to-human transmission and inadequate globalhealth care systems. Pharmaceutical repurposing, an effective drug development technique using existing drugs, could shorten development time and reduce costs compared to those of de novo drug discovery. We carried out virtual screening of antiviral compounds targeting the spike glycoprotein (S), main protease (Mpro), and the SARS-CoV-2 receptor binding domain (RBD)-angiotensin-converting enzyme 2 (ACE2) complex of SARS-CoV-2. PC786, an antiviral polymerase inhibitor, showed enhanced binding affinity to all the targets. Furthermore, the postfusion conformation of the trimeric S protein RBD with ACE2 revealed conformational changes associated with PC786 drug binding. Exploiting immunoinformatics to identify T cell and B cell epitopes could guide future experimental studies with a higher probability of discovering appropriate vaccine candidates with fewer experiments and higher reliability.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Antiviral Agents/pharmacology
- Benzamides
- Benzazepines
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Coronavirus 3C Proteases
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Cysteine Endopeptidases/chemistry
- Cysteine Endopeptidases/immunology
- Cysteine Endopeptidases/metabolism
- Drug Design
- Drug Evaluation, Preclinical
- Epitopes, B-Lymphocyte/drug effects
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/drug effects
- Epitopes, T-Lymphocyte/immunology
- Humans
- Molecular Docking Simulation
- Pandemics/prevention & control
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/immunology
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Protein Binding
- Protein Conformation
- Protein Domains
- Protein Interaction Domains and Motifs
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Spiro Compounds/pharmacology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/immunology
- Viral Nonstructural Proteins/metabolism
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Affiliation(s)
- Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Murugan Natarajan Arul
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, 106 91 Stockholm, Sweden
| | - Paritosh Patel
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Suresh K. Verma
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Wei Luo
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | | | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alsion 2, DK-6400 Sønderborg, Denmark
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Rajeev Ahuja
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology (KTH), SE-100 44 Stockholm, Sweden
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88
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Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations. Biophys Chem 2020; 264:106421. [PMID: 32623047 DOI: 10.1016/j.bpc.2020.106421] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) play many biological roles in the human proteome ranging from vesicular transport, signal transduction to neurodegenerative diseases. The Aβ and tau proteins, and the α-synuclein protein, key players in Alzheimer's and Parkinson's diseases, respectively are fully disordered at the monomer level. The structural heterogeneity of the monomeric and oligomeric states and the high self-assembly propensity of these three IDPs have precluded experimental structural determination. Simulations have been used to determine the atomic structures of these IDPs. In this article, we review recent computer models to capture the equilibrium ensemble of Aβ, tau and α-synuclein proteins at different association steps in aqueous solution and present new results of the PEP-FOLD framework on α-synuclein monomer.
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89
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Ghafouri F, Cohan RA, Noorbakhsh F, Samimi H, Haghpanah V. An in-silico approach to develop of a multi-epitope vaccine candidate against SARS-CoV-2 envelope (E) protein. RESEARCH SQUARE 2020. [PMID: 32702713 PMCID: PMC7336711 DOI: 10.21203/rs.3.rs-30374/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Since the first appearance of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2) in China on December 2019, the world has now witnessed the emergence of the SARS- CoV-2 outbreak. Therefore, due to the high transmissibility rate of virus, there is an urgent need to design and develop vaccines against SARS-CoV-2 to prevent more cases affected by the virus. In this study, a computational approach is proposed for vaccine design against the envelope (E) protein of SARS-CoV-2, which contains a conserved sequence feature. First, we sought to gain potential B-cell and T-cell epitopes for vaccine designing against SARS-CoV-2. Second, we attempted to develop a multi-epitope vaccine. Immune targeting of such epitopes could theoretically provide defense against SARS-CoV-2. Finally, we evaluated the affinity of the vaccine to major histocompatibility complex (MHC) molecules to stimulate the immune system response to this vaccine. We also identified a collection of B-cell and T-cell epitopes derived from E proteins that correspond identically to SARS-CoV-2 E proteins. The in-silico design of our potential vaccine against E protein of SARS-CoV-2 demonstrated a high affinity to MHC molecules, and it can be a candidate to make a protection against this pandemic event.
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90
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Delineating Novel Therapeutic Drug and Vaccine Targets for Staphylococcus cornubiensis NW1T Through Computational Analysis. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10076-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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91
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Rakib A, Sami SA, Islam MA, Ahmed S, Faiz FB, Khanam BH, Uddin MMN, Emran TB. Epitope-Based Peptide Vaccine Against Severe Acute Respiratory Syndrome-Coronavirus-2 Nucleocapsid Protein: An in silico Approach.. [DOI: 10.1101/2020.05.16.100206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractWith an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. SARS-CoV-2 is a member of the Coronaviridae family, which is transmitted from animal to human and because of being contagious, further it transmitted human to human. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019) as a global pandemic. But, no specific medications are available for the treatment of COVID-19 so far. As a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication as well as interferes with host immune responses. We have comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we have predicted the most immunogenic epitope for T-cell as well as B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.
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Secretory Expression of a Chimeric Peptide in Lactococcus lactis: Assessment of its Cytotoxic Activity and a Deep View on Its Interaction with Cell-Surface Glycosaminoglycans by Molecular Modeling. Probiotics Antimicrob Proteins 2020; 11:1034-1041. [PMID: 30552573 DOI: 10.1007/s12602-018-9496-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, cancer remains a major cause of death affecting millions of people. Currently, the antimicrobial peptides (AMPs) as potent anticancer therapeutic agents offer specificity and low levels of side effects in cancer therapy. In the present study, a cationic chimeric peptide (cLFchimera), derived from camel lactoferrin, was expressed as a secretory peptide using P170 expression system in L. lactis. Peptide purification was carried out using Ni-NTA agarose column from culture medium with 21 μ/mL concentration. The recombinant peptide was investigated for its activity against four tumor and one normal cell line. The cLFchimera was more active against two tumor cell lines (chondrosarcoma and colorectal cancer cells), but the activity against two other tumor cell lines (hepatoma and breast cancer cell line) and normal cells was low. Finally, to have better insight into the mode of action of the peptide on cytotoxic activity, we examined the interaction of cationic peptide with two glycosaminoglycans (GAGs), heparan sulfate (HS) and chondroitin sulfate (CS), as the two most anionic molecules on the cell surface by molecular dynamic simulation. The results of in silico analysis showed that the cLFchimera interacted with HS and CS with a totally different amino acid profile. Hydrogen bonding screening in GAGs-peptide complexes revealed K21, V23 and I3, R16 are the dominant amino acids involved in peptide-HS and CS interaction, respectively. Overall, the results of this investigation showed the P170 expression system successfully expressed a cationic peptide with potent anticancer activity. Moreover, molecular docking analysis revealed the pattern of peptide interaction with negatively charged membrane molecules.
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93
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Gurung S, Khan F, Gunassekaran GR, Yoo JD, Poongkavithai Vadevoo SM, Permpoon U, Kim SH, Kim HJ, Kim IS, Han H, Park JH, Kim S, Lee B. Phage display-identified PD-L1-binding peptides reinvigorate T-cell activity and inhibit tumor progression. Biomaterials 2020; 247:119984. [PMID: 32278214 DOI: 10.1016/j.biomaterials.2020.119984] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/16/2020] [Accepted: 03/17/2020] [Indexed: 01/19/2023]
Abstract
Blockade of programmed cell death ligand-1 (PD-L1) restores T-cell activity and enhances anti-tumor immunity. Screening a phage-displayed peptide library for peptides that selectively bind to PD-L1-overexpressing cells identified two peptides, CLQKTPKQC and CVRARTR (PD-L1Pep-1 and PD-L1Pep-2, respectively) that appeared to block PD-L1. PD-L1Pep-1 and PD-L1Pep-2 preferentially bound to high PD-L1-expressing cells over low PD-L1-expressing cells; binding was further enhanced by interferon-γ, an inducer of PD-L1 expression. Binding affinities of PD-L1Pep-1 and PD-L1Pep-2 were approximately 373 and 281 nM, respectively. Cellular binding of the PD-L1-binding peptides was reduced by silencing PD-L1 gene expression or competition with anti-PD-L1 antibody. PD-L1Pep-1 and PD-L1Pep-2 induced the internalization and downregulated cell surface levels of PD-L1. The PD-L1-binding peptides restored cytokine secretion and T-cell proliferation to cells inhibited by co-culture with tumor cells or culture on PD-L1-coated plates. Intravenously injected PD-L1Pep-1 and PD-L1Pep-2 efficiently homed to tumor tissues, inhibited tumor growth, and increased CD8+/FoxP3+ ratio in mice. The PD-L1-binding peptides in combination with doxorubicin or PD-L1-targeted liposomal doxorubicin inhibited tumor growth and increased CD8+/FoxP3+ ratio more efficiently than doxorubicin alone and untargeted liposomal doxorubicin, respectively. These results suggest that PD-L1Pep-1 and PD-L1Pep-2 block PD-L1 and reinvigorate T-cell activity, inhibiting tumor growth by enhancing anti-tumor immunity.
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Affiliation(s)
- Smriti Gurung
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Fatima Khan
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Gowri Rangaswamy Gunassekaran
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Jae Do Yoo
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Sri Murugan Poongkavithai Vadevoo
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Uttapol Permpoon
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Sang-Hyun Kim
- Department of Pharmacology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Ha-Jeong Kim
- Department of Physiology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - In-San Kim
- Biomedical Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14 gil, Seongbuk-gu, Seoul, 02792, Republic of Korea; KU-KIST School, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyeonjeong Han
- Department of Bio and Brain Engineering, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ji-Ho Park
- Department of Bio and Brain Engineering, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Soyoun Kim
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea
| | - Byungheon Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea; CMRI, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu, 41944, Republic of Korea.
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Pirkhezranian Z, Tahmoorespur M, Daura X, Monhemi H, Sekhavati MH. Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study. BMC Genomics 2020; 21:60. [PMID: 31959108 PMCID: PMC6971935 DOI: 10.1186/s12864-020-6458-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/07/2020] [Indexed: 12/31/2022] Open
Abstract
Background Lactoferrampin (LFampin), Lactoferricin (LFcin), and LFchimera are three well-known antimicrobial peptides derived from Lactoferrin and proposed as alternatives for antibiotics. Although the intracellular activity of these peptides has been previously demonstrated, their mode of action is not yet fully understood. Here, we performed a molecular dynamics simulation study to understand the molecular interactions between camel Lactoferrin derived peptides, including CLFampin, CLFcin, and CLFchimera, and DNA as an important intracellular target. Results Our results indicate that all three peptides bind to DNA, albeit with different propensities, with CLFchimera showing the highest binding affinity. The secondary structures of the peptides, modeled on Lactoferrin, did not undergo significant changes during simulation, supporting their functional relevance. Main residues involved in the peptide-DNA interaction were identified based on binding free energy estimates calculated over 200 ns, which, as expected, confirmed strong electrostatic interactions between DNA phosphate groups and positively charged peptide side chains. Interaction between the different concentrations of CLFchimera and DNA revealed that after binding of four copies of CLFchimera to DNA, hydrogen bonds between the two strands of DNA start to break from one of the termini. Conclusions Importantly, our results revealed that there is no DNA-sequence preference for peptide binding, in line with a broad antimicrobial activity. Moreover, the results showed that the strength of the interaction between DNA and CLFchimera is concentration dependent. The insight provided by these results can be used for the rational redesign of natural antimicrobial peptides targeting the bacterial DNA.
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Affiliation(s)
- Zana Pirkhezranian
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mojtaba Tahmoorespur
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Xavier Daura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Hassan Monhemi
- Department of Chemistry, Faculty of Science, University of Neyshabur, Neyshabur, Iran
| | - Mohammad Hadi Sekhavati
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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95
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Glashagen G, de Vries S, Uciechowska-Kaczmarzyk U, Samsonov SA, Murail S, Tuffery P, Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins 2019; 88:1018-1028. [PMID: 31785163 DOI: 10.1002/prot.25860] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 01/17/2023]
Abstract
The ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI rounds 38-45. For 11 out of 16 targets acceptable or better quality solutions have been submitted (~70%). It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions. The option of combining rigid body minimization and simultaneous optimization in collective degrees of freedom based on elastic network modes was employed and systematically evaluated. Application to a large benchmark set indicates a modest improvement in docking performance compared to rigid docking. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
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Affiliation(s)
- Glenn Glashagen
- Physik-Department T38, Technische Universität München, Garching, Germany
| | - Sjoerd de Vries
- Université de Paris, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | | | | | - Samuel Murail
- Université de Paris, CNRS UMR 8251, INSERM ERL U1133, Paris, France
| | - Pierre Tuffery
- Université de Paris, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, Garching, Germany
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96
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Specific metallo-protein interactions and antimicrobial activity in Histatin-5, an intrinsically disordered salivary peptide. Sci Rep 2019; 9:17303. [PMID: 31754129 PMCID: PMC6872563 DOI: 10.1038/s41598-019-52676-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
Histatin-5 (Hst-5) is an antimicrobial, salivary protein that is involved in the host defense system. Hst-5 has been proposed to bind functionally relevant zinc and copper but presents challenges in structural studies due to its disordered conformation in aqueous solution. Here, we used circular dichroism (CD) and UV resonance Raman (UVRR) spectroscopy to define metallo-Hst-5 interactions in aqueous solution. A zinc-containing Hst-5 sample exhibits shifted Raman bands, relative to bands observed in the absence of zinc. Based on comparison to model compounds and to a family of designed, zinc-binding beta hairpins, the alterations in the Hst-5 UVRR spectrum are attributed to zinc coordination by imidazole side chains. Zinc addition also shifted a tyrosine aromatic ring UVRR band through an electrostatic interaction. Copper addition did not have these effects. A sequence variant, H18A/H19A, was employed; this mutant has less potent antifungal activity, when compared to Hst-5. Zinc addition had only a small effect on the thermal stability of this mutant. Interestingly, both zinc and copper addition shifted histidine UVRR bands in a manner diagnostic for metal coordination. Results obtained with a K13E/R22G mutant were similar to those obtained with wildtype. These experiments show that H18 and H19 contribute to a zinc binding site. In the H18A/H19A mutant the specificity of the copper/zinc binding sites is lost. The experiments implicate specific zinc binding to be important in the antimicrobial activity of Hst-5.
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97
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Tahmoorespur M, Azghandi M, Javadmanesh A, Meshkat Z, Sekhavati MH. A Novel Chimeric Anti-HCV Peptide Derived from Camel Lactoferrin and Molecular Level Insight on Its Interaction with E2. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09972-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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98
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Tahir Ul Qamar M, Saleem S, Ashfaq UA, Bari A, Anwar F, Alqahtani S. Epitope-based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: an immune-informatics study. J Transl Med 2019; 17:362. [PMID: 31703698 PMCID: PMC6839065 DOI: 10.1186/s12967-019-2116-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/26/2019] [Indexed: 12/28/2022] Open
Abstract
Background Middle East Respiratory Syndrome Coronavirus (MERS-COV) is the main cause of lung and kidney infections in developing countries such as Saudi Arabia and South Korea. This infectious single-stranded, positive (+) sense RNA virus enters the host by binding to dipeptidyl-peptide receptors. Since no vaccine is yet available for MERS-COV, rapid case identification, isolation, and infection prevention strategies must be used to combat the spreading of MERS-COV infection. Additionally, there is a desperate need for vaccines and antiviral strategies. Methods The present study used immuno-informatics and computational approaches to identify conserved B- and T cell epitopes for the MERS-COV spike (S) protein that may perform a significant role in eliciting the resistance response to MERS-COV infection. Results Many conserved cytotoxic T-lymphocyte epitopes and discontinuous and linear B-cell epitopes were predicted for the MERS-COV S protein, and their antigenicity and interactions with the human leukocyte antigen (HLA) B7 allele were estimated. Among B-cell epitopes, QLQMGFGITVQYGT displayed the highest antigenicity-score, and was immensely immunogenic. Among T-cell epitopes, MHC class-I peptide YKLQPLTFL and MHC class-II peptide YCILEPRSG were identified as highly antigenic. Furthermore, docking analyses revealed that the predicted peptides engaged in strong bonding with the HLA-B7 allele. Conclusion The present study identified several MERS-COV S protein epitopes that are conserved among various isolates from different countries. The putative antigenic epitopes may prove effective as novel vaccines for eradication and combating of MERS-COV infection.
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Affiliation(s)
- Muhammad Tahir Ul Qamar
- College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Saman Saleem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Amna Bari
- College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Safar Alqahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdul Aziz University, Alkharj, Saudi Arabia.
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99
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Santini BL, Zúñiga-Bustos M, Vidal-Limon A, Alderete JB, Águila SA, Jiménez VA. In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy. J Chem Inf Model 2019; 60:786-793. [PMID: 31657548 DOI: 10.1021/acs.jcim.9b00756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The transmembrane glycoprotein mucin 1 (MUC1) is an attractive tumor marker for cancer therapy and diagnosis. The nine amino acid extracellular epitope APDTRPAPG of this protein is selectively recognized by the S2.2 single-stranded DNA anti-MUC1 aptamer, which has emerged as a promising template for designing novel targeting agents for MUC1-directed therapy. In this work, 100 ns molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, and conformational analysis were employed to propose a novel prospective anti-MUC1 aptamer with increased affinity toward the MUC1 epitope resulting from the double mutation of the T11 and T12 residues with PSU and U nucleosides, respectively. The double mutant aptamer exhibits a tight interaction with the MUC1 epitope and adopts a groove conformation that structurally favors the intermolecular contact with the epitope through the intermediate T11-A18 region leaving the 3' and 5' ends free for further chemical conjugation with a nanocarrier or pharmaceutical. These results are valuable to gain understanding about the molecular features governing aptamer-epitope interactions and constitute a first key step for the design of novel aptamer-based nanocarriers for MUC1-targeted cancer therapy.
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Affiliation(s)
- Brianda L Santini
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Matías Zúñiga-Bustos
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andres Bello , Sede Concepción, Autopista Concepción-Talcahuano 7100 , Talcahuano 4260000 , Chile
| | - Abraham Vidal-Limon
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales , Universidad de Talca , Casilla 747 , Talca 3460000 , Chile
| | - Sergio A Águila
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andres Bello , Sede Concepción, Autopista Concepción-Talcahuano 7100 , Talcahuano 4260000 , Chile
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100
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Wisdom EC, Zhou Y, Chen C, Tamerler C, Snead ML. Mitigation of peri-implantitis by rational design of bifunctional peptides with antimicrobial properties. ACS Biomater Sci Eng 2019; 6:2682-2695. [PMID: 32467858 DOI: 10.1021/acsbiomaterials.9b01213] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The integration of molecular and cell biology with materials science has led to strategies to improve the interface between dental implants with the surrounding soft and hard tissues in order to replace missing teeth and restore mastication. More than 3 million implants have been placed in the US alone and this number is rising by 500,000/year. Peri-implantitis, an inflammatory response to oral pathogens growing on the implant surface threatens to reduce service life leading to eventual implant failure, and such an outcome will have adverse impact on public health and create significant health care costs. Here we report a predictive approach to peptide design, which enabled us to engineer a bifunctional peptide to combat bacterial colonization and biofilm formation, reducing the adverse host inflammatory immune response that destroys the tissue surrounding implants and shortens their lifespans. This bifunctional peptide contains a titanium-binding domain that recognizes and binds with high affinity to titanium implant surfaces, fused through a rigid spacer domain with an antimicrobial domain. By varying the antimicrobial peptide domain, we were able to predict the properties of the resulting bifunctional peptides in their entirety by analyzing the sequence-structure-function relationship. These bifunctional peptides achieve: 1) nearly 100% surface coverage within minutes, a timeframe suitable for their clinical application to existing implants; 2) nearly 100% binding to a titanium surface even in the presence of contaminating serum protein; 3) durability to brushing with a commercially available electric toothbrush; and 4) retention of antimicrobial activity on the implant surface following bacterial challenge. A bifunctional peptide film can be applied to both new implants and/or repeatedly applied to previously placed implants to control bacterial colonization mitigating peri-implant disease that threatens dental implant longevity.
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Affiliation(s)
- E Cate Wisdom
- Bioengineering Program, Institute for Bioengineering Research, University of Kansas, Lawrence, USA
| | - Yan Zhou
- Herman Ostrow School of Dentistry of USC, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, USA
| | - Casey Chen
- Herman Ostrow School of Dentistry of USC, Division of Periodontology, Diagnostic Services, & Dental Hygiene University of Southern California, Los Angeles, USA
| | - Candan Tamerler
- Bioengineering Program, Institute for Bioengineering Research, University of Kansas, Lawrence, USA.,Mechanical Engineering Department, University of Kansas, Lawrence, USA
| | - Malcolm L Snead
- Herman Ostrow School of Dentistry of USC, Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, USA
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